Show simple item record

dc.contributor.authorGarber, Manuel
dc.contributor.authorAmit, Ido
dc.date2022-08-11T08:08:36.000
dc.date.accessioned2022-08-23T16:01:05Z
dc.date.available2022-08-23T16:01:05Z
dc.date.issued2012-09-14
dc.date.submitted2018-07-18
dc.identifier.citation<p>Mol Cell. 2012 Sep 14;47(5):810-22. doi: 10.1016/j.molcel.2012.07.030. Epub 2012 Aug 30. <a href="https://doi.org/10.1016/j.molcel.2012.07.030">Link to article on publisher's site</a></p>
dc.identifier.issn1097-2765 (Linking)
dc.identifier.doi10.1016/j.molcel.2012.07.030
dc.identifier.pmid22940246
dc.identifier.urihttp://hdl.handle.net/20.500.14038/31037
dc.description<p>Full author list omitted for brevity. For the full list of authors, see article.</p>
dc.description.abstractUnderstanding the principles governing mammalian gene regulation has been hampered by the difficulty in measuring in vivo binding dynamics of large numbers of transcription factors (TF) to DNA. Here, we develop a high-throughput Chromatin ImmunoPrecipitation (HT-ChIP) method to systematically map protein-DNA interactions. HT-ChIP was applied to define the dynamics of DNA binding by 25 TFs and 4 chromatin marks at 4 time-points following pathogen stimulus of dendritic cells. Analyzing over 180,000 TF-DNA interactions we find that TFs vary substantially in their temporal binding landscapes. This data suggests a model for transcription regulation whereby TF networks are hierarchically organized into cell differentiation factors, factors that bind targets prior to stimulus to prime them for induction, and factors that regulate specific gene programs. Overlaying HT-ChIP data on gene-expression dynamics shows that many TF-DNA interactions are established prior to the stimuli, predominantly at immediate-early genes, and identified specific TF ensembles that coordinately regulate gene-induction.
dc.language.isoen_US
dc.relation<p><a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&list_uids=22940246&dopt=Abstract">Link to Article in PubMed</a></p>
dc.relation.urlhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3873101/
dc.subjectAmino Acids, Peptides, and Proteins
dc.subjectBioinformatics
dc.subjectCell Biology
dc.subjectComputational Biology
dc.subjectGenetic Phenomena
dc.subjectGenomics
dc.subjectMolecular Biology
dc.titleA high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals
dc.typeArticle
dc.source.journaltitleMolecular cell
dc.source.volume47
dc.source.issue5
dc.identifier.legacycoverpagehttps://escholarship.umassmed.edu/garber_lab_pubs/5
dc.identifier.contextkey12504417
html.description.abstract<p>Understanding the principles governing mammalian gene regulation has been hampered by the difficulty in measuring in vivo binding dynamics of large numbers of transcription factors (TF) to DNA. Here, we develop a high-throughput Chromatin ImmunoPrecipitation (HT-ChIP) method to systematically map protein-DNA interactions. HT-ChIP was applied to define the dynamics of DNA binding by 25 TFs and 4 chromatin marks at 4 time-points following pathogen stimulus of dendritic cells. Analyzing over 180,000 TF-DNA interactions we find that TFs vary substantially in their temporal binding landscapes. This data suggests a model for transcription regulation whereby TF networks are hierarchically organized into cell differentiation factors, factors that bind targets prior to stimulus to prime them for induction, and factors that regulate specific gene programs. Overlaying HT-ChIP data on gene-expression dynamics shows that many TF-DNA interactions are established prior to the stimuli, predominantly at immediate-early genes, and identified specific TF ensembles that coordinately regulate gene-induction.</p>
dc.identifier.submissionpathgarber_lab_pubs/5
dc.contributor.departmentGarber Lab
dc.contributor.departmentProgram in Bioinformatics and Integrative Biology
dc.source.pages810-22


Files in this item

Thumbnail
Name:
Publisher version

This item appears in the following Collection(s)

Show simple item record