Flexible promoter architecture requirements for coactivator recruitment

Chiang, Derek Y.; Nix, David A.; Shultzaberger, Ryan K.; Gasch, Audrey P.; Eisen, Michael B.

doi:10.1186/1471-2199-7-16

Flexible promoter architecture requirements for coactivator recruitment

Journal Article · Fri Apr 28 00:00:00 EDT 2006 · BMC Molecular Biology

DOI:https://doi.org/10.1186/1471-2199-7-16· OSTI ID:1626499

Chiang, Derek Y. ^[1]; Nix, David A. ^[2]; Shultzaberger, Ryan K. ^[3]; Gasch, Audrey P. ^[4]; Eisen, Michael B. ^[5]

Univ. of California, Berkeley, CA (United States); Broad Inst. of MIT and Harvard, Cambridge, MA (United States); DOE/OSTI
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Affymetrix, Santa Clara, CA (United States)
Univ. of California, Berkeley, CA (United States)
Univ. of Wisconsin, Madison, WI (United States)
Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

The spatial organization of transcription factor binding sites in regulatory DNA, and the composition of intersite sequences, influences the assembly of the multiprotein complexes that regulate RNA polymerase recruitment and thereby affects transcription. We have developed a genetic approach to investigate how reporter gene transcription is affected by varying the spacing between transcription factor binding sites. We characterized the components of promoter architecture that govern the yeast transcription factors Cbf1 and Met31/32, which bind independently, but collaboratively recruit the coactivator Met4. A Cbf1 binding site was required upstream of a Met31/32 binding site for full reporter gene expression. Distance constraints on coactivator recruitment were more flexible than those for cooperatively binding transcription factors. Distances from 18 to 50 bp between binding sites support efficient recruitment of Met4, with only slight modulation by helical phasing. Intriguingly, we found that certain sequences located between the binding sites abolished gene expression. These results yield insight to the influence of both binding site architecture and local DNA flexibility on gene expression, and can be used to refine computational predictions of gene expression from promoter sequences. In addition, our approach can be applied to survey promoter architecture requirements for arbitrary combinations of transcription factor binding sites.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC02-05CH11231; AC03-76SF00098

OSTI ID:: 1626499

Journal Information:: BMC Molecular Biology, Journal Name: BMC Molecular Biology Journal Issue: 1 Vol. 7; ISSN 1471-2199

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
Biochemistry & Molecular Biology
Minimal Promoter
Reporter Gene Activation
Reporter Gene Expression
Sequence Context
Transcription Factor Binding Site

Flexible promoter architecture requirements for coactivator recruitment

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