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Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq

Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq

Published on: November 13, 2017

TT-seq maps the human transient transcriptome.

Björn Schwalb¹, Margaux Michel¹, Benedikt Zacher²

¹Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen, Germany.

Science (New York, N.Y.)

|June 4, 2016

Summary

This summary is machine-generated.

Transient transcriptome sequencing (TT-seq) maps all RNA types, revealing short-lived enhancer RNAs and identifying transcription termination sites. This method provides a comprehensive view of genome-wide RNA synthesis and degradation dynamics.

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Area of Science:

Genomics
Molecular Biology
Transcriptomics

Background:

The genome continuously produces various RNA molecules, including stable and transient forms.
Understanding the full spectrum of RNA production and turnover is crucial for deciphering gene regulation.

Purpose of the Study:

To develop and apply a novel method, transient transcriptome sequencing (TT-seq), for comprehensive mapping of RNA-producing units.
To estimate RNA synthesis and degradation rates across the genome.
To characterize transient RNAs, including enhancer RNAs, and identify transcription termination sites.

Main Methods:

Development of transient transcriptome sequencing (TT-seq) protocol.
Application of TT-seq to human K562 cells.
Bioinformatic analysis of sequencing data to map RNA species and termination sites.

Main Results:

TT-seq successfully mapped stable messenger RNAs, long noncoding RNAs, and various transient RNAs (enhancer, antisense, promoter-associated).
Enhancer RNAs were characterized as short-lived molecules lacking U1 motifs and significant secondary structure.
Multiple transcription termination sites were identified, associated with a DNA motif promoting RNA polymerase pausing.

Conclusions:

TT-seq offers a uniform approach to profile the entire transcriptome, encompassing both stable and transient RNA species.
The study provides new insights into the characteristics and regulation of transient RNAs, particularly enhancer RNAs.
Identification of transcription termination sites advances the understanding of RNA processing and genome regulation.