A transcription factor hierarchy defines an environmental stress response network

被引：392

作者：

Song, Liang ^{[1
]}

Huang, Shao-shan Carol ^{[1
]}

Wise, Aaron ^{[2
]}

Castanon, Rosa ^{[3
]}

Nery, Joseph R. ^{[3
]}

Chen, Huaming ^{[3
]}

Watanabe, Marina ^{[1
]}

Thomas, Jerushah ^{[1
]}

Bar-Joseph, Ziv ^{[2
]}

Ecker, Joseph R. ^{[1
,3
,4
]}

机构：

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

[2] Carnegie Mellon Univ, Sch Comp Sci, Computat Biol Dept, Pittsburgh, PA 15213 USA

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

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

来源：

SCIENCE | 2016年 / 354卷 / 6312期

基金：

美国国家科学基金会;

关键词：

CHIP-SEQ; BIOCONDUCTOR PACKAGE; FUNCTIONAL ELEMENTS; REGULATORY NETWORKS; POSITIVE REGULATOR; GENE-EXPRESSION; SEED DORMANCY; GENOME; ENCODE; TOLERANCE;

D O I：

10.1126/science.aag1550

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Environmental stresses are universally encountered by microbes, plants, and animals.Yet systematic studies of stress-responsive transcription factor (TF) networks in multicellular organisms have been limited.The phytohormone abscisic acid (ABA) influences the expression of thousands of genes, allowing us to characterize complex stress-responsive regulatory networks. Using chromatin immunoprecipitation sequencing, we identified genome-wide targets of 21 ABA-related TFs to construct a comprehensive regulatory network in Arabidopsis thaliana. Determinants of dynamic TF binding and a hierarchy among TFs were defined, illuminating the relationship between differential gene expression patterns and ABA pathway feedback regulation. By extrapolating regulatory characteristics of observed canonical ABA pathway components, we identified a new family of transcriptional regulators modulating ABA and salt responsiveness and demonstrated their utility to modulate plant resilience to osmotic stress. Copyright © 2016 by the American Association for the Advancement of Science.

引用

页数：10

共 66 条

[1] HTSeq-a Python']Python framework to work with high-throughput sequencing data [J].

Anders, Simon ;

Pyl, Paul Theodor ;

Huber, Wolfgang .

BIOINFORMATICS, 2015, 31 (02) :166-169

[2]

[Anonymous], 2015, DIFFBIND DIFFERENTIA

[3]

[Anonymous], METHODS MOL BIOL

[4] The MEME Suite [J].

Bailey, Timothy L. ;

Johnson, James ;

Grant, Charles E. ;

Noble, William S. .

NUCLEIC ACIDS RESEARCH, 2015, 43 (W1) :W39-W49

[5] Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project [J].

Birney, Ewan ;

Stamatoyannopoulos, John A. ;

Dutta, Anindya ;

Guigo, Roderic ;

Gingeras, Thomas R. ;

Margulies, Elliott H. ;

Weng, Zhiping ;

Snyder, Michael ;

Dermitzakis, Emmanouil T. ;

Stamatoyannopoulos, John A. ;

Thurman, Robert E. ;

Kuehn, Michael S. ;

Taylor, Christopher M. ;

Neph, Shane ;

Koch, Christoph M. ;

Asthana, Saurabh ;

Malhotra, Ankit ;

Adzhubei, Ivan ;

Greenbaum, Jason A. ;

Andrews, Robert M. ;

Flicek, Paul ;

Boyle, Patrick J. ;

Cao, Hua ;

Carter, Nigel P. ;

Clelland, Gayle K. ;

Davis, Sean ;

Day, Nathan ;

Dhami, Pawandeep ;

Dillon, Shane C. ;

Dorschner, Michael O. ;

Fiegler, Heike ;

Giresi, Paul G. ;

Goldy, Jeff ;

Hawrylycz, Michael ;

Haydock, Andrew ;

Humbert, Richard ;

James, Keith D. ;

Johnson, Brett E. ;

Johnson, Ericka M. ;

Frum, Tristan T. ;

Rosenzweig, Elizabeth R. ;

Karnani, Neerja ;

Lee, Kirsten ;

Lefebvre, Gregory C. ;

Navas, Patrick A. ;

Neri, Fidencio ;

Parker, Stephen C. J. ;

Sabo, Peter J. ;

Sandstrom, Richard ;

Shafer, Anthony .

NATURE, 2007, 447 (7146) :799-816

[6] Gene Ontology Consortium: going forward [J].

Blake, J. A. ;

Christie, K. R. ;

Dolan, M. E. ;

Drabkin, H. J. ;

Hill, D. P. ;

Ni, L. ;

Sitnikov, D. ;

Burgess, S. ;

Buza, T. ;

Gresham, C. ;

McCarthy, F. ;

Pillai, L. ;

Wang, H. ;

Carbon, S. ;

Dietze, H. ;

Lewis, S. E. ;

Mungall, C. J. ;

Munoz-Torres, M. C. ;

Feuermann, M. ;

Gaudet, P. ;

Basu, S. ;

Chisholm, R. L. ;

Dodson, R. J. ;

Fey, P. ;

Mi, H. ;

Thomas, P. D. ;

Muruganujan, A. ;

Poudel, S. ;

Hu, J. C. ;

Aleksander, S. A. ;

McIntosh, B. K. ;

Renfro, D. P. ;

Siegele, D. A. ;

Attrill, H. ;

Brown, N. H. ;

Tweedie, S. ;

Lomax, J. ;

Osumi-Sutherland, D. ;

Parkinson, H. ;

Roncaglia, P. ;

Lovering, R. C. ;

Talmud, P. J. ;

Humphries, S. E. ;

Denny, P. ;

Campbell, N. H. ;

Foulger, R. E. ;

Chibucos, M. C. ;

Giglio, M. Gwinn ;

Chang, H. Y. ;

Finn, R. .

NUCLEIC ACIDS RESEARCH, 2015, 43 (D1) :D1049-D1056

[7]

Buenrostro Jason D, 2015, Curr Protoc Mol Biol, V109, DOI 10.1002/0471142727.mb2129s109

[8]

Celli Fabrizio, 2015, F1000Res, V4, P110, DOI 10.12688/f1000research.6354.1

[9] Floral dip:: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana [J].

Clough, SJ ;

Bent, AF .

PLANT JOURNAL, 1998, 16 (06) :735-743

[10] Improved DNase-seq protocol facilitates high resolution mapping of DNase I hypersensitive sites in roots in Arabidopsis thaliana [J].

Cumbie, Jason S. ;

Filichkin, Sergei A. ;

Megraw, Molly .

PLANT METHODS, 2015, 11

← 1 2 3 4 5 6 7 →