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  Classifying human promoters by occupancy patterns identifies recurring sequence elements, combinatorial binding, and spatial interactions

Yang, X., & Vingron, M. (2018). Classifying human promoters by occupancy patterns identifies recurring sequence elements, combinatorial binding, and spatial interactions. BMC Biology, 16(1): 138. doi:10.1186/s12915-018-0585-5.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0003-6C2D-3 Version Permalink: http://hdl.handle.net/21.11116/0000-0003-6C2E-2
Genre: Journal Article

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© Yang and Vingron. 2018

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 Creators:
Yang, Xinyi1, Author
Vingron, Martin1, Author              
Affiliations:
1Gene regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479639              

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Free keywords: *Biclustering *Promoter-enhancer interaction *Promoters *Transcription factor combinatorics
 Abstract: BACKGROUND: Characterizing recurring sequence patterns in human promoters has been a challenging undertaking even nowadays where a near-complete overview of promoters exists. However, with the more recent availability of genomic location (ChIP-seq) data, one can approach that question through the identification of characteristic patterns of transcription factor occupancy and histone modifications. RESULTS: Based on the ENCODE annotation and integration of sequence motifs as well as three-dimensional chromatin data, we have undertaken a re-analysis of occupancy and sequence patterns in human promoters. We identify clear groups of CAAT-box and E-box sequence motif containing promoters, as well as a group of promoters whose interaction with an enhancer appears to be mediated by CCCTC-binding factor (CTCF) binding on the promoter. We also extend our analysis to inactive promoters, showing that only a surprisingly small number of inactive promoters is repressed by the polycomb complex. We also identify combinatorial patterns of transcription factor interactions indicated by the ChIP-seq signals. CONCLUSION: Our analysis defines subgroups of promoters characterized by stereotypic patterns of transcription factor occupancy, and combinations of specific sequence patterns which are required for their binding. This grouping provides new hypotheses concerning the assembly and dynamics of transcription factor complexes at their respective promoter groups, as well as questions on the evolutionary origin of these groups.

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 Dates: 2018-10-042018-11-15
 Publication Status: Published online
 Pages: -
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 Table of Contents: -
 Rev. Method: -
 Identifiers: DOI: 10.1186/s12915-018-0585-5
ISSN: 1741-7007
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Title: BMC Biology
Source Genre: Journal
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Publ. Info: Berlin ; Heidelberg : Springer
Pages: - Volume / Issue: 16 (1) Sequence Number: 138 Start / End Page: - Identifier: ISSN: 1741-7007
CoNE: https://pure.mpg.de/cone/journals/resource/111071069889000