Articles, Blog

18. Analysis of Chromatin Structure

October 16, 2019

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visit MIT OpenCourseWare at PROFESSOR: All right, well,
good afternoon and welcome back. We have an exciting fun-filled
program for you this afternoon. I’m David Gifford. I’m delighted to
be back with you again, here in computational
systems biology. Today we’re going to talk
about chromatin structure and how we can analyze it. And to give you the narrative
arc for our discussion today, we’re first going to
begin with looking at computational methods that
we can break the, quote unquote code, that describes
the epigenome. Now, epigenetic state is
extraordinarily important and one way you
can visualize this is that the genome is
like a hotel filled with lots of different rooms. And a lot of the doors are
locked and some of the doors are unlocked. And only in the doors
that we can go into, where the genome is
open and accessible can there actually be work
done, regulation performed and transcripts
and proteins made. So we’re going to talk about
how to actually analyze epigenetic state. And then we’re going
to talk about how to use epigenetic
information to understand the entire regulatory
occupancy of the genome. We’ve already talked about
ChIP-seq and the idea that we can understand where
individual regulators sit on the genome, and how they
regulate proximal genes. We’re now going to see if we
can learn more about the genome. How it’s state– whether
it’s open or closed. Is it self-regulated? And answer a puzzle. The puzzle is, if there
are hundreds of thousands of possible binary
locations that are equally good
for a regulator, why are only tens of
thousands occupied? And how are those sites picked? Because that level of regulation
is extraordinarily important to establish a basal
level of what genes are accessible and operating. And finally, we’re going to
talk about how we can map, which regulatory
regions in the genome are affecting which genes. It turns out that about
1/3 of the regulatory sites in the genome skip over a
gene that’s closest to them to regulate a gene
that’s farther away. This is a million genomes. And so given that
rough approximation, how is it that we
can make connections between regulatory sites and
the genes that they control? Now, in computational
systems biology, we always talk a
lot about biology, but we also need to reflect
upon the computational methods that we’re bringing to
bear on these questions. And so, today, we’re
going to be talking about three different methods. We’ll talk about dynamic
Bayesian networks as a way to approach, understanding
the histone code. We’ll talk about how to
classify factor binding, using log likelihood ratios. And finally, we’ll
turn to our friend, the hypergeometric
distribution to analyze which locations
in the genome are interacting with one another. So let’s begin with
establishing a vocabulary. I’m sure some of you
have seen this before. This is the way
that chromatin can be thought of being organized
at different levels. There’s the primary
DNA sequence, which can include
methylated CPGs. That’s cysteine,
phosphate, guanine. And the nice thing about
that is that it’s symmetrical so that when you have a CPG,
a methyltransferase during DNA replication can copy
that methy mark over. So it’s a mark that’s heritable. The next level down
are histone tails. On the amino terminus
of histones H3 and H4, different chemical
modifications can be made, and they serve as
sign posts, as we’ll see, to give us
clues about what’s going on in the genome in
that proximal location. The next level down
is, whether or not the chromatin is
compacted or not. Whether it’s open or closed. And that relates
to whether or not DNA binding proteins are
actually on the genome. And finally, certain
domains of the genome can be associated with
the nuclear lamina. And so they’re different levels
of organization of chromatin. And we’ll be exploring
all of these today. So the cartoon
version of the way that the genome is
organized is that at the top we have a transcribed gene. And you can see that
there’s an enhancer that is interacting with the RNA
polymerase II start site. And you can see
varied histone marks that are associated with
this activated gene. There are also marks
that are associated with that active enhancer. Down below, you see
an inactive gene. And you can see that there’s
a boundary element that’s bound by CTCF, which,
one of its function is to serve as a genomic
insulator, which insulates the effect of the enhancer
above from the gene below. So through careful biochemical
analysis over the years, these different marks have been
analyzed and characterized. And a general paradigm
for understanding how the marks transition
as genes are activated is shown here. So genes that are
fairly active and cycle between active and
inactive states typically have a high CPG content
in their promoters. And transition is
shown on the left. Where in the repressed
state on the bottom, they’re marked by
H3K27 trimethyl marks. When they’re poised, they have
both H3K4 trimethyl and H3K27 trimethyl. And when they’re active, they
only have H3K4 trimethyl. And on the right hand side are
genes that are less active. So in their completely shut down
state, they may have no marks, but the DNA is
methylated, silencing that region of the genome. And other marks then,
culminating in H3K4 trimethyl once again when they
become active at the top. So I’m summarizing
for you here, decades of research in histone marks. And it has been
summarized in figures like this, where you can
look at different classes of genetic elements– whether
they be promoters in front of genes, gene bodies
themselves, enhancers, or the large scale
repression of the genome– and you can look
at the associated marks with those
characteristic elements. OK, so, how can we
learn this de novo? That is, you could
memorize, and of course it’s important to
understand, for example, if you want to look
for active enhancers in the genome, that
looking for things like H3K4 monomethyl and H3K7
27 acetyl marks together, would give you a good clue
where the enhancers are in the genome that are active. But if we want to
learn all this de novo, without having to memorize it
or rely upon the literature, the great thing is that there’s
a lot of data out there now that characterizes, or profiles
all these marks, genome-wide, in variety of cellular states. And there’s the epigenome
roadmap initiative to look at this in hundreds
of different cell types. So, what is the histone code? That is, how can we
unravel the different marks present in the genome and
understand what they mean? Because the genome doesn’t come
ready-made with those little cute labels that we had on
it– enhancer, gene body, and so forth. So somehow, if we
want to understand the grammar of the
genome and its function, we’re going to need to be
able to annotate it, hopefully with computational help. So here’s a picture of
what typical data looks like along the genome. So, obviously you can’t
read any of the legends on the left-hand side. If you want to look
at the slides that are posted on Stellar, you
can see the actual marks. But the reason I posted
this is because you can see the little pink
thing at the top– that’s where the RNA transcript has
been mapped to the genome. The actual annotated
genes are above. And then down below you
can see a whole collection of histone marks and other
kinds of chromatin information that have been
mapped to the genome and spatially
create patterns that are suggestive of the function
of the genomic elements, if they’re properly interpreted. And below, you see in blue,
the binding of different TFs, as determined by ChIP-seq. So, what we would
like to do then, is to take this
kind of information and automatically learn,
or automatically annotate the genome as to its
functional elements. Let me stop here and
ask, how many people have seen histone mark
information before? OK. And how many people have
used it in their research? Not too many– a couple people? OK. So it’s getting
quite easy to collect and there are a couple of ways
of analyzing this kind of data, genome-wide. One way is that we could
run a hidden Markov model over these data
and predict states at regular intervals. For example, every 200
bases down the genome, and see how the HMM transition
from state to state and let the state suggest what the
underlying genome elements that we’re doing. Another way is to use a
dynamic Bayesian network. So a dynamic Bayesian network
is simply a Bayesian network. We’ve talked about those before. And it models data
sampled along the genome. And so it’s a directed
acyclic graph. There are tools out
there that allow us to learn these
models directly. And it allows us, as we’ll
see, to analyze the genome at high resolution, and
to handle missing data. So we’ll be talking
about Segway, which is a particular
dynamic Bayesian network that takes the kind of data
we saw on the slide before and essentially parses
it into labels that allow us to assign function to
different genomic elements. And it does this in
an unsupervised way. What I mean by that is
that it is automatically learning the states,
and then afterwards we can look at the states and
assign meaning to them. So here is the dynamic Bayesian
network that Segway uses. And let me explain
this somewhat scary looking diagram of lots of
little boxes and pointers to you. The genome is described
through the variables on the bottom– the
observation variables, going from left to
right, where each base is a separate observation
variable which consists of the level of a
particular histone mark at a particular based position
as described by mapped reads to that location. The little square
box– the little boxes that says “x” on it with the
other small print you can’t read– is simply an
indicator, whether or not the data is present. If the data is absent, we
don’t try and model it. If that box contains a zero,
we don’t model the data. If the box is one, then we
attempt to model the data. And the most important part of
the dynamic Bayesian network is the q box above, where
those are the states. And each state describes an
ensemble of different histone marks that are output. And so the key thing
is that for each state we learn what marks
it’s outputting. And the model learns
this automatically through a learning phase. The boxes above
simply are a counter. And the counter allows us
to define maximum lengths for particular states, so
states don’t run on forever. So unlike a hidden
Markov model that doesn’t have that
kind of control, we can adjust how long we
want the states to last. So this model, if you
turned it 90 degrees and rotated it clockwise,
would be more familiar to you because all the arrows
would be flowing from the top of the screen down. There are no cycles in this
directed acyclic graph. And therefore, it can be
probabilistically viewed and learned in
the same framework that we learn a
Bayesian network. In fact, it is a
Bayesian network. The reason it’s
called dynamic is because we are learning
temporal information, or in this case,
spatial information with these different
observations along the bottom of the model. Now before I go on,
perhaps somebody could ask me a question
about the details of these dynamic
Bayesian networks, because the ability to
automatically assign labels to genome function, given
the histone marks is really a key thing that’s gone on
the last couple of years. Yes? AUDIENCE: Could you
re-explain that– what the labeled– the second
[INAUDIBLE] was all about? PROFESSOR: Sure. So the Q label is right
here, these labels. And each of these
Q labels defines one of a number of states. For example, 24
different states. In a given state, describes
the expected output in terms of what histone marks
are present in that state. So it’s going to
describe the means of all those different histone marks. 24 different means,
let’s say, of the marks it’s going to output. And the job of fitting the model
is picking the right states, or a set of 24
states, each of which is most descriptive of its
particular subset of chromatin marks. And then defining how we
transition between states. So we not only need to
define what a state means in terms of the marks
that it outputs, but also when we transition from
one state to another. Does that make sense to you? AUDIENCE: So I know it
states the information that tells at each of the Q boxes. Is that a series
of probabilities? Or is it something else? PROFESSOR: It’s actually
a discrete number, right. So it actually is a
single– there’s only a single state in each Q box. So it might be a
number between 1 and 24 that we’re going to learn. And based upon
that number, we’re going to have a
description of the marks that we would expect to
see at the observation at that particular
genomic location. And so our job here is to
learn those 24 different states and what they output
in the training phase, and then once we’ve
trained the model, we can go back and look
at other held out data, and then we can
decode the genome. Because we know what
the states are, and we know what they are
supposed to be producing, we can use a Verterbi decoder
and go back and– as we did with the HMM and we
learned the HMM– go back and read off on the
histone mark sequence and figure out what
their relative states are for each base position
of the genome. Is that helpful? Yes? Any other questions about
dynamic Bayesian networks? Yes? AUDIENCE: How do you choose
the number of states? PROFESSOR: That’s a
very good question. How do you choose
the number of states? Well, if you choose
too many states, they obviously don’t
really become descriptive and you can become
over fit and then can start fitting
noise to your model. And if you choose too few
states, what will happen is, that states can
get collapsed together and they won’t be
adequately descriptive. The answer is, it’s more
or less trial and error. There really isn’t
a principled way to choose the right
number of states in this particular context. Now, you could do– AUDIENCE: What’s
the trial, then? You run it and you
get a set of things, and what do you do
with those labels? PROFESSOR: What do
you do with labels? AUDIENCE: Yeah, how
do you evaluate it? PROFESSOR: You
typically, in both of these cases– both in the
case of chrome HMM and this– you rely upon the
previous literature. And we saw on that
slide earlier, what marks are associated
with what kinds of features. So you use the prior
literature and you use what the states are telling
you they’re describing to try and associate those
states with what’s known about genome function. All right, yes? AUDIENCE: Where does that
information concerning the distance between
states go again? Like, the counter? Like, how does that
control how long the states go on
and whether or not– PROFESSOR: What happens is that
the counter at the top, the C variables, influence the J
variables you can see there. When the J variable
terms to a 1, it forces the state transition. So the counters count
down and can then force a state
transition which will cause the Q variable to change. It’s sort of a– that particular
formulation of this model is a bit of a, sort
of Rube Goldberg kind of hackish kind of thing. I think to make it get
out of particular states. But it works, as we’ll
see in just a moment. OK. So here’s an example
of it operating. And you can see the different
states on the y-axis here. You can see the different
state transitions as we go down the genome. And you can see the
annotations that it’s outputting, corresponding
to the histone marks. And so what this
is doing is it’s decoding for us what it thinks
is going on in the genome, solely with reference
to the histone marks, without reference to primary
sequence or anything else. And this kind of
decoding is most useful when we want to discover things
like regulatory elements. When we want to look for H3K4
mono or dimethyl, and H3K27 acetyl for example, and identify
those regions of the genome that we think are
active enhancers. OK. OK. So, any questions at all about
histone marks and decoding? Do you get the
general idea that you can assay these histone
marks through ChIP-seq using antibodies that are specific
to a particular mark. Pull down the histones that
are associated with DNA with that mark and map
them to the genome. So we get one track for
each ChIP-seq experiment. We can profile all the marks
that we think are relevant, and then we can look at
what those parks imply about both the static
structure of our genome, and also how it’s being
used as cells differentiate or in different
environmental conditions. OK. OK. So, let’s go on, then,
to the next step, which is that if we understand the
sort of epigenetics state, how is that established and
how is the opening of chromatin regulated and how is it that
factors find particular places in the genome to bind? So, the puzzle I talked
to you about earlier was that there are
hundreds of thousands of particular motifs
in the genome, but a very small
number are actually bound by regulatory factors. And you might think
that the difference is that the ones that are bound
have different DNA sequences. But in fact, on the
right-hand side, what we see is that identical DNA sequences
are bound differentially in two different conditions. Shown there are
sites that are only bound, for example,
in endodermal tissues or in ES cells. So it isn’t the sequence
that’s controlling the specificity of the
binding, it’s something else. And we’d like to figure out
what that something else is. We’d like to understand
the rules that govern where those factors
are binding in the genome. So a set of factors are
known that bind to the genome and open it. They’re called pioneer factors. There are some well known
pioneer factors like FoxA and some of the iPS
reprogramming factors. And the idea is that
they’re able to bind to closed chromatin
and to open it up to provide accessibility
to other factors. So what we would
like to do, is to see if there’s a way that we
could, both understand how to discover those
factors automatically, using a computational
method, and secondarily, understand where factors are
binding in a single experiment across the genome. So the results I’m going to
show you can be summarized here. I’m going to show
you a method called PIQ that can predict where
TFs bind from DNase-seq data that I’ll describe in a moment. We’ll identify pioneer factors. We’ll show that certain of these
pioneer factors are directional and only operate in
one way on the genome. And finally, that the
opening of the genome allow subtler factors to come
in and to bind to the genome. So let’s begin with
what DNase-seq data is, and how we can use
it to predict where TFs are binding to the genome. So DNase-seq is a
methodology for exploring what parts of the
genome are open. So here’s the idea. You take your cell
and you expose it, once you’ve isolated the
chromatin to DNase-1 which will cut or nick
DNA at locations where the DNA is open. You then can collect the
DNA, size separate it and sequence it. And thus, you’re
going to have more reads where the
DNA has been open, and less reads were it’s
protected by proteins. So the cartoon below
gives you an idea that, where there are
histones– each histone has about 147 bases of
DNA wrapped around it. Or where there are other
proteins hiding the DNA, you’re going to cast
shadows on this. So we’re going to be looking
at the shadows and also the accessible parts,
by looking directly at the DNase-seq reads. So if we sequence
deeply enough we can understand that
each binding protein has its own particular
profile of protection. So if you look at these
different proteins, they cast particular
shadows on the genome. I’m showing here a window
that’s 400 base pairs wide. This is the average of thousands
of different binding instances. So this is not one binding
instance on the top row. You can see how CTCF
and other factors have particular shadows
they cast or profiles. Yes? AUDIENCE: How do you know
which factor was at which site? [INAUDIBLE]. PROFESSOR: How do we know
which factor is at which site? By the motifs that
are under the site. And what’s
interesting about CTCF is that you can actually see
how it phase the nucleosomes. You can see the, sort of,
periodic pattern in CTCF. And those dips are where
the nucleosomes are. There’s a lot you can
tell from these patterns about the underlying molecular
mechanism of what’s going on. Now, you can see at the very
bottom, the aggregate CTCF profile. And if all the CTCF
bindings looked like that, it’d be really easy. But above it, as I’ve shown
you what an individual CTCF site looks like, you can
see how sparse it is. We just don’t get
enough re-density to be able to recover a beautiful
protection profile like that. So we’re always working
against a lot of noise in this kind of
biological environment. And so our
computational technique will need to come up
with an adequate model to overcome that noise. But if we can, right,
the great promise is that with a single
experiment we’ll be able to identify where all
these different factors are binding to the genome
from one set of data. So, just reiterating now,
if you think about the input to this algorithm– we’re
going to have three things that we input to the algorithm. We input the original
genome sequence. We input the motifs
of the factors that we care about, that
we think are interesting. And we input the
DNase-seq data that has been aligned to the genome. So those are the three inputs. And the output of
the algorithm is going to be the predictions
of which motifs are occupied by the factors,
probabilistically. And in order to do
that, for each protein we need to learn its
protection profile. And we need to
score that profile against each
instance of the motif to see whether or not we
think the protein is actually sitting at that
location in the genome. Any questions at all about that? No? OK. Don’t hesitate to stop me. So the design goals for this
particular computational algorithm, as I said earlier,
is resistance to low coverage and lots of noise. To be able to handle
multiple experiment once, it has to work on the
entire mammalian genome. It has to have high
spatial accuracy and it has to have good
behavior in bad cases. So in order to model the
underlying re-distribution of the genome, what
we’re going to do is something that
is in principle quite straightforward. Which is that we’re going to
model all accounts that we see in the genome by a
Poisson distribution. So in each base of
the genome, the counts that we see there in
the DNase-seq data are modeled by a Poisson. And this is assuming that
there’s no protein bound there. So what we’re trying to do
is to model the background distribution of counts
without any kind of binding. And the log rate
of that Poisson is going to be taken from
a multivariate normal. And the particular structure
of that multivariate normal provides a lot of smoothing. So we can learn from
that multivariate normal how to fill in
missing information. It’s very important
to build strength from neighboring bases. So, even though we may not
have lots of information for this base, if
we have information for all the bases around us,
we can use that information to build strength to estimate
what we should see at this base if it’s not occupied. So the details of how we
learn the mean and the sigma matrix you see up
there for estimating the multivariate normal
are outside the scope of what I’m going
to talk about today. But suffice to say, they
can be effectively learned. And the second thing we need
to learn are these profiles. And so each protein is
going to have a profile. Here shown 400 bases wide. And it describes how that
protein, so to speak, casts a shadow on the genome. And we judge the significance
of these profiles– and remember that
one of my points was I wanted this to be robust. So I will not make calls for
proteins where I cannot get a robust profile that is
significant above background. And I also exclude the
middle region of the profile because it’s been shown that
the actual cutting enzymes are sequence specific
to some extent. The DNase-1 cutting enzyme. And so we don’t
simply want to be but picking up sequence
bias in our profile. So we learn these
profiles that describe for each particular
motif– and typically we can take in hundreds of motifs,
over 500 motifs at once– for each motif, what its
protection looks like. So what we then have– we’re
going to learn this, actually, in an iterative process, but
what we’re going to have is– now we have a model of what the
unoccupied genome looks like. And we have a model of the
reads that a particular protein at a motif location
is going to produce. And we can put those two
things together and the way that we do that is that we
have a binding variable. Showing there is delta. And we can either add or
not add the binding profile of a particular protein in
a location in the genome. And that will change the
expected number of counts that we see. So the key part of this is that
we use a likelihood ratio shown as the second probability. It’s not really a
probability, it’s a ratio, which is the
probability of a count, given that a protein j is
binding at that location, versus the probability of the
counts, were it not binding. And that quantity
is key because it’s going to be– once
we log transform it, will be a key component
of our test statistic to figure out whether
or not a protein’s binding at a
particular location. And so the way that we go about
that is it we log that ratio and we add it to some other
prior information that gives us an overall measure
for whether or not the protein is binding
at a particular location. And then we can rank
these for all the motifs for that particular
protein in the genome. And then we can make
calls using a null set. So we could look in the
genome for locations that we know are not occupied,
compute a distribution of that statistic,
and then we can say, for what values of this
statistic that we observe, at the actual motif sites,
is it so unlikely that this would occur at random. At some desired p
value by looking at the area in the
tail of the null set. So, just summarizing, we
learn a background model of the genome, which
is a Poisson that takes log rates from
a multivariate normal. We learn patterns, or
profiles of protection, or the production of
reads for each motif. And at each motif location,
we ask the question whether or not, it’s
likely that the protein was there and actually caused
the reads that we’re seeing, using a log likelihood ratio. So what we’re
integrating together, when we take all
these things, is that we’re taking our
original DNA seq-reads, we’re taking our TF-specific
specific binding profiles. We can build strength across
experiments for the background model and we can also learn,
to what extent, the strength of binding is influenced by
the match of the position– a specific weight matrix–
to a particular location in the genome. And then we can
produce binding calls. And when we do so,
it works quite well. So here you see three
different mouse ESO factors. And the area under
this receiver operating curve– we’ve talked
about this before. Remember a receiver
operating characteristic curve– has false
positives increasing on the x-axis and true positives
increasing on the y-axis. And if we had a perfect method,
the area under that curve would be 1.0. And so for this method,
the area under the ROC curve for these three
factors, using ChIP-seq data, is the absolute gold
standard, is over 0.9. And you might say,
well that’s great, but how well does
it work in general? I mean, for example,
the On-code project has used hundreds and hundreds
of ChIP-seq experiments to profile where
factors are binding in different cellular states. If you take the DNase-seq data
from those matched cell types and you ask, can you reproduce
the ChIP-seq seq data? The answer is, a lot
of the time we can, using this kind of methodology. And that is, the
AUC mean is 0.93 compared to 313 different
ChIP-seq experiments. So this methodology of
looking at open chromatin allows us to identify where
lots of different factors bind to the genome. And about 75 different
factors are strongly detectable using
this methodology. So it’s detectable if
it has a strong motif, if it binds in
DNase-accessible regions and has strong
DNA-binding affinity. So I tell you this
just so you know that there are
new methods coming that allow us to take
a single experiment and analyze it and determine
where a large number of factors bind from that single
experimental data set. Now, a second question
we wanted to answer was, how is it that chrome,
opening and closing is controlled? And since we had a direct read
out of what chromatin is open, because reads are
being produced there, we could look in a
experimental system where we measured
chromatin accessibility through developmental time. And the idea was that as we
measured this accessibility, we could look at the
places that changed and determine what underlying
motifs were present that perhaps were causing the
genome to undergo this opening process. So we developed an
underlying theory that pioneer factors would bind
to closed chromatin as shown in the middle panel
and open it up, and that we could observe those
by looking at the differential accessibility of the genome
at two different time points that were related. And we couldn’t observe pioneers
they didn’t open up chromatin. And for non-pioneers–
obviously the left-hand panel– they would not, in
our design here, lead to increased accessibility. So we then looked at designing
computational indices that measured the–
oh, question, yes? AUDIENCE: When you
say pioneer factors, are you looking at what proteins
are pioneer factors, or are you looking at what sequences they
bind to that are [INAUDIBLE]. PROFESSOR: So the
question is, are we looking at what
proteins are factors, or are we looking at
what sequence, right? What we’re doing is,
we’re making an assumption that the underlying sequence
denotes one or more proteins and thus, we are
hypothesizing, there’s the proteins that are actually
binding to the sequence, that’s causing that. And then later on, we’ll go back
and test that experimentally, as you’ll see in a second. OK? So here there are three
different metrics, which is the dynamic opening
of chromatin from one time point to the next, the
static openness of chromatin around a particular factor,
and a social index showing how many other factors
are around where a particular factor binds. And you can see that these
things are distributed in a way that certain of the factors have
a very high index in multiple of these scores. And thus, we were
able to classify a certain set of factors
as what we classified as computational pioneers,
that would open up the genome. Now, in any kind of
computational work, we’re actually looking
at correlative analysis, which is never causal. Right. So we have to go back and we
have to test whether or not our computational
predictions are correct. So in order to do
that, we built a test construct where we
could put the pioneers in on the left-hand side
and ask, whether or not the pioneer would
open up chromatin and enable the expression
of a GFP marker. And the red bars
show the factors that we thought were pioneers. And as you can see, in
this case, all but one of the predictive pioneers
produces GFP activity. And this construct was
designed in an interesting way. We had to design it so that
the pioneers themselves were not simply activators. And so it was upstream of
another activator, which is a retinoic acid
receptor site. And so in the absence of
retinoic acid receptor, we had to ensure that when
we turned on the pioneer, GFP was not turned on. It was only with the
addition of the pioneer to open the chromatin
and the activator that we actually
got GFP expression. OK. So, through this
methodology we discovered about 120 different motifs
corresponding to proteins that we found computationally
open– chromatin out. Yes? AUDIENCE: [INAUDIBLE]
concentrations of different pioneer
factors are different, wouldn’t that show up
differentially [INAUDIBLE]? PROFESSOR: The question
is, if the concentration of different pioneer
factors was different, wouldn’t that show
up differentially? And that’s precisely, we
think how chromatin structures are regulated. That we think that the
concentration, or presence of different pioneer factors,
is regulating the openness or closeness of different
parts of the genome, based upon where their
motifs are occurring. Is that, in part,
answering your question? AUDIENCE: Yes, but,
if a concentration of a particular
pioneer factor is low, do they necessarily have lesser
binding sites on the genome? PROFESSOR: So you’re
asking, how is the concentration
of a pioneer factor related to its ability
to open chromatin and whether or not a
higher dosage would open more chromatin? AUDIENCE: Yes. PROFESSOR: I don’t have a
good answer to that question. Those experiments
haven’t been done. However, one thing you may have
noticed about these profiles– remember these are the same
profiles that we talked about earlier of DNase-1
read reproduction around a particular factor. And what you might notice is
that some of these profiles are asymmetric. And that they appear to be
producing more region one direction than the
other direction. And so this is all
computational analysis, right. But when you see
something like that you say, well gee, why
is that going on? Why is it that for NRF-1 the
left-hand side has a lot more reads than the right hand side. Now, of course, the only reason
that we can produce an oriented profile like that is that the
NRF-1 motif is not palindromic, right. We can actually orient
it in the genome and so we know that the
more reads, in this case, are coming from
the five prime end then from the three prime end. So what do you think
would cause that? Does anybody have a–
when we first saw this, we didn’t know what it was. But anybody have an idea
of what that could be? Oh, yes. AUDIENCE: It’s the remodelers
that these transcription factors are calling in tend to
open the chromatin more on one side of the motif
than the other. PROFESSOR: Right,
so if the remodelers are working in some sort
of directional way, right. So that’s what we thought. We didn’t know whether
they were or not. And so we went back to our
assay and we tested the motifs, both in the forward and
the reverse direction. Right. To see whether or
not it mattered which way the motif
went into the construct, based upon selecting factors,
based upon a symmetry score that we computed for
their read profile, right? And what we found was that, in
fact, it was the case that when the motif was properly
oriented it would turn on GFP and was in the other
direction it would not. So it appeared, for the
factors that we tested, that they did have directional
chromatin opening properties. And so that’s an
interesting concept that you actually
can have chromatin being opened in one direction
but not the other direction, because it admits
the idea of some sort of genomic parentheses,
where you could imagine part of the genome
being accessible where the other part is not. And overall this led us to
classifying protein factors that are operating in
genome accessibility into three classes. Here shown as two, where
we have pioneers which are the things that
open up the genome, and settlers that follow
behind and actually bind in the regions where
the chromatin is open. That is, it’s much more likely
that those factors are going to bind where the doors
of the rooms are open, and the pioneers are
the proteins that come along and open the doors,
in particular, chromatin domains. And there were a couple of other
tests that we wanted to do. We wanted to test whether
or not we could knock out this pioneering activity by
taking a pioneer and just only including its
DNA-binding domain and knocking out the
rest of its domain which might be operative
in doing this chromatin remodeling. And then asked,
whether or not, when we expressed this sort
of poisoned pioneer, whether or not it would affect
the binding of nearby factors. And, in fact, when
you do express the sort of poison
pioneer, it does reduce the binding
of nearby factors. Here, we have a dominant
negative for NFYA and dominant negative for NRF1. It reduces the binding
of nearby factors. And finally, we wanted
to know, if we included a dominant negative for
the directional pioneer, if it actually
would preferentially affect the binding
of [INAUDIBLE] on one side of its binding
occurrences or the other side. And so we looked
at mix sites that were oriented with
respect to NFYA. And when we add
the NFYA, you can see that it actually– the
dominant negative NFYA– when the mix site is down of where
we think NFYA is opening up the chromatin, the binding
is substantially reduced. Whereas, when the
Myc site is not on the side where we think
that NFYA is opening, it doesn’t really
have an effect. So this is further
confirmation of the idea that in vivo, these
factors are actually operating in a directional way. Now I tell you all
this because, you know, we do a lot of
computational analysis and it’s important to
follow up and understand what the correlations tell us. So when you do
computational analysis and you see a very
interesting pattern, the thing to keep in mind
is, what kind of experiment can I design to
test whether or not my hypothesis is correct or not? We also did an analysis across
human and mouse data sets and found that
for a given motif, and thus, protein
family, it appeared that the chromatin
opening index was largely preserved, evolutionarily. So that there are
similar pioneers between human and mouse. Are there any questions
at all about the idea? So I told you, I mean, when you
go to cocktail party tonight, you say hey, you know, did
you know that DNase-seq is this really cool technique
that not only tells you whether or not chromatin is
open or not, but, you know, where factors bind? And some of those factors
open up the chromatin itself and, plus, get this,
some of the factors only do it in one direction, right. That’d be a good
conversation starter, right? That’d be the end of
the conversation, no. You get the idea, right. So are there any questions
about DNase-1 seq analysis? Yes? AUDIENCE: A little unrelated,
but I was just wondering– in the literature where people
have identified factors that neither directly reprogram
between different cell types, or go through some sort of
[INAUDIBLE] intermediate– PROFESSOR: Yes. AUDIENCE: There are a number
of transcription factors that have been
identified. [INAUDIBLE] but there are others. Do you often see, or always
see some of the pioneers that you’ve identified
in those cases. And then– PROFESSOR: Yes. AUDIENCE: And then,
a follow-up question would be, do you think that if
you took some of the pioneers that you generated that
were not known before and expressed them
in cell types, that they would open
up the chromatin sufficiently to potentially
reprogram the mistakes? PROFESSOR: Right. So the question
was, is it the case that known
reprogramming factors, at times are powerful pioneers? The answer is yes. The second question was,
now that you have a broader repertoire of pioneer
factors, and you can identify what they’re
doing, is a possible to, in a principled way, engineer
the opening of chromatin by perhaps expressing those
factors to see whether or not you could match a particular
desired epigenetic state, let’s say? Our preliminary results are yes
on the second count as well. That there appear to
be pioneer factors that operate, sort of at a
basal level that keep, sort of, the sort of usual
rooms open in the genome. And then there are
factors that operate in a lineage-specific
specific way. And when we express
lineage-specific pioneer factors, they don’t completely
mimic but largely mimic the chromatin state
that’s present in the corresponding
lineage committed cells. And so we think that for
principal reprogramming of cells, the basal level
of establishing matched open states is going to be
an interesting and important avenue to explore. Does that answer your question? Yeah. OK. So, now we’re going to
turn to another– well let me just first summarise
what I just told you about, which is that we
can predict where TFs bind from DNase-seq data. We can identify these
pioneer factors. Some of them are directional. And other factors follow
these pioneers and bind sort of in their wake. In where they are actually
open up the chromatin. And returning to our
narrative arc for today, we’ve talked about the
idea of histone marks. We’ve talked about the
idea of chromatin openness and closeness. And now I’d like to talk about
the important question of how we can understand which
regulatory regions are regulating which genes. Now the traditional
way to approach this, is that if you have a regulatory
region, the thing that you do is you look for
the closest gene. And you go, aha, that’s the one
that that regulatory region is controlling. This applies not only
for regulatory regions but for snips, right. If you find a snip
or a polymorphism you are likely to
assume that it’s regulating the closest gene. It could have an effect
on the closest gene. But there are other ways of
approaching that question with molecular protocols. And drawing you once again
a cartoon of genome looping, you can see how an enhancer is
coming in contact with the Pol II holoenzyme apparatus. And this enhancer will
include regulators that will cause Pol II
to begin transcription. And if somehow we could
capture these complexes so that we could examine them
and figure out what bits of DNA are associated with
one another, we could map, directly, what
enhancers are controlling what genes, when they’re
active in this form. So the essential idea of a
variety of different protocols, whether it be protocols
like high c or ChIA-PET that we’re going to
talk about are the same. The difference is that
in the case of ChIA-PET, we’re only going to look
at interactions that are defined by a
particular protein. So what we’re going to do in
the slides I’m going to show you today, is we’re
going to only look at interactions that are
mediated through RNA polymerase II. And those are particularly
interesting interactions as you can see,
because they involve actively transcribed genes. So if we could capture all
the RNA polymerase II mediated interactions, we’d
be in great shape. So, we have a lot of very
talented biologists here. So would anybody like to make
a suggestion for a protocol for actually revealing
these interactions? Does anybody have any ideas
how you’d go about that? Or what enzyme
might be involved? Any ideas? Don’t be bashful now. Yes. AUDIENCE: How about fixing
everything in place where it is and then getting
[INAUDIBLE] through DNA. PROFESSOR: OK. Fixing everything
where it is in place. That’s good. So we might cross link this
whole thing, for example. OK. And then any other
ideas what we would do? That’s done, this
protical– yes. AUDIENCE: Well, [INAUDIBLE] that
you’ve going to be [INAUDIBLE]. And then digesting the
DNA that’s coming out, and then that lingers
to the DNA that are closest together
in the sequence. PROFESSOR: OK. So I think what you’re
suggesting goes something like this. All right. Which is, that imagine that
we cross link those complexes and we precipitate them. And then what we do is we,
in a very dilute solution, we ligate the DNA together. And so we get two kinds
of ligation products. On the left-hand side we
get self-ligation products where a DNA molecule
ligates to itself. And on the right-hand side we
get inner ligation products, where the piece of DNA
that the enhancer was on, ligates to the pieces of DNA
that the RNA polymerase was transcribing the gene on. And those inter-ligation
bits of DNA, the ones that are red and blue,
are really interesting, right. Because they contain both
the enhancer sequence and the promoter sequence. And all we need to do now is
to sequence those molecules from the ends and figure out
where they are in the genome. Yes? AUDIENCE: How much variation
would there be in the sequence? I guess I’m just wondering– the
RNA polymerase is not static, is it? In terms of its interaction
with the intenser and the gene. I just don’t know what
would be capturing in this– PROFESSOR: Right. AUDIENCE: [INAUDIBLE]
doesn’t just touch at the beginning
and then [INAUDIBLE]. PROFESSOR: Right. And I think that’s a
very good question. And in fact, a PhD thesis was
just written on this topic. Which is, when you have
proteins that are moving down the genome, in
some sense, you’re looking at a blurred picture. So how do you
de-blur the picture so that it’s brought
sharply into focus? And so a compute is something
called a point spread function which describes how things are
spread out down the genome. And then you invert that to get
a more focused picture of where the protein is actually,
primarily located. But you’re right. Things like RNA
polymerase II are not thought of as
point-binding proteins. They’re actually proteins
in motion most time when they’re doing their work. AUDIENCE: [INAUDIBLE]
that it’s polymerizing, does that it mean that it’s
still continually bound to the [INAUDIBLE]? PROFESSOR: No. Although, I don’t
think we really understand all of the
details of that mechanism. But, suffice to say
that what I can do is I can start showing
you data and from the data we can try and
understand mechanism. These are all great
questions, right. Yes. AUDIENCE: When we did the
citations and ligation, you’re going to get a lot
of random ligation, right? PROFESSOR: A lot
of random ligation? AUDIENCE: Yeah, between DNA
sequences that aren’t aren’t, I guess, as close? Or you shouldn’t really be
ligating certain things? PROFESSOR: Well, this picture is
a little bit deceiving, right? Because there’s actually another
complex just like the one at the top, right
to its left, right? And you could imagine those
things ligating together. And so now you’re going to
get ligation products that are noise. They don’t mean anything. AUDIENCE: Do you just
throw those out, I guess? PROFESSOR: Well, the problem is,
you don’t know which ones are noise and which ones aren’t. Right? Now, there are some clever
tricks you can play. One clever trick is
to change the protocol to do these kinds
of reactions, not in solution, but
in some sort of gel or other thing that
keeps the products apart. The other thing you
can do is estimate how bad the situation is. And how might you do that? What you do is, you
take one set of– you take your original preparation
and you split it into two. OK. And you color this one red and
this one blue using linkers, right. And then you put them together
and you do this reaction. And then you ask,
how many molecules have the red and the
blue linkers on them. And then you know those are
bad ones because they actually came from different
complexes, right. And so by estimating the amount
of critical chimeric products you get, from that split and
then recombined approach, you can optimize the protocol to
reduce the chimeric production rate. Current chimeric production
rates are about 20%. Something of that order. OK. It used to be 50%,
that’s really bad. OK. So you can try
and optimize that. Now, if the protocol
has these issues– you have a moving protein
that was brought up here, right, that you’re
trying to capture. You’ve got a lot of noise
coming from the background of these reactions, right. Why are we doing this? Well, it’s the only
game in town right now. If you want to have
a mechanistic way of understanding what enhancers
are communicating with what genes, this and its
family– I broadly call this a family
of protocols– is really the only way to go. OK. The interesting thing
is that when you do, you get data like this. And so, what you’re
looking at here is exactly the same
location in the genome. It’s about 600,000 bases
across from left to right. OK. And at the very bottom,
you see the SOX2 gene. And you have three
different cellular states. The top state–
our motor neurons have been programmed through
the ectopic expression of three transcription factors. The second set of
interactions are motor neurons that have been
produced by exposure to small molecules
over a 7-day period. And the bottom set
of interactions are from mouse ES cells
that are plueripotent. And what’s interesting
is that you can see how– I’m
going to point here. You can see here– this is the
SOX2 gene down at the bottom. And you can see here–
this regulatory region is interacting heavily with
the SOX2 gene at the ESL state. And above here, I have
put SOX2 ChIP-seq data. So you can actually see that
SOX2 is regulating itself. And up here, we have the
same SOX2 gene locus. And OLIG2 is a key regulator
of this motor neuron fate. And you can see that it
appears that OLIG2 is now regulating SOX2. And we don’t have as complete
dependence upon the SOX2 locus as we had before. And up here in the induced
motor neuron state, LHX4 is one of the
reprogramming factors and you can see how it is
interacting with SOX2 here and over here. So what this methodology
allows us to do, is to tie these regulatory
regions to the genes that they are regulating,
albeit it with some issues. So, we’ll talk about the
issues in just a second. Are there any questions at all
about the idea of capturing, in essence, the folding of the
genome with this methodology to link regulatory
regions to genes? Yes? AUDIENCE: I have a question. So in each of
those charts you’ve got parts describing regions
that are interacting. PROFESSOR: Yes. AUDIENCE: Is that correct? PROFESSOR: Yes. The little loops underneath
are the actual read pairs that came out of the sequencer. And the green dotted
lines are the interactions I’m suggesting are significant. So I’m showing you
the raw data and I’m showing you the hypothesized
or purported interactions with the green dotted lines. Right? Right? AUDIENCE: So how is you raw
sequencing then transformed into this set of interactions? PROFESSOR: How is the raw
sequencing data– remember that what came out
of the protocol were molecules on the
right-hand side that had little bits of DNA from two
different places in the genome. AUDIENCE: I’m
sorry, I meant, how did you determine– because
I’m assuming each of these arcs has to have a single base start
side and a single base end site. PROFESSOR: Correct. AUDIENCE: However,
your reads are going to span– your
joined paired reads are going to span a number of bases. So you have a number
of bases coming from the red part
and a number of bases coming from the blue part. PROFESSOR: We’ve got
20, 20 something, yeah. AUDIENCE: How do you determine
which of these red bases and which of these blue
bases are your start and end points for
the [INAUDIBLE]. PROFESSOR: Well, you are
looking at a 600,000 base pair window of the
genome and we’re not quite at the resolution
of 28 bases yet. AUDIENCE: OK. PROFESSOR: So, you know– AUDIENCE: So this is not
necessarily single base pair resolution, but this
is a region resolution? Is that correct? PROFESSOR: Once
again, the question of how to improve the spatial
resolution of these results is a subject of active research. And once again, you
can deconvolve things like the shearing to
actually get things down to within, say, 10 to
100 base pairs resolution. AUDIENCE: OK. PROFESSOR: OK? AUDIENCE: Got it. PROFESSOR: But you can’t
identify the exact motif that the things land on, right. They can get in the
ballpark, so to speak, right. You can figure out where
you need to look for motifs. And so one thing
that we and others do is look at these
regions and we ask what motifs are present
into these regions. Or if you have match DNase-seq
data, you can go back and you can say, aha,
I have DNase-seq data. I have this data and
I know that there’s something going on at
that region of the genome. What proteins do I
think are sitting there, based upon the protection
profiles I see. Right. So you can take an
integrative approach where you use different
data types to begin to pick apart the
regulatory network. Where you see the connections
directly molecularly, and you see the
regulatory proteins that are binding
at those locations. OK? Was that helpful? Good. Good questions. Any other questions? Yes? AUDIENCE: Would you consider
Hi-C and 5C and all of those to be the same
family of technique? PROFESSOR: I would. They’re all, sort of the same
family and they’re improving. I’m about to tell you why
this doesn’t work very well. But, that said, it’s the
best thing we have going. Right. 5C is not any to any. It’s to one to any. This protocol, when you do
one experiment with this, it tells you all the interacting
regions in the genome. Right. I believe 5C– help
me if I’m wrong. You pick one anchor
location and then you can tell all the
regions and genomes that are interacting with
that anchor location. AUDIENCE: Isn’t that 3C? PROFESSOR: What? AUDIENCE: 3C’s one to one. 4C’s one to any. AUDIENCE: And 5C is– AUDIENCE: 5C’s any to any. PROFESSOR: And 5C’s any to any? OK. I stand correct. Thank you. Yeah. OK. You didn’t critique
my bond type. See I was trying to
get you and you didn’t. OK. And other questions about this? OK. What could go wrong? What could go wrong? Well, I can tell you
what will go wrong. What will go wrong is that it
has a low true positive rate. OK. And how can you tell that? You do the experiment
twice and you get thousands of interactions
from each experiment in exactly matched conditions and
there’s a very small overlap between the conditions. Oops. So, that’s a pretty
big oops, right? Because you would like it
to be the case that when you do an experiment multiple
times, you get the same answer. So let us just
suppose that you get 10,000 interactions
in experiment one. 10,000 interactions in
experiment two, but only 2,000 of them are the same. What could possibly
be going wrong? Any ideas? If you’re looking at the
data, what would you think? Well? Yeah? AUDIENCE: [INAUDIBLE]
could be really high, so you’re just seeing
a couple of things that are above the background. And they don’t necessarily– PROFESSOR: Right. So is it maybe
that, you know, it’s just tough to get
these interactions out. And so you got a lot
of background trash. And the things that
are significant are tough to pick out. Yeah? AUDIENCE: Maybe it’s a real
biological noise issue? So rather than the technique,
actually any given time that the interactions as so diverse
that when you take the snap shot you can’t– PROFESSOR: I like
that explanation because it’s very pleasing
and makes me feel good. And I would be hopeful
that that would be true that there’s enough biological
noise that that’s actually what I’m observing. It doesn’t make me feel
too warm and fuzzy, but you know, I’d
go with that, right. The other thing you
might think is, gee, if we just sequenced
that library more, we’d get more interactions
out them, right? So you go off and you compute
the library complexity of your library and you go,
oops, that’s not going to work. There just isn’t enough
diversity in the library. Meaning that the underlying
biological protocol did not produce enough of those
interesting inner ligation events to allow you to reveal
more information about what’s going on. OK. Now if I ask you to judge the
significance of an interaction pair here. Let’s think about
this using what we know already
from the subject. OK. So I’m going to draw a picture. So I have my genome. And let’s just say that I have
a location, CA and a location CB and I have a pile of ends that
wind up in those two locations. OK. And what I would like
to know is– and I have, let me just see what
variable I used for this. And I have a certain number of
interactions between a and b. That is I have a certain
number of reads that cross between these two
locations in the genome. And I’d like to know whether
or not this number of reads is significant. OK. How could I estimate that? Any ideas? Oh, I’m also going
to tell you that n is the total number
of read ends observed. OK. Well, here is the idea. I’ve got n total
read ends, right? I’ve got ca read ends here. I’ve got cv read
ends here, and I have iab that are overlapping. So now, this is just our old
friend, the hypergeometric, right. We can ask what is the
probability of that happening at random? This many interactions or
fewer would happen at random. And if it’s very
unlikely, we would reject the null hypothesis
and accept that there’s really an interaction going on here. OK? So, just to be more
precise about that. This is what it looks like. You’ve seen this before. That the probability of
those interactions happening on a null model, given a total
number of interactions end in ca and cb is given by
the hypergeometric. OK. So that’s one way of going
about assessing whether or not the interactions we
see are significant. Now, let me ask you a
slightly different question. Right. Imagine that I have– and
I’m being very generous here. Imagine that I have
two experiment– that’s the wrong size bubbles. I don’t want to mislead you. One of your friends
comes to you and say, “I’ve done this
experiment twice.” Twice, OK. “And each time I get
1,000 interactions. So each one gives
you 1,000, let’s say. And I have 900 that are common
between the two replicates. And your friend says,
“how many interactions do you think there
are in total?” How could we estimate that? Well, what’s interesting
about this problem is that what we’re
asking is what’s n? Right. What’s the total number of
interactions of which we’re observing this set and this set
of which 900 is overlapping. There’s the hyperlink
geometric again. So all we need to do is to find
the maximum value, the best value for n that predicts the
observed overlap given that we have two experiments
of size, with m and n different observations,
and we have an overlap of k. OK. Does that makes
sense to everybody? Of how to estimate the
total number of interactions out there making a
set of assumption that they’re all equally likely. Any questions about that at all? OK. And, just so you know, you can
approximate this, this way. Which is that the maximum
likelihood estimate of the total number
of interactions is approximately
n times n over k, as seen by the
approximation on the bottom. OK? Just so that you can
approximate how many things are out there that you
haven’t seen when you’ve done a couple of replicates. OK, you guys have
been totally great. We’ve talked about a
lot of different things today in chromatin
architecture and structure. Sort of the DC to light
version of chromatin structure and architecture lecture. Next time we’re going
to talk about building genetic models of EQTLs. And the time after
that we’re going to talk about human genetics. Thank you so much. Have a great, long weekend. We’ll see you next Thursday.

1 Comment

  • Reply Lotus Sreerengini May 11, 2017 at 6:39 pm

    Thank you.

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