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PMID: 28137873 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Systematic dissection of genomic features determining transcription factor binding and enhancer function.

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 114 ·No. 7 ·2017-00-14 ·Pages E1291-E1300

Grossman SR, Zhang X, Wang L, Engreitz J, Melnikov A, Rogov P, Tewhey R, Isakova A, Deplancke B, Bernstein BE, Mikkelsen TS, Lander ES

Abstract

Enhancers regulate gene expression through the binding of sequence-specific transcription factors (TFs) to cognate motifs. Various features influence TF binding and enhancer function-including the chromatin state of the genomic locus, the affinities of the binding site, the activity of the bound TFs, and interactions among TFs. However, the precise nature and relative contributions of these features remain unclear. Here, we used massively parallel reporter assays (MPRAs) involving 32,115 natural and synthetic enhancers, together with high-throughput in vivo binding assays, to systematically dissect the contribution of each of these features to the binding and activity of genomic regulatory elements that contain motifs for PPARγ, a TF that serves as a key regulator of adipogenesis. We show that distinct sets of features govern PPARγ binding vs. enhancer activity. PPARγ binding is largely governed by the affinity of the specific motif site and higher-order features of the larger genomic locus, such as chromatin accessibility. In contrast, the enhancer activity of PPARγ binding sites depends on varying contributions from dozens of TFs in the immediate vicinity, including interactions between combinations of these TFs. Different pairs of motifs follow different interaction rules, including subadditive, additive, and superadditive interactions among specific classes of TFs, with both spatially constrained and flexible grammars. Our results provide a paradigm for the systematic characterization of the genomic features underlying regulatory elements, applicable to the design of synthetic regulatory elements or the interpretation of human genetic variation.

Keywords
gene regulation systems biology transcription factor binding
MeSH Terms
3T3-L1 Cells Animals Binding Sites/genetics Enhancer Elements, Genetic/genetics Gene Expression Regulation Genomics/methods Mice Mutation Nucleotide Motifs/genetics PPAR gamma/metabolism Protein Binding Transcription Factors/metabolism
Chemicals
PPAR gamma Transcription Factors
Authors & Affiliations
12 authors, click to expand affiliations / ORCID
Grossman Sharon R
Broad Institute, Cambridge, MA 02142. | Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139. | Health Sciences and Technology, Harvard Medical School, Boston, MA 02215.
Zhang Xiaolan
Broad Institute, Cambridge, MA 02142.
Wang Li
Broad Institute, Cambridge, MA 02142.
Engreitz Jesse
Broad Institute, Cambridge, MA 02142. | Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139.
Melnikov Alexandre
Broad Institute, Cambridge, MA 02142.
Rogov Peter
Broad Institute, Cambridge, MA 02142.
Tewhey Ryan
Broad Institute, Cambridge, MA 02142. | Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138. | Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138.
Isakova Alina
Institute of Bioengineering, CH-1015 Lausanne, Switzerland. | Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland.
Deplancke Bart
Institute of Bioengineering, CH-1015 Lausanne, Switzerland. | Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland.
Bernstein Bradley E
Broad Institute, Cambridge, MA 02142. | Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114. | Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114.
Mikkelsen Tarjei S
Broad Institute, Cambridge, MA 02142. | Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138. | Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138.
Lander Eric S
Broad Institute, Cambridge, MA 02142; lander@broadinstitute.org. | Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139. | Department of Systems Biology, Harvard Medical School, Boston, MA 02215.
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Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
1091-6490
DOI
10.1073/pnas.1621150114
Email
lander@broadinstitute.org
Published
2017-00-14
Epub
2017-00-30
Pages
E1291-E1300
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC5321001
Subset
IM
Grants
NHGRI NIH HHS · K99 HG008179 · United States
NHGRI NIH HHS · R01 HG006785 · United States
NIGMS NIH HHS · T32 GM007753 · United States
NHGRI NIH HHS · U54 HG003067 · United States
External Links
PubMed source DOI: 10.1073/pnas.1621150114 PMC Full Text View journal details
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