Toggle involving cis-interfering noncoding RNAs controls variegated gene expression in yeast

被引：154

作者：

Bumgarner, Stacie L. ^{[2
]}

Dowell, Robin D. ^{[1
]}

Grisafi, Paula ^{[2
]}

Gifford, David K. ^{[1
]}

Fink, Gerald R. ^{[2
]}

机构：

[1] MIT, Comp Sci & Artificial Intelligence Lab, Cambridge, MA 02139 USA

[2] 9 Cambridge Ctr, Whitehead Inst Biomed Res, Cambridge, MA 02142 USA

来源：

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA | 2009年 / 106卷 / 43期

基金：

美国国家卫生研究院;

关键词：

FLO11; intergenic transcription; Rpd3L histone deacetylase; transcriptional interference; regulatory RNAs; RPD3 HISTONE DEACETYLASE; SACCHAROMYCES-CEREVISIAE; X-CHROMOSOME; BIDIRECTIONAL PROMOTERS; ANTISENSE TRANSCRIPTION; GLOBAL IDENTIFICATION; BUDDING YEAST; KINASE; UME6; STABILIZATION;

D O I：

10.1073/pnas.0909641106

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：

The identification of specific functional roles for the numerous long noncoding (nc)RNAs found in eukaryotic transcriptomes is currently a matter of intense study amid speculation that these ncRNAs have key regulatory roles. We have identified a pair of cis-interfering ncRNAs in yeast that contribute to the control of variegated gene expression at the FLO11 locus by implementing a regulatory circuit that toggles between two stable states. These capped, polyadenylated ncRNAs are transcribed across the large intergenic region upstream of the FLO11 ORF. As with mammalian long intervening (ii)ncRNAs, these yeast ncRNAs (ICR1 and PWR1) are themselves regulated by transcription factors (Sfl1 and Flo8) and chromatin remodelers (Rpd3L) that are key elements in phenotypic transitions in yeast. The mechanism that we describe explains the unanticipated role of a histone deacetylase complex in activating gene expression, because Rpd3L mutants force the ncRNA circuit into a state that silences the expression of the adjacent variegating gene.

引用

页码：18321 / 18326

页数：6

共 64 条

[1] Genes expressed in neurons of adult male Drosophila [J].

Amrein, H ;

Axel, R .

CELL, 1997, 88 (04) :459-469

[2]

[Anonymous], 1989, Molecular Cloning: A Laboratory Manual

[3]

[Anonymous], 2000, Transcription Regulation in Prokaryotes

[4] Global identification of human transcribed sequences with genome tiling arrays [J].

Bertone, P ;

Stolc, V ;

Royce, TE ;

Rozowsky, JS ;

Urban, AE ;

Zhu, XW ;

Rinn, JL ;

Tongprasit, W ;

Samanta, M ;

Weissman, S ;

Gerstein, M ;

Snyder, M .

SCIENCE, 2004, 306 (5705) :2242-2246

[5]

BOEKE JD, 1987, METHOD ENZYMOL, V154, P164

[6] Target hub proteins serve as master regulators of development in yeast [J].

Borneman, AR ;

Leigh-Bell, JA ;

Yu, HY ;

Bertone, P ;

Gerstein, M ;

Snyder, M .

GENES & DEVELOPMENT, 2006, 20 (04) :435-448

[7] Antisense RNA stabilization induces transcriptional gene silencing via histone deacetylation in s.: cerevisiae [J].

Camblong, Jurgi ;

Iglesias, Nahid ;

Fickentscher, Céline ;

Dieppois, Guennaelle ;

Stutz, Françoise .

CELL, 2007, 131 (04) :706-717

[8] The transcriptional landscape of the mammalian genome [J].

Carninci, P ;

Kasukawa, T ;

Katayama, S ;

Gough, J ;

Frith, MC ;

Maeda, N ;

Oyama, R ;

Ravasi, T ;

Lenhard, B ;

Wells, C ;

Kodzius, R ;

Shimokawa, K ;

Bajic, VB ;

Brenner, SE ;

Batalov, S ;

Forrest, ARR ;

Zavolan, M ;

Davis, MJ ;

Wilming, LG ;

Aidinis, V ;

Allen, JE ;

Ambesi-Impiombato, X ;

Apweiler, R ;

Aturaliya, RN ;

Bailey, TL ;

Bansal, M ;

Baxter, L ;

Beisel, KW ;

Bersano, T ;

Bono, H ;

Chalk, AM ;

Chiu, KP ;

Choudhary, V ;

Christoffels, A ;

Clutterbuck, DR ;

Crowe, ML ;

Dalla, E ;

Dalrymple, BP ;

de Bono, B ;

Della Gatta, G ;

di Bernardo, D ;

Down, T ;

Engstrom, P ;

Fagiolini, M ;

Faulkner, G ;

Fletcher, CF ;

Fukushima, T ;

Furuno, M ;

Futaki, S ;

Gariboldi, M .

SCIENCE, 2005, 309 (5740) :1559-1563

[9] Stable incorporation of sequence specific repressors Ash1 and Ume6 into the Rpd3L complex [J].

Carrozza, MJ ;

Florens, L ;

Swanson, SK ;

Shia, WJ ;

Anderson, S ;

Yates, J ;

Washburn, MP ;

Workman, JL .

BIOCHIMICA ET BIOPHYSICA ACTA-GENE STRUCTURE AND EXPRESSION, 2005, 1731 (02) :77-87

[10] Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription [J].

Carrozza, MJ ;

Li, B ;

Florens, L ;

Suganuma, T ;

Swanson, SK ;

Lee, KK ;

Shia, WJ ;

Anderson, S ;

Yates, J ;

Washburn, MP ;

Workman, JL .

CELL, 2005, 123 (04) :581-592

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