<i>C. elegans</i> sequences that control <i>trans</i>-splicing and operon pre-mRNA processing

Graber, Joel H.; Salisbury, Jesse; Hutchins, Lucie N.; Blumenthal, Thomas

doi:10.1261/rna.596707

Cited by 38 publications

(41 citation statements)

References 54 publications

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“…C. elegans contains clear homologs of all CPSF subunits 44 and has been shown to contain the canonical 3 0 end formation sequences at both internal and terminal 3 0 ends. 41 RNAPII pausing is a known characteristic of poly-A signal transcription. Indeed, RNAPII pausing at 3 0 ends of mammalian core histone genes, which code for non-polyadenylated transcripts, is brief or absent.…”

Section: Discussionmentioning

confidence: 99%

“…They have a somewhat less highly conserved AAUAAA »30 nt upstream of their 3 0 end cleavage site and a U-or GU-rich region »20 nt downstream. 41 In addition, the C. elegans genome encodes clear homologs of all the subunits of the 3 0 end formation complex. 42,43 Importantly, several 3 0 end formation factors were identified in a C. elegans suppressor screen for genes that play roles in 3 0 end formation.…”

Section: Introductionmentioning

confidence: 99%

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Localization of RNAPII and 3′ end formation factor CstF subunits onC. elegansgenes and operons

2016

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Transcription termination is mechanistically coupled to pre-mRNA 3 0 end formation to prevent transcription much beyond the gene 3 0 end. C. elegans, however, engages in polycistronic transcription of operons in which 3 0 end formation between genes is not accompanied by termination. We have performed RNA polymerase II (RNAPII) and CstF ChIP-seq experiments to investigate at a genome-wide level how RNAPII can transcribe through multiple poly-A signals without causing termination. Our data shows that transcription proceeds in some ways as if operons were composed of multiple adjacent single genes. Total RNAPII shows a small peak at the promoter of the gene cluster and a much larger peak at 3 0 ends. These 3 0 peaks coincide with maximal phosphorylation of Ser2 within the C-terminal domain (CTD) of RNAPII and maximal localization of the 3 0 end formation factor CstF. This pattern occurs at all 3 0 ends including those at internal sites in operons where termination does not occur. Thus the normal mechanism of 3 0 end formation does not always result in transcription termination. Furthermore, reduction of CstF50 by RNAi did not substantially alter the pattern of CstF64, total RNAPII, or Ser2 phosphorylation at either internal or terminal 3 0 ends. However, CstF50 RNAi did result in a subtle reduction of CstF64 binding upstream of the site of 3 0 cleavage, suggesting that the CstF50/CTD interaction may facilitate bringing the 3 0 end machinery to the transcription complex.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Localization of RNAPII and 3′ end formation factor CstF subunits onC. elegansgenes and operons

2016

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“…Nonetheless, the independent origin of the same features in dinoflagellates raises an intriguing alternative explanation, namely that the evolutionary origins of polycistronic mRNAs and trans-splicing are linked. This is all of the more compelling when one considers that both features are also found together in the nematode Caenorhabditis elegans (26). It is unlikely that this is either functionally advantageous or an evolutionary relict, but rather that the evolution of one feature preconditions the genome by removing deleterious effects of the second feature.…”

Section: The Nucleus: Spliced Leaders and Polycistronic Mrna Processingmentioning

confidence: 99%

Cascades of convergent evolution: The corresponding evolutionary histories of euglenozoans and dinoflagellates

Lukeš

Leander

Keeling

2009

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

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The majority of eukaryotic diversity is hidden in protists, yet our current knowledge of processes and structures in the eukaryotic cell is almost exclusively derived from multicellular organisms. The increasing sensitivity of molecular methods and growing interest in microeukaryotes has only recently demonstrated that many features so far considered to be universal for eukaryotes actually exist in strikingly different versions. In other words, during their long evolutionary histories, protists have solved general biological problems in many more ways than previously appreciated. Interestingly, some groups have broken more rules than others, and the Euglenozoa and the Alveolata stand out in this respect. A review of the numerous odd features in these 2 groups allows us to draw attention to the high level of convergent evolution in protists, which perhaps reflects the limits that certain features can be altered. Moreover, the appearance of one deviation in an ancestor can constrain the set of possible downstream deviations in its descendents, so features that might be independent functionally, can still be evolutionarily linked. What functional advantage may be conferred by the excessive complexity of euglenozoan and alveolate gene expression, organellar genome structure, and RNA editing and processing has been thoroughly debated, but we suggest these are more likely the products of constructive neutral evolution, and as such do not necessarily confer any selective advantage at all. mitochondria ͉ plastids ͉ comparative genomics ͉ molecular evolution ͉ Trypanosoma

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“…We show here that the RNAPII CTD is phosphorylated on Ser-2 residues near internal 3Ј-end formation sites just like terminal sites are, so something else must differentiate internal from terminal sites. Internal sites could have a sequence that prevents termination (14), or they might lack a sequence needed for termination. It was recently shown that cis splicing of the first intron of downstream genes in operons may play a role in preventing transcription termination from occurring at these internal sites (15).…”

Section: Vol 30 2010 Rnapii Ctd Phosphorylation In C Elegans Operomentioning

confidence: 99%

RNA Polymerase II C-Terminal Domain Phosphorylation Patterns in Caenorhabditis elegans Operons, Polycistronic Gene Clusters with Only One Promoter

Garrido-Lecca

Blumenthal

2010

Molecular and Cellular Biology

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The heptad repeat of the RNA polymerase II (RNAPII) C-terminal domain is phosphorylated at serine 5 near gene 5 ends and serine 2 near 3 ends in order to recruit pre-mRNA processing factors. Ser-5(P) is associated with gene 5 ends to recruit capping enzymes, whereas Ser-2(P) is associated with gene 3 ends to recruit cleavage and polyadenylation factors. In the gene clusters called operons in Caenorhabditis elegans, there is generally only a single promoter, but each gene in the operon forms a 3 end by the usual mechanism. Although downstream operon genes have 5 ends, they receive their caps by trans splicing rather than by capping enzymes. Thus, they are predicted to not need Ser-5 phosphorylation. Here we show by RNAPII chromatin immunoprecipitation (ChIP) that internal operon gene 5 ends do indeed lack Ser-5(P) peaks. In contrast, Ser-2(P) peaks occur at each mRNA 3 end, where the 3-end formation machinery binds. These results provide additional support for the idea that the serine phosphorylation of the C-terminal domain (CTD) serves to bring RNA-processing enzymes to the transcription complex. Furthermore, these results provide a novel demonstration that genes in operons are cotranscribed from a single upstream promoter.Pre-mRNAs of protein-coding genes must be processed into mature mRNAs for translation. This transcription is carried out by RNA polymerase II (RNAPII) in association with a wide range of nuclear proteins that serve at different stages in the transcription cycle. Shortly after the nascent RNA emerges from RNAPII, its 5Ј end is cotranscriptionally capped (6,8,26,29). The addition of the cap is performed in three steps: first, the 5Ј phosphate is removed by RNA triphosphatase; second, GMP is added by RNA guanyltransferase; and third, the cap is methylated by RNA methyltransferase (33). At the other end of the gene, the pre-mRNA is cotranscriptionally cleaved by the 3Ј-end formation machinery composed of the multisubunit proteins cleavage and polyadenylation specificity factor (CPSF) and cleavage-stimulatory factor (CstF) as well as several additional proteins. However, transcription does not terminate (i.e., release from the template) until the polymerase has continued synthesizing RNA for an additional kilobase or more (10,12,15). The 3Ј-end formation machinery, and perhaps pre-mRNA cleavage itself, plays a key role in the termination event. One popular idea is that cleavage exposes a free 5Ј phosphate end on the downstream RNA, thereby allowing access to the 5Ј-to-3Ј exonuclease XRN2 (11,18,38,39).To accommodate the large number of proteins required for these and other cotranscriptional events, RNAPII includes a unique and flexible tail-like domain at the carboxy terminus of its largest subunit, referred to as its carboxy-terminal domain (CTD). The CTD is composed of numerous heptad repeats with the consensus sequence Y 1 S 2 P 3 T 4 S 5 P 6 S 7 , a sequence conserved among all eukaryotes (35). The number of these heptad repeats correlates with genomic complexity, varying from 26 repeats in th...

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C. elegans sequences that control trans-splicing and operon pre-mRNA processing

Cited by 38 publications

References 54 publications

Localization of RNAPII and 3′ end formation factor CstF subunits onC. elegansgenes and operons

Localization of RNAPII and 3′ end formation factor CstF subunits onC. elegansgenes and operons

Cascades of convergent evolution: The corresponding evolutionary histories of euglenozoans and dinoflagellates

RNA Polymerase II C-Terminal Domain Phosphorylation Patterns in Caenorhabditis elegans Operons, Polycistronic Gene Clusters with Only One Promoter

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