We've updated our Privacy Policy to make it clearer how we use your personal data.

We use cookies to provide you with a better experience. You can read our Cookie Policy here.

Advertisement
A Workflow for Genome-Wide Mapping of Archaeal Transcription Factors with ChIP-seq
News

A Workflow for Genome-Wide Mapping of Archaeal Transcription Factors with ChIP-seq

A Workflow for Genome-Wide Mapping of Archaeal Transcription Factors with ChIP-seq
News

A Workflow for Genome-Wide Mapping of Archaeal Transcription Factors with ChIP-seq

Read time:
 

Want a FREE PDF version of This News Story?

Complete the form below and we will email you a PDF version of "A Workflow for Genome-Wide Mapping of Archaeal Transcription Factors with ChIP-seq"

First Name*
Last Name*
Email Address*
Country*
Company Type*
Job Function*
Would you like to receive further email communication from Technology Networks?

Technology Networks Ltd. needs the contact information you provide to us to contact you about our products and services. You may unsubscribe from these communications at any time. For information on how to unsubscribe, as well as our privacy practices and commitment to protecting your privacy, check out our Privacy Policy

Abstract

Deciphering the structure of gene regulatory networks across the tree of life remains one of the major challenges in postgenomic biology. We present a novel ChIP-seq workflow for the archaea using the model organism Halobacterium salinarum sp. NRC-1 and demonstrate its application for mapping the genome-wide binding sites of natively expressed transcription factors. This end-to-end pipeline is the first protocol for ChIP-seq in archaea, with methods and tools for each stage from gene tagging to data analysis and biological discovery. Genome-wide binding sites for transcription factors with many binding sites (TfbD) are identified with sensitivity, while retaining specificity in the identification the smaller regulons (bacteriorhodopsin-activator protein). Chromosomal tagging of target proteins with a compact epitope facilitates a standardized and cost-effective workflow that is compatible with high-throughput immunoprecipitation of natively expressed transcription factors. The Pique package, an opensource bioinformatics method, is presented for identification of binding events. Relative to ChIPChip and qPCR, this workflow offers a robust catalog of protein–DNA binding events with improved spatial resolution and significantly decreased cost. While this study focuses on the application of ChIP-seq in H. salinarum sp. NRC-1, our workflow can also be adapted for use in other archaea and bacteria with basic genetic tools.

This article is published online in Nucleic Acids Research and is free to view.

Advertisement