ATAC-seq regulatory element types such as promoters and enhancers.

ATAC-seq report

Main aim

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The ATAC-seq assay is mainly aiming at
identifying the accessible DNA regions and then interpret the interaction
between genomic locations of open-chromatin, individual nucleosomes,
nucleosome-free region and DNA-binding proteins.

 

Introduction

ATAC-seq is a technology which can be used
to investigate the chromatin accessibility.

In human cells, the long DNA strands are
always being packaged by wrapping it around histones and then further condensed
into chromatin. The ATAC-seq can utilizing the transposase Tn5 which act on the
genomic DNA, cleaving the open chromatin region specifically. By using the NGS
sequencing we can easily get the information about the chromatin accessibility
and nucleosome positioning.

 

Procedure:

1. Cell preparation:

In this step, ATAC-seq using the same means
of methods for cell separation and isolation, including cell sorting, cell
collecting, cell lysing (e.g. cold lysis buffer).

2. Transposition reaction:

The key step of ATAC-seq procedure is
transposition. The adaptor-loaded transposase Tn5 can act preferentially on the
nucleosome-free region or the exposed DNA, then catalyze both the movement of
adaptors to the regions and the fragmentation process, this progression is also
called “tagmentation”.

The natural transposases have low reactive
efficiency so they have been previously mutated in order to increase their
activity significantly. After the transposition, the sequencing adaptors are
inserted into accessible regions of chromatin which contribute to the following
PCR amplification and sequencing step.

 

3. Analysis

The ATAC-seq will produce a large amount of
NGS reads that can be mapped on the reference genome. Based on this, we can get
a cut count for each genomic position and create a signal with base-pair
resolution.

The accessible regions during this
experiment will contain more sequencing reads because they are the region which
the transposase acts specifically, and then it will form some peaks in the
signal graph.

These regions can then be categorized into
various regulatory element types such as promoters and enhancers. Further ,the
position of nucleosomes and nucleosome-free regions can be visualized as well.

Advantages:

1. Low requirements of the input materials:
500-50000 cells are sufficient for this experiment to get a reliable result.

2. High speed: The whole experiment only
cost 3 hours in total.

3. High-resolution mapping.

4. The entire assay and library
construction can be performed in a simple protocol, significantly reduce the
error which take placed in the multistep protocols or many potentially
loss-prone steps.

 

Main challenge:

Analyzing ATAC-seq experiments has a big
challenge that the datasets which we finally got tend to be large, sparse and
binary. So, some normal single-cell analysis approaches will not appropriate in
this experiment, for instance, the principal component analysis.

 

Article: Exhaustion-associated regulatory
regions in CD8+ tumor-infiltrating T cells

 

Main aim

The main aim of this article is to find out
regulatory regions associated with T-cells exhaustion in CD8+
tumor-infiltrating T cells, and define chromatin accessibility and
transcriptional profiles in tumor-reactive and non-reactive tumor-infiltrating
T-cells by combining RNA sequencing (RNA-seq) and Assay for transposase
accessible chromatin sequencing (ATAC-seq).

 

How is the ATAC-seq being used and
conclusions

In earlier part of the experiments, NFAT
transcription factor is investigated to substantially contribute to exhaustion
of CD8+ T-cells.

1. genome-wide changes in chromatin
accessibility of in vitro-generated CTLs caused by re-stimulation.

To detect what changes happened to
chromatin accessibility of in vitro-generated CTLs after re-stimulation. And
check the effect of NFAT and other transcription factors in the exhaustion
program.

(Although for histone modifications,
ChIP-seq can be performed on small number of cells, ChIP-seq in this experiment
with limited cell numbers has a low technically feasible. Thus, ATAC-seq was
used to probe chromatin accessibility with very few of cells.

ATAC-seq can identify accessible regions,
and find out enriched known sequence motifs that are bound by specific families
of transcription factors. The exact type of transcription factors occupying
accessible regions can be indicated by RNA-seq.)

ATAC-seq was performed on in unstimulated
vitro-differentiated CTLs.

Re-stimulation was performed.

(1) re-stimulated by ionomycin (Iono) –
activated NFAT

(2) re-stimulated by PMA + Iono – activated
NFAT, AP-1, NF?B

(3) re-stimulated by PMA + anti-CD3 –
activated AP-1, NF?B, less activated NFAT.

ATAC-seq was performed on re-stimulated
CTLs.

A set of about 4,300 regions were
identified which showed differential accessibility, and classified into five
clusters. Enrichment level analysis of motifs was performed.

Different accessible regions caused by
different stimulation condition were identified based on ATAC-seq experiments.
Combined with motif enrichment analysis, showed a series of known transcription
factors that may drive gene expression under different stimulation conditions.

This part set a foundation of subsequent
analysis of accessible regions in CD8+ tumor-infiltrating T cells.

 

2. Genome-wide chromatin accessibility
overview of OT-I (exhausted) and P14 (non-exhausted) TILs.

ATAC-seq was performed on OT-I and P14
TILs.

1,864 regions that more accessible in OT-I
than in P14 (red dots), and 453 regions more accessible in P14 than in OT-I
(blue dots) were identified.

They mainly focused on the regions with a
higher accessibility in OT-I, and found that these regions showed enrichment
for transcription factor motifs associated with T-cell activation, i.e. AP-1,
NF?B, and NFAT:AP-1.

Motifs for NFAT (without adjacent AP-1)
were enriched in specific regions of OT-I TILs.

The strongest enrichment of accessible
regions specific of OT-I TILs is Nur77.

The working hypothesis “NFAT binding
without AP-1 contributes to exhaustion of T-cells” and the result of experiment
reach an agreement.

 

3. Identification of specific accessible
regions of exhaustion in OT-I TILs.

ATAC-seq was promoted on the 1864 regions
that have a higher accessibility in OT-I than in P14, 1,414 of them showed
different accessibility in CD8+ T-cells re-stimulated by PMA + Iono or PMA +
anti-CD3 in vitro and OT-I TILs, these 1,414 regions were defined to be related
to activation. By contrast, other 450 regions were defined as exhaustion
associated.