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RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
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A Semiautomated ChIP-Seq Procedure for Large-scale Epigenetic Studies

A Semiautomated ChIP-Seq Procedure for Large-scale Epigenetic Studies

Published on: August 13, 2020

A Scalable Epitope Tagging Approach for High Throughput ChIP-Seq Analysis.

Xiong Xiong¹, Yanxiao Zhang², Jian Yan^2,3

¹Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.

ACS Synthetic Biology

|February 21, 2017

Summary

This summary is machine-generated.

Researchers developed cmChIP-Seq, a new method using CRISPR and MMEJ to tag transcription factors (TFs) genetically. This technique enables efficient mapping of TF-DNA interactions, overcoming antibody limitations for ChIP-Seq analysis.

Keywords:

CRISPR/Cas9 ChIP-Seq FLAG tagging genome engineering microhomology mediated end joining

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Generation of High Quality Chromatin Immunoprecipitation DNA Template for High-throughput Sequencing ChIP-seq

Generation of High Quality Chromatin Immunoprecipitation DNA Template for High-throughput Sequencing ChIP-seq

Published on: April 19, 2013

Area of Science:

Genomics
Molecular Biology
Epigenetics

Background:

Transcription factors (TFs) regulate gene expression by binding to specific DNA sequences.
Mapping TF-DNA interactions is vital for understanding cellular gene regulatory networks.
Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) is a common method, but relies on specific TF antibodies, which are often unavailable.

Purpose of the Study:

To develop a novel, antibody-independent method for mapping TF-DNA interactions.
To overcome the limitations of traditional ChIP-Seq due to the lack of suitable antibodies.
To establish a scalable strategy for TF-DNA interaction analysis across various cell types and species.

Main Methods:

Developed cmChIP-Seq, combining CRISPR technology with microhomology mediated end joining (MMEJ).
Genetically engineered transcription factors (TFs) with an epitope tag using the CRISPR-MMEJ system.
Applied the cmChIP-Seq strategy to four TFs in a human colorectal cancer cell line.

Main Results:

Successfully demonstrated the utility of the cmChIP-Seq strategy for TF-DNA interaction mapping.
Showcased the efficiency and scalability of the developed method.
Provided a viable alternative to antibody-dependent ChIP-Seq for TF analysis.

Conclusions:

The cmChIP-Seq strategy offers an efficient and scalable approach for mapping TF-DNA interactions.
This method overcomes the critical limitation of antibody availability in traditional ChIP-Seq.
cmChIP-Seq is suitable for broad application in TF analysis across diverse biological contexts.