Transcripts synthesized by RNA polymerase III can be polyadenylated in an AAUAAA-dependent manner

Borodulina, Olga R.; Крамеров, Д. А.

doi:10.1261/rna.1006608

Cited by 45 publications

(42 citation statements)

References 41 publications

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“…the binding site of TFIIH). Alternatively, the chimeric constructs used here may not reconstitute elongation and termination complexes properly as has been seen for RNAP III transcripts that can be polyadenylated only if an appropriate polyadenylation signal and RNAP III terminator are present (45).…”

Section: Discussionmentioning

confidence: 99%

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The Carboxyl-terminal Domain of RNA Polymerase II Is Not Sufficient to Enhance the Efficiency of Pre-mRNA Capping or Splicing in the Context of a Different Polymerase

Natalizio

Robson-Dixon

García-Blanco

2009

Journal of Biological Chemistry

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Eukaryotic messenger RNA precursors (pre-mRNAs) synthesized by RNA polymerase II (RNAP II) are processed cotranscriptionally. The carboxyl-terminal domain (CTD) of the largest subunit of RNA polymerase II is thought to mediate the coupling of transcription with pre-mRNA processing by coordinating the recruitment of processing factors during synthesis of nascent transcripts. Previous studies have demonstrated that the phosphorylated CTD is required for efficient co-transcriptional processing. In the study presented here we investigated whether the CTD is sufficient to coordinate transcription with pre-mRNA capping and splicing in the context of two other DNA-dependent RNA polymerases, mammalian RNAP III and bacteriophage T7 RNAP. Our results indicate that the CTD fused to the largest subunit of RNAP III (POLR3A) is not sufficient to enhance co-transcriptional pre-mRNA splicing or capping in vivo. Additionally, we analyzed a T7 RNAP-CTD fusion protein and examined its ability to enhance pre-mRNA splicing and capping of both constitutively and alternatively spliced substrates. We observed that the CTD in the context of T7 RNAP was not sufficient to enhance pre-mRNA splicing or capping either in vitro or in vivo. We propose that the efficient coupling of transcription to pre-mRNA processing requires not only the phosphorylated CTD but also other RNAP II specific subunits or associated factors.In recent years many studies have focused on deciphering the mechanisms by which RNA polymerase II (RNAP II) 4 transcription is coupled with pre-messenger RNA (pre-mRNA) processing, including 5Ј capping, splicing, and 3Ј end formation (1-8). These studies have revealed a role of the carboxyl-terminal domain (CTD) of the largest subunit of RNAP II (POLR2A) in the coupling of transcription to pre-mRNA processing. The CTD is unique to POLR2A, as it is not present in homologous subunits of RNA polymerases I and III (9, 10). The highly conserved CTD comprises 25-52 heptapeptide repeats with the consensus sequence 1 YSPTSPS 7 . This sequence can be highly modified in vivo via glycosylation, phosphorylation, and isomerization of specific residues (11-13). The repetitive nature of the CTD and its ability to be differentially modified has led to the proposal of a CTD code (11,14). This idea suggests that the modification state of the heptapeptide repeats can serve to coordinate transcription with pre-mRNA processing by recruiting the appropriate processing factors at appropriate stages of the transcription cycle (15).CTD phosphorylation and dephosphorylation are critical for proper CTD function (15). The hypophosphorylated form of RNAP II, RNAP II a , is associated with the preinitiation complex positioned at the promoter, whereas the hyperphosphorylated form, RNAP II O , is associated with transcript elongation and pre-mRNA processing (12). The general transcription factor TFIIH phosphorylates Ser 5 residues of the CTD soon after transcription initiation. RNAP II with Ser 5 -phosphorylated CTD repeats undergoes promoter-proximal pausin...

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Section: Discussionmentioning

confidence: 99%

“…Although there is evidence that RNAP III transcripts can be polyadenylated (45), transcripts made by RNAP III are not substrates for splicing (38). Several splicing constructs were generated that were derived from the 5S␤3 plasmid (38).…”

Section: Polr3a Recombinant Proteinsmentioning

confidence: 99%

The Carboxyl-terminal Domain of RNA Polymerase II Is Not Sufficient to Enhance the Efficiency of Pre-mRNA Capping or Splicing in the Context of a Different Polymerase

Natalizio

Robson-Dixon

García-Blanco

2009

Journal of Biological Chemistry

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“…We found 9.5 RPKM in exonic sequence but only 0.1 RPKM in introns, indicating great specificity for expressed mRNA and rejection of genomic DNA and unspliced pre-mRNA. Reads aligning to repeats were dominated by the B2 family of short interspersed elements, which are known to generate polyadenylated transcripts (Borodulina and Kramerov 2008) and are abundantly expressed in many tissues including the early embryo (Taylor and Piko 1987).…”

Section: Single-cell Tagged Reverse Transcriptionmentioning

confidence: 99%

Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq

Islam

Kjällquist²,

Moliner³

et al. 2011

Genome Res.

872

726

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Our understanding of the development and maintenance of tissues has been greatly aided by large-scale gene expression analysis. However, tissues are invariably complex, and expression analysis of a tissue confounds the true expression patterns of its constituent cell types. Here we describe a novel strategy to access such complex samples. Single-cell RNA-seq expression profiles were generated, and clustered to form a two-dimensional cell map onto which expression data were projected. The resulting cell map integrates three levels of organization: the whole population of cells, the functionally distinct subpopulations it contains, and the single cells themselves—all without need for known markers to classify cell types. The feasibility of the strategy was demonstrated by analyzing the transcriptomes of 85 single cells of two distinct types. We believe this strategy will enable the unbiased discovery and analysis of naturally occurring cell types during development, adult physiology, and disease.

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“…The cis-preference violation can be mediated by poly(A)-binding protein, which can bind proteins of the translational machinery (Roy-Engel et al, 2002b); in this case, the acquisition of an A-tail should be an essential step in the evolution of SINEs mobilized by an RT with cis-preference. In some SINEs (for example, rodent B2), a polyadenylation signal at the 3 0 end provides for the A-tail synthesis (Borodulina and Kramerov, 2008).…”

Section: Reverse Transcriptional Competencementioning

confidence: 99%

“…There is evidence that polyadenylation radically increases the lifetime of SINE RNA (Borodulina and Kramerov, 2008). The transport of SINE RNA is likely mediated by the interaction of its domains with cellular factors.…”

Section: Reverse Transcriptional Competencementioning

confidence: 99%

Origin and evolution of SINEs in eukaryotic genomes

2011

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Transcripts synthesized by RNA polymerase III can be polyadenylated in an AAUAAA-dependent manner

Cited by 45 publications

References 41 publications

The Carboxyl-terminal Domain of RNA Polymerase II Is Not Sufficient to Enhance the Efficiency of Pre-mRNA Capping or Splicing in the Context of a Different Polymerase

The Carboxyl-terminal Domain of RNA Polymerase II Is Not Sufficient to Enhance the Efficiency of Pre-mRNA Capping or Splicing in the Context of a Different Polymerase

Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq

Origin and evolution of SINEs in eukaryotic genomes

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