التفاصيل البيبلوغرافية
| العنوان: |
A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq |
| المؤلفون: |
Wilbanks, Elizabeth G, Larsen, David J, Neches, Russell Y, Yao, Andrew I, Wu, Chia-Ying, Kjolby, Rachel AS, Facciotti, Marc T |
| المصدر: |
Nucleic Acids Research, vol 40, iss 10 |
| بيانات النشر: |
eScholarship, University of California |
| سنة النشر: |
2012 |
| المجموعة: |
University of California: eScholarship |
| مصطلحات موضوعية: |
Biochemistry and Cell Biology, Bioinformatics and Computational Biology, Genetics, Biological Sciences, Human Genome, Bioengineering, Biotechnology, Generic health relevance, Archaeal Proteins, Binding Sites, Chromatin Immunoprecipitation, Genome, Archaeal, Halobacterium salinarum, High-Throughput Nucleotide Sequencing, Sequence Analysis, DNA, Software, Transcription Factors, Environmental Sciences, Information and Computing Sciences, Developmental Biology, Chemical sciences |
| جغرافية الموضوع: |
e74 - e74 |
| الوصف: |
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. |
| نوع الوثيقة: |
article in journal/newspaper |
| وصف الملف: |
application/pdf |
| اللغة: |
unknown |
| العلاقة: |
qt1pb9j2mf; https://escholarship.org/uc/item/1pb9j2mfTest |
| الإتاحة: |
https://escholarship.org/uc/item/1pb9j2mfTest |
| حقوق: |
public |
| رقم الانضمام: |
edsbas.69026693 |
| قاعدة البيانات: |
BASE |
