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ATAC-Seq Optimization for Cancer Epigenetics Research

ATAC-Seq Optimization for Cancer Epigenetics Research

Published on: June 30, 2022

Protocol for base resolution mapping of ac4C using RedaC:T-seq.

David Sturgill¹, Daniel Arango², Shalini Oberdoerffer¹

¹Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.

|January 3, 2023

Summary

This summary is machine-generated.

This study introduces RedaC:T-seq, a novel method to map N4-acetylcytidine (ac4C) mRNA modifications at base resolution. This technique enables precise identification of ac4C positions, crucial for understanding mRNA translation regulation.

Keywords:

Bioinformatics Molecular Biology RNAseq Sequencing

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High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

Published on: October 5, 2018

Area of Science:

Molecular Biology
Epigenetics
RNA Biology

Background:

N4-acetylcytidine (ac4C) is a dynamic mRNA modification impacting translation.
The enzyme N-acetyltransferase 10 (NAT10) catalyzes ac4C formation.
Understanding ac4C distribution is key to deciphering gene expression regulation.

Purpose of the Study:

To develop a high-resolution method for mapping ac4C modifications on mRNA.
To enable base-specific detection of ac4C across the transcriptome.
To provide a tool for investigating the functional roles of ac4C.

Main Methods:

Developed RedaC:T-seq protocol for ac4C mapping.
Utilized NaBH4 to reduce ac4C to tetrahydro-ac4C.
Leveraged altered base pairing during cDNA synthesis for detection via Illumina sequencing.

Main Results:

Successfully mapped ac4C at base resolution.
Demonstrated specific detection of ac4C sites.
Established a protocol for transcriptome-wide ac4C profiling.

Conclusions:

RedaC:T-seq is an effective method for precise ac4C mapping.
This technique facilitates the study of ac4C's role in mRNA translation.
Provides a valuable tool for RNA epigenetics research.