Dynamics of bacterial operons during genome-wide stresses is influenced by premature terminations and internal promoters
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ABSTRACT:
PROVIDER: PRJNA1009069 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25757619_1.fastq.gz | Fastqsanger.gz | |||
| SRR25757619_2.fastq.gz | Fastqsanger.gz | |||
| SRR25757620_1.fastq.gz | Fastqsanger.gz | |||
| SRR25757620_2.fastq.gz | Fastqsanger.gz | |||
| SRR25757621_1.fastq.gz | Fastqsanger.gz |
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Project description:Transcription termination is mechanistically coupled to pre-mRNA 3’ end formation to prevent transcription much beyond the gene 3’ end. C. elegans, however, engages in polycistronic transcription of operons in which 3’ 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’ ends. These 3’ peaks coincide with maximal phosphorylation of Ser2 within the C-terminal domain (CTD) of RNAPII and maximal localization of the 3’ end formation factor CstF. This pattern occurs at all 3’ ends including those at internal sites in operons where termination does not occur. Thus the normal mechanism of 3’ 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’ ends. However, CstF50 RNAi did result in a subtle reduction of CstF64 binding upstream of the site of 3’ cleavage, suggesting that the CstF50/CTD interaction may facilitate bringing the 3’ end machinery to the transcription complex.
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Project description:Transcription termination is mechanistically coupled to pre-mRNA 3’ end formation to prevent transcription much beyond the gene 3’ end. C. elegans, however, engages in polycistronic transcription of operons in which 3’ 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’ ends. These 3’ peaks coincide with maximal phosphorylation of Ser2 within the C-terminal domain (CTD) of RNAPII and maximal localization of the 3’ end formation factor CstF. This pattern occurs at all 3’ ends including those at internal sites in operons where termination does not occur. Thus the normal mechanism of 3’ 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’ ends. However, CstF50 RNAi did result in a subtle reduction of CstF64 binding upstream of the site of 3’ cleavage, suggesting that the CstF50/CTD interaction may facilitate bringing the 3’ end machinery to the transcription complex.
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Project description:Caenorhabditis elegans and its relatives are unique among animals, possibly even among eukaryotes, in having operons. In these regulated multigene transcription units, a polycistronic pre-mRNA is processed to monocistronic mRNAs by 3' end formation and trans-splicing utilizing a special snRNP, the SL2 snRNP, for downstream mRNAs1. Previously, the correlation between downstream location in an operon and SL2 trans-splicing has been strong, but anecdotal. Although only 28 operons have been reported previously, the complete sequence of the genome reveals numerous gene clusters. To determine how many represent operons, we probed full-genome microarrays for SL2-containing mRNAs. We found significant enrichment for about 1200 genes including most of a group of several hundred genes represented by cDNAs that contain SL2 sequence. Analysis of their genomic arrangements indicates that >90% are downstream genes, falling in 790 distinct operons. We conclude that the genome contains at least 1000 operons, 2- 8 genes in length, that contain ~15% of C. elegans genes. Most of the operons have not been reported previously, and numerous examples of co-transcription of genes encoding functionally related proteins are evident. Inspection of the operon list should reveal heretofore unknown functional relationships. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set Computed
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Project description:Transcription termination is mechanistically coupled to pre-mRNA 3â end formation to prevent transcription much beyond the gene 3â end. C. elegans, however, engages in polycistronic transcription of operons in which 3â 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 3â ends. These 3â peaks coincide with maximal phosphorylation of Ser2 within the C-terminal domain (CTD) of RNAPII and maximal localization of the 3â end formation factor CstF. This pattern occurs at all 3â ends including those at internal sites in operons where termination does not occur. Thus the normal mechanism of 3â 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 3â ends. However, CstF50 RNAi did result in a subtle reduction of CstF64 binding upstream of the site of 3â cleavage, suggesting that the CstF50/CTD interaction may facilitate bringing the 3â end machinery to the transcription complex. RNA-seq analysis of wild type (empty vector) and RNAi CstF50 mRNA (polyA-selected) and rRNA-depleted RNA (total RNA).
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