Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

被引：1149

作者：

Weirauch, Matthew T. ^{[1
,2
,3
,4
,5
]}

Yang, Ally ^{[4
,5
]}

Albu, Mihai ^{[4
,5
]}

Cote, Atina G. ^{[4
,5
]}

Montenegro-Montero, Alejandro ^{[6
]}

Drewe, Philipp ^{[7
]}

Najafabadi, Hamed S. ^{[4
,5
]}

Lambert, Samuel A. ^{[8
]}

Mann, Ishminder ^{[4
,5
]}

Cook, Kate ^{[8
]}

Zheng, Hong ^{[4
,5
]}

Goity, Alejandra ^{[6
]}

van Bakel, Harm ^{[4
,5
,9
]}

Lozano, Jean-Claude ^{[10
]}

Galli, Mary ^{[11
]}

Lewsey, Mathew G. ^{[11
,12
]}

Huang, Eryong ^{[13
]}

Mukherjee, Tuhin ^{[14
]}

Chen, Xiaoting ^{[14
]}

Reece-Hoyes, John S. ^{[15
]}

Govindarajan, Sridhar ^{[16
]}

Shaulsky, Gad ^{[13
]}

Walhout, Albertha J. M. ^{[15
]}

Bouget, Francois-Yves ^{[10
]}

Ratsch, Gunnar ^{[7
]}

Larrondo, Luis F. ^{[6
]}

Ecker, Joseph R. ^{[11
,17
]}

Hughes, Timothy R. ^{[4
,5
,8
]}

机构：

[1] Cincinnati Childrens Hosp Med Ctr, CAGE, Cincinnati, OH 45229 USA

[2] Cincinnati Childrens Hosp Med Ctr, Div Biomed Informat, Cincinnati, OH 45229 USA

[3] Cincinnati Childrens Hosp Med Ctr, Div Dev Biol, Cincinnati, OH 45229 USA

[4] Univ Toronto, Banting & Best Dept Med Res, Toronto, ON M5S 3E1, Canada

[5] Univ Toronto, Donnelly Ctr, Toronto, ON M5S 3E1, Canada

[6] Pontificia Univ Catolica Chile, Fac Ciencias Biol, Dept Genet Mol & Microbiol, Santiago 8331150, Chile

[7] Sloan Kettering Inst, Computat Biol Ctr, New York, NY 10065 USA

[8] Univ Toronto, Dept Mol Genet, Toronto, ON M5S 1A8, Canada

[9] Icahn Sch Med Mt Sinai, Icahn Inst Genom & Multiscale Biol, Dept Genet & Genom Sci, New York, NY 10029 USA

[10] Univ Paris 06, Sorbonne Univ, CNRS, Lab Oceanog Microbienne,Observ Oceanol,UMR 7621, F-66650 Banyuls Sur Mer, France

[11] Salk Inst Biol Studies, Genom Anal Lab, La Jolla, CA 92037 USA

[12] Salk Inst Biol Studies, Plant Biol Lab, La Jolla, CA 92037 USA

[13] Baylor Coll Med, Dept Mol & Human Genet, Houston, TX 77030 USA

[14] Univ Cincinnati, Dept Elect & Comp Syst, Cincinnati, OH 45221 USA

[15] Univ Massachusetts, Sch Med, Program Syst Biol, Worcester, MA 01655 USA

[16] DNA2 0 Inc, Menlo Pk, CA 94025 USA

[17] Salk Inst Biol Studies, Howard Hughes Med Inst, La Jolla, CA 92037 USA

来源：

CELL | 2014年 / 158卷 / 06期

基金：

加拿大健康研究院; 美国国家科学基金会;

关键词：

DNA-BINDING SPECIFICITIES; GENOME-WIDE ASSOCIATION; NUCLEOSOME OCCUPANCY; RECOGNITION; DATABASE; MICROARRAY; PREDICTION; REVEALS; MODELS; MOTIFS;

D O I：

10.1016/j.cell.2014.08.009

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Transcription factor (TF) DNA sequence preferences direct their regulatory activity, but are currently known for only similar to 1% of eukaryotic TFs. Broadly sampling DNA-binding domain (DBD) types from multiple eukaryotic clades, we determined DNA sequence preferences for >1,000 TFs encompassing 54 different DBD classes from 131 diverse eukaryotes. We find that closely related DBDs almost always have very similar DNA sequence preferences, enabling inference of motifs for similar to 34% of the similar to 170,000 known or predicted eukaryotic TFs. Sequences matching both measured and inferred motifs are enriched in chromatin immunoprecipitation sequencing (ChIP-seq) peaks and upstream of transcription start sites in diverse eukaryotic lineages. SNPs defining expression quantitative trait loci in Arabidopsis promoters are also enriched for predicted TF binding sites. Importantly, our motif "library" can be used to identify specific TFs whose binding may be altered by human disease risk alleles. These data present a powerful resource for mapping transcriptional networks across eukaryotes.

引用

页码：1431 / 1443

页数：13

共 63 条

[1] Identification of Specific DNA Binding Residues in the TCP Family of Transcription Factors in Arabidopsis [J].

Aggarwal, Pooja ;

Das Gupta, Mainak ;

Joseph, Agnel Praveen ;

Chatterjee, Nirmalya ;

Srinivasan, N. ;

Nath, Utpal .

PLANT CELL, 2010, 22 (04) :1174-1189

[2] Predicting the binding preference of transcription factors to individual DNA k-mers [J].

Alleyne, Trevis M. ;

Pena-Castillo, Lourdes ;

Badis, Gwenael ;

Talukder, Shaheynoor ;

Berger, Michael F. ;

Gehrke, Andrew R. ;

Philippakis, Anthony A. ;

Bulyk, Martha L. ;

Morris, Quaid D. ;

Hughes, Timothy R. .

BIOINFORMATICS, 2009, 25 (08) :1012-1018

[3]

[Anonymous], GENOME BIOL

[4] Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines [J].

Atwell, Susanna ;

Huang, Yu S. ;

Vilhjalmsson, Bjarni J. ;

Willems, Glenda ;

Horton, Matthew ;

Li, Yan ;

Meng, Dazhe ;

Platt, Alexander ;

Tarone, Aaron M. ;

Hu, Tina T. ;

Jiang, Rong ;

Muliyati, N. Wayan ;

Zhang, Xu ;

Amer, Muhammad Ali ;

Baxter, Ivan ;

Brachi, Benjamin ;

Chory, Joanne ;

Dean, Caroline ;

Debieu, Marilyne ;

de Meaux, Juliette ;

Ecker, Joseph R. ;

Faure, Nathalie ;

Kniskern, Joel M. ;

Jones, Jonathan D. G. ;

Michael, Todd ;

Nemri, Adnane ;

Roux, Fabrice ;

Salt, David E. ;

Tang, Chunlao ;

Todesco, Marco ;

Traw, M. Brian ;

Weigel, Detlef ;

Marjoram, Paul ;

Borevitz, Justin O. ;

Bergelson, Joy ;

Nordborg, Magnus .

NATURE, 2010, 465 (7298) :627-631

[5] Diversity and Complexity in DNA Recognition by Transcription Factors [J].

Badis, Gwenael ;

Berger, Michael F. ;

Philippakis, Anthony A. ;

Talukder, Shaheynoor ;

Gehrke, Andrew R. ;

Jaeger, Savina A. ;

Chan, Esther T. ;

Metzler, Genita ;

Vedenko, Anastasia ;

Chen, Xiaoyu ;

Kuznetsov, Hanna ;

Wang, Chi-Fong ;

Coburn, David ;

Newburger, Daniel E. ;

Morris, Quaid ;

Hughes, Timothy R. ;

Bulyk, Martha L. .

SCIENCE, 2009, 324 (5935) :1720-1723

[6] A kingdom-level phylogeny of eukaryotes based on combined protein data [J].

Baldauf, SL ;

Roger, AJ ;

Wenk-Siefert, I ;

Doolittle, WF .

SCIENCE, 2000, 290 (5493) :972-977

[7] Genomic Location Analysis by ChIP-Seq [J].

Barski, Artem ;

Zhao, Keji .

JOURNAL OF CELLULAR BIOCHEMISTRY, 2009, 107 (01) :11-18

[8]

Bateman A, 2004, NUCLEIC ACIDS RES, V32, pD138, DOI [10.1093/nar/gkp985, 10.1093/nar/gkh121, 10.1093/nar/gkr1065]

[9] Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences [J].

Berger, Michael F. ;

Badis, Gwenael ;

Gehrke, Andrew R. ;

Talukder, Shaheynoor ;

Philippakis, Anthony A. ;

Pena-Castillo, Lourdes ;

Alleyne, Trevis M. ;

Mnaimneh, Sanie ;

Botvinnik, Olga B. ;

Chan, Esther T. ;

Khalid, Faiqua ;

Zhang, Wen ;

Newburger, Daniel ;

Jaeger, Savina A. ;

Morris, Quaid D. ;

Bulyk, Martha L. ;

Hughes, Timothy R. .

CELL, 2008, 133 (07) :1266-1276

[10] Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities [J].

Berger, Michael F. ;

Philippakis, Anthony A. ;

Qureshi, Aaron M. ;

He, Fangxue S. ;

Estep, Preston W., III ;

Bulyk, Martha L. .

NATURE BIOTECHNOLOGY, 2006, 24 (11) :1429-1435

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