High-Copy-Number Expression of Sub2p, a Member of the RNA Helicase Superfamily, Suppresses <i>hpr1</i>-Mediated Genomic Instability

Fan, Hua-Ying; Merker, Robert J.; Klein, Hannah L.

doi:10.1128/mcb.21.16.5459-5470.2001

Cited by 53 publications

(78 citation statements)

References 55 publications

(67 reference statements)

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“…Hpr1 is a component of the THO complex, which consists of Tho2, Mft1, and Thp2, in addition to Hpr1 (Chavez et al 2000). Interestingly, the splicing and export factor Sub2 (UAP56 in humans) genetically suppressed Hpr1 and Cdc73 (PAF subunit) phenotypes, potentially linking these complexes to splicing and export activities (Fan et al 2001). Independent work discovered genetic interactions between THO and additional mRNA export factors including Sub2 and Yra1/REF (ALY in humans) (Jimeno et al 2002;Merker and Klein 2002;Strasser et al 2002).…”

Section: Rna Surveillance and Nuclear Exportmentioning

confidence: 99%

Elongation by RNA polymerase II: the short and long of it

Sims¹,

Belotserkovskaya²,

Reinberg³

2004

Genes Dev.

614

586

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Appreciable advances into the process of transcript elongation by RNA polymerase II (RNAP II) have identified this stage as a dynamic and highly regulated step of the transcription cycle. Here, we discuss the many factors that regulate the elongation stage of transcription. Our discussion includes the classical elongation factors that modulate the activity of RNAP II, and the more recently identified factors that facilitate elongation on chromatin templates. Additionally, we discuss the factors that associate with RNAP II, but do not modulate its catalytic activity. Elongation is highlighted as a central process that coordinates multiple stages in mRNA biogenesis and maturation.The regulation of gene expression is one of the most intensely studied areas in all of science. Differential gene expression in multicellular organisms forms the foundation of cell-type specificity. Deregulation of the appropriate pattern of gene expression has profound effects on cellular function and underlies many diseases. Although there are many cellular processes that control gene expression, the most direct regulation occurs during transcription. The transcription of protein-coding genes in eukaryotes is performed by RNA polymerase II (RNAP II). Up until recently, the vast majority of studies aimed at elucidating the molecular mechanisms of transcription regulation have focused on early stages, such as the formation of a transcription initiation complex (preinitiation) and initiation (see below). For many years, transcript elongation has been thought of as the trivial addition of ribonucleoside triphosphates to the growing mRNA chain. It is now apparent that this process is a dynamic and highly regulated stage of the transcription cycle capable of coordinating downstream events. Numerous factors have been identified that specifically target the elongation stage of transcription. Importantly, multiple steps in mRNA maturation, including premRNA capping, splicing, 3Ј-end processing, surveillance, and export, are modulated through interactions with the RNAP II transcript elongation complex (TEC). It also appears that distinct elongation factors function in specific transcriptional contexts; the requirements for these specialized factors are largely unknown and highlight the need to better understand elongation in vivo. Many molecular and biochemical approaches have been used to quantify the different aspects of elongation, many of which are discussed below. It remains important to assimilate both in vitro and in vivo experimental systems when discussing what constitutes an elongation factor. An elongation factor can be defined as any molecule that affects the activities of or is associated with the TEC. We suggest that there are at least two major types of transcript elongation factors: one family, referred to as active elongation factors, and a second family, denoted as passive elongation factors. The difference resides in whether the factor affects the catalytic activity of RNAP II, regardless of whether the factor remains associate...

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Section: Rna Surveillance and Nuclear Exportmentioning

confidence: 99%

Elongation by RNA polymerase II: the short and long of it

Sims¹,

Belotserkovskaya²,

Reinberg³

2004

Genes Dev.

614

586

View full text Add to dashboard Cite

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“…Sub2p is a highly conserved RNA helicase with orthologs in Schizosaccharomyces pombe, Caenorhabditis elegans, Drosophila melanogaster, mouse, and man (Fan et al 2001;Jimeno et al 2002). As such, it contains the typical DEAD-box helicase core in addition to an extended N-terminal region of unknown function.…”

Section: Introductionmentioning

confidence: 99%

“…Sub2p is involved in multiple stages of mRNA maturation and its inactivation leads to nonproductive spliceosome assembly (Kistler and Guthrie 2001;Libri et al 2001), decreased polyadenylation efficiency and mRNA instability (Rougemaille et al 2007;Saguez et al 2008), as well as nuclear accumulation of poly(A) + RNA (Jensen et al 2001a;Strasser and Hurt 2001;Rougemaille et al 2007;Schmid et al 2008). In addition, Sub2p is important for chromatin maintenance as its overexpression suppresses the genomic instability caused by deletion of the HPR1 THO component gene (Chavez et al 2000;Fan et al 2001), which otherwise causes a recombination rate of >3000 times that of wild-type (wt) cells (Aguilera and Klein 1988;Piruat and Aguilera 1998). The reason for involvement of an RNA helicase in DNA stability is not understood, but it may be related to the unwinding of RNA:DNA hybrid structures (R-loops) formed during transcription (Gomez-Gonzalez et al 2011).…”

Section: Introductionmentioning

confidence: 99%

Mutational analysis of the yeast RNA helicase Sub2p reveals conserved domains required for growth, mRNA export, and genomic stability

Saguez

Gonzales-Zubiate

Schmid

et al. 2013

RNA

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Sub2p/UAP56 is a highly conserved DEAD-box RNA helicase involved in the packaging and nuclear export of mRNA/protein particles (mRNPs). In Saccharomyces cerevisiae, Sub2p is recruited to active chromatin by the pentameric THO complex and incorporated into the larger transcription-export (TREX) complex. Sub2p also plays a role in the maintenance of genome integrity as its inactivation causes severe transcription-dependent recombination of DNA. Despite the central role of Sub2p in early mRNP biology, little is known about its function. Here, we report the presence of an N-terminal motif (NTM) conserved specifically in the Sub2p branch of RNA helicases. Mutation of the NTM causes nuclear accumulation of poly(A) + RNA and impaired growth without affecting core helicase functions. Thus, the NTM functions as an autonomous unit. Moreover, two sub2 mutants, that are deficient in ATP binding, act in a trans-dominant negative fashion for growth and induce high recombination rates in vivo. Although wild-type Sub2p is prevented access to transcribed loci in such a background, this does not mechanistically explain the phenotype.

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“…The Saccharomyces cerevisiae multisubunit THO complex, which has been identified as a possible elongation component, has been associated with many aspects of RNA and DNA metabolism (9)(10)(11)(12). The complex consists of four tightly bound proteins (Hpr1, Tho2, Thp1, and Mft1) (13), two of which (Hpr1 and Tho2) are conserved from yeast to humans (14).…”

mentioning

confidence: 99%

Genes with internal repeats require the THO complex for transcription

Voynov

Verstrepen

Jansen

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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The evolutionarily conserved multisubunit THO complex, which is recruited to actively transcribed genes, is required for the efficient expression of FLO11 and other yeast genes that have long internal tandem repeats. FLO11 transcription elongation in Tho ؊ mutants is hindered in the region of the tandem repeats, resulting in a loss of function. Moreover, the repeats become genetically unstable in Tho ؊ mutants. A FLO11 gene without the tandem repeats is transcribed equally well in Tho ؉ or Tho ؊ strains. The Tho ؊ defect in transcription is suppressed by overexpression of topoisomerase I, suggesting that the THO complex functions to rectify aberrant structures that arise during transcription.T ranscription involves a highly orchestrated series of events in which the core polymerase is joined by many additional proteins that promote initiation, elongation, and termination (1-3). Efficient transcription also depends on the configuration of the DNA template because transcription creates negative supercoils behind the polymerase and positive supercoils ahead of it (4-6). These alterations in the superhelical density could permit repetitive sequences to form structures that impede the progress of the polymerase and promote recombination. For example, excessive supercoiling in yeast leads to hyperrecombination at the highly repetitive rRNA-encoding DNA locus (7,8). The DNA landscape may therefore influence the efficiency of transcription, and some of the elongation factors could be required to remodel the template to permit efficient transcription.The Saccharomyces cerevisiae multisubunit THO complex, which has been identified as a possible elongation component, has been associated with many aspects of RNA and DNA metabolism (9-12). The complex consists of four tightly bound proteins (Hpr1, Tho2, Thp1, and Mft1) (13), two of which (Hpr1 and Tho2) are conserved from yeast to humans (14). Biochemical studies using natural templates have implicated the THO complex in recruiting the mRNA export proteins Sub2 (UAP56 in humans) and Yra1 (Aly1) to the mRNA in both yeast (15) and humans (14). In yeast, ChIP immunoprecipitation experiments indicate that the THO complex is recruited to actively transcribed genes (16)(17)(18).The biochemical analysis of the function of the THO complex has not led to a consistent picture. Experiments using a GAL1 promoted Escherichia coli lacZ reporter construct expressed in yeast suggested that transcription elongation of the lacZ gene is reduced in an hpr1⌬ mutant (19). Further analysis using a P GAL -lacZ system indicated that in a Tho Ϫ mutant DNA:RNA hybrids are formed in vivo between the nascent transcript and the DNA template (20). Because the transcription of GC-rich lacZ constructs was THO-dependent, whereas that of many endogenous yeast genes was not, it was proposed that the THO complex is required for efficient transcription elongation of long and GC-rich genes (21). Moreover, the role of the THO complex in elongation has been questioned based on the insensitivity of Tho Ϫ mutants to ...

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High-Copy-Number Expression of Sub2p, a Member of the RNA Helicase Superfamily, Suppresses hpr1-Mediated Genomic Instability

Cited by 53 publications

References 55 publications

Elongation by RNA polymerase II: the short and long of it

Elongation by RNA polymerase II: the short and long of it

Mutational analysis of the yeast RNA helicase Sub2p reveals conserved domains required for growth, mRNA export, and genomic stability

Genes with internal repeats require the THO complex for transcription

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