Advances in understanding cis regulation of the plant gene with an emphasis on comparative genomics
作者： Diane G Burgess , Jie Xu , Michael Freeling
DOI: 10.1016/J.PBI.2015.07.001
关键词:
摘要: The plant gene model remains largely an extrapolation from animals, with the cis functional unit, gene, cast as a dynamic looping structure. Molecular genetics plants continues to make advances; highlighted here are quantitative-occupancy results Arabidopsis thaliana (Arabidopsis) Phytochrome-Interacting bHLH transcription Factors (PIF) quartet. Compared this complex snapshot, chromatin occupancy and other Encyclopedia of DNA Elements (ENCODE)-like approaches increase our factor-motif cognate library, but regulation cannot by itself be inferred binding. Complementary published conserved noncoding sequence lists compared, evaluated, merged, released. Comparative genomic have identified modifier gene's expression-hypothetically, transposon-based 'rheostat'-that works in all cells, times places.
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Michael Freeling, Jie Xu, Margaret Woodhouse, Damon Lisch, A Solution to the C-Value Paradox and the Function of Junk DNA: The Genome Balance Hypothesis Molecular Plant. ,vol. 8, pp. 899- 910 ,(2015) , 10.1016/J.MOLP.2015.02.009
Marieke Louwers, Erik Splinter, Roel van Driel, Wouter de Laat, Maike Stam, Studying physical chromatin interactions in plants using Chromosome Conformation Capture (3C) Nature Protocols. ,vol. 4, pp. 1216- 1229 ,(2009) , 10.1038/NPROT.2009.113
Jan Van de Velde, Ken S. Heyndrickx, Klaas Vandepoele, Inference of Transcriptional Networks in Arabidopsis through Conserved Noncoding Sequence Analysis The Plant Cell. ,vol. 26, pp. 2729- 2745 ,(2014) , 10.1105/TPC.114.127001
Federico Ariel, Teddy Jegu, David Latrasse, Natali Romero-Barrios, Aurélie Christ, Moussa Benhamed, Martin Crespi, Noncoding Transcription by Alternative RNA Polymerases Dynamically Regulates an Auxin-Driven Chromatin Loop Molecular Cell. ,vol. 55, pp. 383- 396 ,(2014) , 10.1016/J.MOLCEL.2014.06.011
B. Sun, L.-S. Looi, S. Guo, Z. He, E.-S. Gan, J. Huang, Y. Xu, W.-Y. Wee, T. Ito, Timing Mechanism Dependent on Cell Division Is Invoked by Polycomb Eviction in Plant Stem Cells Science. ,vol. 343, pp. 1248559- 1248559 ,(2014) , 10.1126/SCIENCE.1248559
Marjori A Matzke, Rebecca A Mosher, None, RNA-directed DNA methylation: an epigenetic pathway of increasing complexity Nature Reviews Genetics. ,vol. 15, pp. 394- 408 ,(2014) , 10.1038/NRG3683
Annabelle Haudry, Adrian E Platts, Emilio Vello, Douglas R Hoen, Mickael Leclercq, Robert J Williamson, Ewa Forczek, Zoé Joly-Lopez, Joshua G Steffen, Khaled M Hazzouri, Ken Dewar, John R Stinchcombe, Daniel J Schoen, Xiaowu Wang, Jeremy Schmutz, Christopher D Town, Patrick P Edger, J Chris Pires, Karen S Schumaker, David E Jarvis, Terezie Mandáková, Martin A Lysak, Erik van den Bergh, M Eric Schranz, Paul M Harrison, Alan M Moses, Thomas E Bureau, Stephen I Wright, Mathieu Blanchette, An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions Nature Genetics. ,vol. 45, pp. 891- 898 ,(2013) , 10.1038/NG.2684
M. R. Woodhouse, F. Cheng, J. C. Pires, D. Lisch, M. Freeling, X. Wang, Origin, inheritance, and gene regulatory consequences of genome dominance in polyploids Proceedings of the National Academy of Sciences of the United States of America. ,vol. 111, pp. 5283- 5288 ,(2014) , 10.1073/PNAS.1402475111
A. B. Stergachis, E. Haugen, A. Shafer, W. Fu, B. Vernot, A. Reynolds, A. Raubitschek, S. Ziegler, E. M. LeProust, J. M. Akey, J. A. Stamatoyannopoulos, Exonic transcription factor binding directs codon choice and affects protein evolution Science. ,vol. 342, pp. 1367- 1372 ,(2013) , 10.1126/SCIENCE.1243490
Liya Wei, Lianfeng Gu, Xianwei Song, Xiekui Cui, Zhike Lu, Ming Zhou, Lulu Wang, Fengyi Hu, Jixian Zhai, Blake C Meyers, Xiaofeng Cao, None, Dicer-like 3 produces transposable element-associated 24-nt siRNAs that control agricultural traits in rice Proceedings of the National Academy of Sciences of the United States of America. ,vol. 111, pp. 3877- 3882 ,(2014) , 10.1073/PNAS.1318131111