To Visually Observe Easily Accessible Chromatin Using ATAC-see

Techniques

In the limited space of the nucleus, the most parts of genome are tightly folded, and only the
transcription part is accessible. Howard Chang from Stanford University said, "people have
great interest to determine which regions of the genome of a given cell type is active, which
is just the motivation to develop a technology called ATAC-seq (Assay for
Transposase-Accessible Chromatin with highthroughput sequencing) by Chang. With
ATAC-seq, DNA markers (function as transposon) are integrated into the open regions of the
genome by enzymatic reaction, then by sequencing, they are used for the identification of
these areas.

Chang described ATAC-seq in 2013, but he said, "We get this information from broken cells,
so we can't understand the three-dimensional structure of these accessible genomic regions."

Over the past three years, Chang has developed the ATAC-see technology, also known as
assay of transposase-accessible chromatin with visualization. This technology uses the same
enzymatic method with ATAC-seq to integrate the DNA markers. Differently, the
fluorophores coupled with these DNA markers allow to observe the 3D structure of fixed
nucleus visually. Moreover, once these cells are observed, a marked area can be identified by
sequencing. .

With ATAC-see technology, the Chang team found that unlike most cells, in neutrophils,
accessible chromatin tends to appear in the nucleus edge. This distribution seems to promote
neutrophil extracellular traps (NET) forming. NET is the important bactericidal weapon of
neutrophil. This kind of cell directly spits out its own DNA and histones to form a mesh of
traps to catch and kill pathogens. However, NET can also promote cancer metastasis.

The Chang team also uses ATAC-see technology to study how the entire genome's
accessibility changes during the cell cycle.

Job Dekker (who was not involved in the study) at University of Massachusetts Medical
School said, "One of the major challenges in the field of chromatin research is to integrate the
data obtained by genomic and imaging methods together. Therefore, for the detection
technology, one of the things I love is that it's a combination of the above two".

Easily Detection Technical Visualization The number of

Accessible Principles Difficulty cells required
Chromatin for sequencing
Detection
Techniques
 DNase I biased Particularly No At least of
digests the difficult. millions
accessible DNA. Optimized
Ligate adapters digestion
to these digested conditions are
DNA chains, required.
DNase-seq
and then use
these adapters to
isolate and
sequence these
digested
regions.

ATAC-see Transposases For those who are Yes 50 thousand.

insert adapters skilled in the ATAC-seq (lack
labeled by standard molecular of
fluorescent technology, it is fluorescence-lab
groups into relatively simple. eled visual
accessible observation
chromatin, and techniques) has
then DNA can detected in a
be visually single cell, so
observed, the number of
amplified and required cells
sequenced by may be feasible.
using these
adapters

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Source:
https://www.creative-biogene.com/blog/index.php/2017/09/05/to-visually-observe-easily-acce
ssible-chromatin-using-atac-see-techniques/