Emerging Views on the CTD Code

Zhang, David W.; Rodríguez-Molina, Juan B; Tietjen, Joshua R.; Nemec, Corey M.; Ansari, Aseem Z.

doi:10.1155/2012/347214

Cited by 47 publications

(61 citation statements)

References 251 publications

(247 reference statements)

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“…The CTD consists of consensus repeats Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7, with the number varying from 26 in yeast to 52 in vertebrates (159)(160)(161)(162)(163). The CTD is necessary for efficient polyadenylation both in vivo (33) and in vitro (34), but exactly how it promotes mRNA 3=-end formation is still not well understood.…”

Section: Rnap II Ctdmentioning

confidence: 99%

“…The ability of the RNAP II CTD to interact with a variety of 3= processing factors and thus to link polyadenylation to transcription can be largely explained by its structural diversity, which results from its intrinsic nonuniform and overall disordered architecture (135,165), various dynamic posttranslational modifications, especially phosphorylation, as well as cis-trans isomerization of prolyl peptide bonds (159)(160)(161)(162)(163). Although structural information about the full-length RNAP II CTD is not available, a number of segments ranging from less than one repeat to nearly three repeats have been captured associated with RNAP II CTDbinding proteins.…”

Section: Rnap II Ctdmentioning

confidence: 99%

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Delineating the Structural Blueprint of the Pre-mRNA 3′-End Processing Machinery

Xiang

Tong

Manley

2014

Molecular and Cellular Biology

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Processing of mRNA precursors (pre-mRNAs) by polyadenylation is an essential step in gene expression. Polyadenylation consists of two steps, cleavage and poly(A) synthesis, and requires multiple cis elements in the pre-mRNA and a megadalton protein complex bearing the two essential enzymatic activities. While genetic and biochemical studies remain the major approaches in characterizing these factors, structural biology has emerged during the past decade to help understand the molecular assembly and mechanistic details of the process. With structural information about more proteins and higher-order complexes becoming available, we are coming closer to obtaining a structural blueprint of the polyadenylation machinery that explains both how this complex functions and how it is regulated and connected to other cellular processes.

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Section: Rnap II Ctdmentioning

confidence: 99%

Section: Rnap II Ctdmentioning

confidence: 99%

Delineating the Structural Blueprint of the Pre-mRNA 3′-End Processing Machinery

Xiang

Tong

Manley

2014

Molecular and Cellular Biology

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“…We therefore considered whether elongating RNA Pol II recruits ASH1 to sites downstream of active gene promoters. This possibility was attractive because the CTD of RNA Pol II recruits a wide variety of factors involved in transcription (Zhang et al, 2012).…”

Section: Research Articlementioning

confidence: 99%

“…The phosphorylated C-terminal domain (CTD) of elongating Pol II recruits a host of factors required for the transcription and processing of nascent transcripts to the body of active genes, including the histone methyltransferase SET2, the histone deacetylase RPD3, transcription elongation factor SPT6, and the histone H3 K27 demethylase UTX (Bartkowiak et al, 2011;Smith et al, 2008;Zhang et al, 2012). Transcription elongation also promotes the replacement of histone H3 with the histone variant H3.3, which harbors covalent modifications characteristic of active genes, including elevated H3K4me3 and low H3K27me3 Mito et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

The trithorax group proteins Kismet and ASH1 promote H3K36 dimethylation to counteract Polycomb group repression inDrosophila

Dorighi

Tamkun

2013

Development

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SUMMARYMembers of the Polycomb group of repressors and trithorax group of activators maintain heritable states of transcription by modifying nucleosomal histones or remodeling chromatin. Although tremendous progress has been made toward defining the biochemical activities of Polycomb and trithorax group proteins, much remains to be learned about how they interact with each other and the general transcription machinery to maintain on or off states of gene expression. The trithorax group protein Kismet (KIS) is related to the SWI/SNF and CHD families of chromatin remodeling factors. KIS promotes transcription elongation, facilitates the binding of the trithorax group histone methyltransferases ASH1 and TRX to active genes, and counteracts repressive methylation of histone H3 on lysine 27 (H3K27) by Polycomb group proteins. Here, we sought to clarify the mechanism of action of KIS and how it interacts with ASH1 to antagonize H3K27 methylation in Drosophila. We present evidence that KIS promotes transcription elongation and counteracts Polycomb group repression via distinct mechanisms. A chemical inhibitor of transcription elongation, DRB, had no effect on ASH1 recruitment or H3K27 methylation. Conversely, loss of ASH1 function had no effect on transcription elongation. Mutations in kis cause a global reduction in the di-and tri-methylation of histone H3 on lysine 36 (H3K36) -modifications that antagonize H3K27 methylation in vitro. Furthermore, loss of ASH1 significantly decreases H3K36 dimethylation, providing further evidence that ASH1 is an H3K36 dimethylase in vivo. These and other findings suggest that KIS antagonizes Polycomb group repression by facilitating ASH1-dependent H3K36 dimethylation.

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“…This was named as the CTD Code by Buratowski, a term currently in use [7][8][9][10]. CTD is considered as a recruitment platform for the different factors that are associated to the enzyme during initiation, elongation or the steps related to splicing, transcriptional termination and RNA processing.…”

Section: Commentmentioning

confidence: 99%

RNA Polymerase II: Reading in Loops to get Different Tails

Freire-Picos¹

2016

Biochem Mol Biol J

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CommentThe RNA polymerase II is the multi-subunit enzyme able to transcribe the protein-encoding genes in eukaryotic cells producing the messenger RNA (mRNA). Two critical steps in eukaryotic mRNA biogenesis, for its correct 3´-end processing are: cleavage and polyadenylation. This is necessary to achieve a message that can be recognized by the proteins that properly export it to the cytosol and so that it can be efficiently translated by the ribosomes or mediate its turnover [1,2].But what happens with the RNA polymerase after a first round of transcription? It is necessary to recycle the RNA polymerase back to the promoter for a new round of transcription. For this last purpose, the formation of DNA-loops, establishing physical interactions between the promoter and the sequences downstream from the coding region, are necessary [3][4][5][6]. The current view is that these loops are transcriptional memories for the cells.However, it is not that simple, the major subunit of the RNA polymerase II has a Carboxy-Terminal Domain (CTD) with multiple repeats of a seven amino-acid sequence (YSTPSPS), each position can be covalently modified and there are multiple combinations possible. This was named as the CTD Code by Buratowski, a term currently in use [7][8][9][10]. CTD is considered as a recruitment platform for the different factors that are associated to the enzyme during initiation, elongation or the steps related to splicing, transcriptional termination and RNA processing. While riding the loop the polymerase will undergo multiple changes in the CTD Code and, to finally be recycled back to the promoter, its CTD must be hypo-phosphorylated.Things become more complicated by the fact that many genes are under alternative 3´-end processing (alternative polyadenylation, APA) [11][12][13]. One of these genes is the yeast KlCYC1 gene [14,15]. The regulated APA for this gene causes two transcripts with different 3´-UTR lengths. We have recently shown in the related article of this comment that for genes with regulated APA there is alternative DNA-loops formation also. Moreover, the predominant processing region is included in the predominant loop. Changes in RNA polymerase II positioning or the CTD phosphatase Ssu72 also correlate with both, the loop and APA predominance [16]. From the data attained for a gene with APA, it is clear the dependence of RNA processing in DNA-loop formation and, as indicated in the title, the RNA polymerase has to read the different loops in order to get messages with different tails which will depend on the cellular requirements. RNA Polymerase II: Reading in Loops to get Different Tails AbstractThe DNA-loops are necessary to recycle the RNA polymerase for the multiple transcription rounds of a gene. The nascent transcript needs to be 3'-end processed: cleaved in a specific position and added a 3´-end poly-(A)-tail to become an mRNA. Under regulated conditions, genes undergo 3´-end RNA processing at different positions. This is called alternative polyadenylation (APA) and, as a consequence,...

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Emerging Views on the CTD Code

Cited by 47 publications

References 251 publications

Delineating the Structural Blueprint of the Pre-mRNA 3′-End Processing Machinery

Delineating the Structural Blueprint of the Pre-mRNA 3′-End Processing Machinery

The trithorax group proteins Kismet and ASH1 promote H3K36 dimethylation to counteract Polycomb group repression inDrosophila

RNA Polymerase II: Reading in Loops to get Different Tails

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