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A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq
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 ge...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3378898/ https://www.ncbi.nlm.nih.gov/pubmed/22323522 http://dx.doi.org/10.1093/nar/gks063 |
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author | Wilbanks, Elizabeth G. Larsen, David J. Neches, Russell Y. Yao, Andrew I. Wu, Chia-Ying Kjolby, Rachel A. S. Facciotti, Marc T. |
author_facet | Wilbanks, Elizabeth G. Larsen, David J. Neches, Russell Y. Yao, Andrew I. Wu, Chia-Ying Kjolby, Rachel A. S. Facciotti, Marc T. |
author_sort | Wilbanks, Elizabeth G. |
collection | PubMed |
description | 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 open-source bioinformatics method, is presented for identification of binding events. Relative to ChIP-Chip 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. |
format | Online Article Text |
id | pubmed-3378898 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-33788982012-06-20 A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq Wilbanks, Elizabeth G. Larsen, David J. Neches, Russell Y. Yao, Andrew I. Wu, Chia-Ying Kjolby, Rachel A. S. Facciotti, Marc T. Nucleic Acids Res Methods Online 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 open-source bioinformatics method, is presented for identification of binding events. Relative to ChIP-Chip 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. Oxford University Press 2012-05 2012-02-09 /pmc/articles/PMC3378898/ /pubmed/22323522 http://dx.doi.org/10.1093/nar/gks063 Text en © The Author(s) 2012. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Methods Online Wilbanks, Elizabeth G. Larsen, David J. Neches, Russell Y. Yao, Andrew I. Wu, Chia-Ying Kjolby, Rachel A. S. Facciotti, Marc T. A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq |
title | A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq |
title_full | A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq |
title_fullStr | A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq |
title_full_unstemmed | A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq |
title_short | A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq |
title_sort | workflow for genome-wide mapping of archaeal transcription factors with chip-seq |
topic | Methods Online |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3378898/ https://www.ncbi.nlm.nih.gov/pubmed/22323522 http://dx.doi.org/10.1093/nar/gks063 |
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