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Lamas-Maceiras M, Singh BN, Hampsey M, Freire-Picos MA. Promoter-Terminator Gene Loops Affect Alternative 3'-End Processing in Yeast. J Biol Chem 2016; 291:8960-8. [PMID: 26929407 DOI: 10.1074/jbc.m115.687491] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Indexed: 11/06/2022] Open
Abstract
Many eukaryotic genes undergo alternative 3'-end poly(A)-site selection producing transcript isoforms with 3'-UTRs of different lengths and post-transcriptional fates. Gene loops are dynamic structures that juxtapose the 3'-ends of genes with their promoters. Several functions have been attributed to looping, including memory of recent transcriptional activity and polarity of transcription initiation. In this study, we investigated the relationship between gene loops and alternative poly(A)-site. Using the KlCYC1 gene of the yeast Kluyveromyces lactis, which includes a single promoter and two poly(A) sites separated by 394 nucleotides, we demonstrate in two yeast species the formation of alternative gene loops (L1 and L2) that juxtapose the KlCYC1 promoter with either proximal or distal 3'-end processing sites, resulting in the synthesis of short and long forms of KlCYC1 mRNA. Furthermore, synthesis of short and long mRNAs and formation of the L1 and L2 loops are growth phase-dependent. Chromatin immunoprecipitation experiments revealed that the Ssu72 RNA polymerase II carboxyl-terminal domain phosphatase, a critical determinant of looping, peaks in early log phase at the proximal poly(A) site, but as growth phase advances, it extends to the distal site. These results define a cause-and-effect relationship between gene loops and alternative poly(A) site selection that responds to different physiological signals manifested by RNA polymerase II carboxyl-terminal domain phosphorylation status.
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Affiliation(s)
- Mónica Lamas-Maceiras
- From the Departamento de Biología Celular e Molecular, Facultad de Ciencias, Universidade da Coruña, Campus de A Coruña, Rúa da Fraga 10, 15008 A Coruña, Spain and
| | - Badri Nath Singh
- the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey 08854
| | - Michael Hampsey
- the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey 08854
| | - María A Freire-Picos
- From the Departamento de Biología Celular e Molecular, Facultad de Ciencias, Universidade da Coruña, Campus de A Coruña, Rúa da Fraga 10, 15008 A Coruña, Spain and
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Fang ZA, Wang GH, Chen AL, Li YF, Liu JP, Li YY, Bolotin-Fukuhara M, Bao WG. Gene responses to oxygen availability in Kluyveromyces lactis: an insight on the evolution of the oxygen-responding system in yeast. PLoS One 2009; 4:e7561. [PMID: 19855843 PMCID: PMC2763219 DOI: 10.1371/journal.pone.0007561] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Accepted: 09/16/2009] [Indexed: 11/18/2022] Open
Abstract
The whole-genome duplication (WGD) may provide a basis for the emergence of the very characteristic life style of Saccharomyces cerevisiae—its fermentation-oriented physiology and its capacity of growing in anaerobiosis. Indeed, we found an over-representation of oxygen-responding genes in the ohnologs of S. cerevisiae. Many of these duplicated genes are present as aerobic/hypoxic(anaerobic) pairs and form a specialized system responding to changing oxygen availability. HYP2/ANB1 and COX5A/COX5B are such gene pairs, and their unique orthologs in the ‘non-WGD’ Kluyveromyces lactis genome behaved like the aerobic versions of S. cerevisiae. ROX1 encodes a major oxygen-responding regulator in S. cerevisiae. The synteny, structural features and molecular function of putative KlROX1 were shown to be different from that of ROX1. The transition from the K. lactis-type ROX1 to the S. cerevisiae-type ROX1 could link up with the development of anaerobes in the yeast evolution. Bioinformatics and stochastic analyses of the Rox1p-binding site (YYYATTGTTCTC) in the upstream sequences of the S. cerevisiae Rox1p-mediated genes and of the K. lactis orthologs also indicated that K. lactis lacks the specific gene system responding to oxygen limiting environment, which is present in the ‘post-WGD’ genome of S. cerevisiae. These data suggested that the oxygen-responding system was born for the specialized physiology of S. cerevisiae.
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Affiliation(s)
- Zi-An Fang
- Université Paris Sud-11, CNRS UMR 8621, Institut de Génétique et Microbiologie, Orsay, France
- Institute of Genetics, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Guang-Hui Wang
- School of Mathematics, Shandong University, Jinan, Shandong, China
- Laboratoire Mathématiques Appliquées aux Systèmes, Ecole Centrale Paris, Châtenay-Malabry, France
| | - Ai-Lian Chen
- Department of Mathematics, Fuzhou University, Fuzhou, Fujian, China
| | - You-Fang Li
- Université Paris Sud-11, CNRS UMR 8621, Institut de Génétique et Microbiologie, Orsay, France
| | - Jian-Ping Liu
- Institute of Genetics, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Yu-Yang Li
- Institute of Genetics, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | | | - Wei-Guo Bao
- Université Paris Sud-11, CNRS UMR 8621, Institut de Génétique et Microbiologie, Orsay, France
- * E-mail:
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Seoane S, Lamas-Maceiras M, Rodríguez-Torres AM, Freire-Picos MA. Involvement of Pta1, Pcf11 and a KlCYC1 AU-rich element in alternative RNA 3'-end processing selection in yeast. FEBS Lett 2009; 583:2843-8. [PMID: 19646984 DOI: 10.1016/j.febslet.2009.07.042] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2009] [Revised: 07/23/2009] [Accepted: 07/23/2009] [Indexed: 11/24/2022]
Abstract
This work reports the involvement of yeast RNA processing factors Pta1 and Pcf11 in alternative 3'-end RNA processing. The pta1-1 and pcf11-2 mutations changed the predominance of KlCYC1 1.14 and 1.5 kb transcript isoforms. Mutation of the KlCYC1 3'-UTR AU-rich sequence at positions 679-690 (mutant M1) altered transcript predominance. Moreover, expression of M1 in the yeast mutants partially suppressed their effects in the predominance pattern. The combination of the M1 and M2 (694-698 deletion) mutations abolished the alternative processing. Pta1 involvement in this selection was confirmed using the Pta1-td degron strain.
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Affiliation(s)
- Silvia Seoane
- Universidade da Coruña, Facultad de Ciencias, Campus da Zapateira S/N, 15071 A Coruña, Spain
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Rosende SS, Becerra M, Salgado M, Lamas-Maceiras M, González M, Picos MF. Growth phase-dependent expression of Kluyveromyces lactis genes and involvement of 3′-UTR elements. Process Biochem 2008. [DOI: 10.1016/j.procbio.2008.06.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Mutations in KlCYC1 3′-UTR altering post-transcriptional steps and causing changes in protein levels. J Biotechnol 2007. [DOI: 10.1016/j.jbiotec.2007.07.502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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