Identification and analysis of internal promoters in <i>Caenorhabditis elegans</i> operons

Huang, Peiming; Pleasance, Erin; Maydan, Jason S.; Hunt-Newbury, Rebecca; O’Neil, Nigel J.; Mah, Allan K.; Baillie, David L.; Marra, Marco A.; Moerman, Donald G.; Jones, Steven J.M.

doi:10.1101/gr.6824707

Cited by 44 publications

(49 citation statements)

References 56 publications

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“…We used H3K9ac to mark the position of promoters near the 5 0 end of each operon (Fig. 3), and at a known internal promoter within the eight-gene operon, providing independent evidence for this internal initiation site 45,60,61 ( Fig. 3C).…”

Section: Rnapii Distribution On C Elegans Operonsmentioning

confidence: 99%

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: Rnapii Distribution On C Elegans Operonsmentioning

confidence: 99%

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

2016

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“…Interestingly, however, some genes annotated as downstream in operons receive a mixture of SL1 and SL2. Could these be downstream in hybrid operons (Huang et al 2007)? Perhaps pre-mRNAs receive SL2 when transcribed from promoters at the 59 ends of operons, and SL1 when transcribed from a proximal promoter between the operon genes.…”

Section: Sl Percentage and Internal Operon Promotersmentioning

confidence: 99%

“…Interestingly, however, there are many genes that receive a mixture of SL1 and SL2, and these genes are properly annotated as operons. These genes are members of hybrid operons (Huang et al 2007). Genes with as low as 10% SL2 have a restricted distance to the upstream gene (Fig.…”

Section: Sl2 Trans-splicing and The Annotation Of Operonsmentioning

confidence: 99%

“…The small amount of SL2 trans-spliced mRNA remaining could come from the adjacent promoter or from residual promoter activity upstream. Huang et al (2007) concluded that trans-splicing with a mixture of SL1 and SL2 is not a sufficient indicator for the prediction of an internal promoter. This may well be true, but our data indicate clearly that such a mixture is associated with hybrid operons overall, and that it is therefore capable of predicting the presence of an internal promoter.…”

Section: Sl2 Trans-splicing and The Annotation Of Operonsmentioning

confidence: 99%

“…Furthermore, a few genes receive a mixture of SL1 and SL2. In addition, as many as 25% of operons were estimated to be ''hybrid operons'' in which there are internal promoters (Huang et al 2007). Hybrid operons, therefore, add an additional layer of complexity to the annotation of operons.…”

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A global analysis of C. elegans trans-splicing

Allen¹,

Hillier²,

Waterston³

et al. 2010

Genome Res.

158

256

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Trans-splicing of one of two short leader RNAs, SL1 or SL2, occurs at the 59 ends of pre-mRNAs of many C. elegans genes. We have exploited RNA-sequencing data from the modENCODE project to analyze the transcriptome of C. elegans for patterns of trans-splicing. Transcripts of~70% of genes are trans-spliced, similar to earlier estimates based on analysis of far fewer genes. The mRNAs of most trans-spliced genes are spliced to either SL1 or SL2, but most genes are not transspliced to both, indicating that SL1 and SL2 trans-splicing use different underlying mechanisms. SL2 trans-splicing occurs in order to separate the products of genes in operons genome wide. Shorter intercistronic distance is associated with greater use of SL2. Finally, increased use of SL1 trans-splicing to downstream operon genes can indicate the presence of an extra promoter in the intercistronic region, creating what has been termed a ''hybrid'' operon. Within hybrid operons the presence of the two promoters results in the use of the two SL classes: Transcription that originates at the promoter upstream of another gene creates a polycistronic pre-mRNA that receives SL2, whereas transcription that originates at the internal promoter creates transcripts that receive SL1. Overall, our data demonstrate that >17% of all C. elegans genes are in operons.[Supplemental material is available for this article. The sequence data from this study have been submitted to the NCBI Sequence Read Archive (http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi) under accession nos. SRA008646 and SRA003622.] C. elegans uses two RNA processing features that distinguish it from other model organisms. First, the transcripts of many genes are trans-spliced to a spliced leader (SL). Trans-splicing is a process in which an SL replaces the 59 end of a transcript by spliceosomal splicing. The 22-nucleotide (nt) SL is donated by an ;100-nt SL snRNP (small nuclear ribonucleoprotein) to a pre-mRNA with an intron-like region, the outron, containing an unpaired 39 splice site located near the 59 end. The second distinguishing feature is that many genes are transcribed in polycistronic units, known as operons, where a single promoter serves several genes. The operons can be up to eight genes long, and the polycistronic pre-mRNAs are separated into individual cistrons by 39 end formation accompanied by SL trans-splicing.These two features have important implications for C. elegans research. For instance, deletions/insertions within an operon may affect not only the expression of the gene containing the mutation, but also the genes downstream from it in the operon (Cui et al. 2008). Similarly, in a strain with enhanced RNAi sensitivity, RNAi of an operon gene can also affect expression of genes downstream (Guang et al. 2010). Finally, the trans-splice site is at the 59 end of the mRNA, not the pre-mRNA, and thus, the promoter is often not directly adjacent to the gene, but rather upstream of the outron or the entire operon (Blumenthal and Spieth 1996). SL trans-splicing has been repor...

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Fifteen Years of Evolutionary Genomics inCaenorhabditis elegans

Jovelin

Dey

Cutter

2013

Encyclopedia of Life Sciences

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The nematode worm Caenorhabditis elegans , introduced by Sydney Brenner for the genetic analysis of nervous system formation, is now a powerful model organism for studying nearly all aspects of biology, from development to diseases to evolution. Sequencing and analysis of the worm genome revealed intriguing nonrandom patterns of genome organisation and unusual features such as abundant operons. Surprising upon first discovery, worms and humans have a similar number of genes that are comprised of a similar proportion of transcription factors to regulate their genomes. However, differences in small ribonucleic acid content may contribute to differences in organismal complexity. In nature, the bacterivorous C. elegans is found primarily on rotting vegetation in temperate regions across the world. Natural selection, combined with the low effective recombination rate associated with selfing, strongly reduces nucleotide variation across the genome, yielding similarly low polymorphism to other selfing hermaphrodite species of Caenorhabditis . The genus Caenorhabditis provides a superb model system for ecological and evolutionary genetics, benefiting from C. elegans tools and information when applied to investigations of species with a higher polymorphism and better known ecological context. Key Concepts: The nematode Caenorhabditis elegans , introduced by Sydney Brenner for the genetic analysis of nervous system development, was the first metazoan to have a complete sequenced genome and is now a model organism for nearly all fields of biology. Many genomic features are not randomly distributed along C. elegans chromosomes and are prevalent either in the chromosome arms or in its centre. An unusually large fraction of protein‐coding genes is organised in operons, possibly optimising transcriptional resources during recovery from developmental arrest. Gene duplication and alternative splicing contribute to extensive diversification of gene function, with 10.5% of protein‐coding genes having paralogs and 25% of genes being alternatively spliced. The ratio of transcription factors to protein‐coding genes is similar in worms and humans but the two species differ greatly in their microRNA content. The differences in chromatin states contribute to phenotypic variation and the transgenerational epigenetic inheritance suggests a role for epigenetic information in evolution. The rate of duplication is two orders of magnitude greater than the nucleotide mutation rate, highlighting the role of gene duplication in the evolution of the C. elegans genome. Caenorhabditis is not a soil nematode but instead proliferates and feeds on bacteria in rotting vegetation. Population genetic variation is strongly affected by the mating system of Caenorhabditis , with very low polymorphism in selfing hermaphroditic species relative to outcrossing gonochoristic species.

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Identification and analysis of internal promoters in Caenorhabditis elegans operons

Cited by 44 publications

References 56 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

A global analysis of C. elegans trans-splicing

Fifteen Years of Evolutionary Genomics inCaenorhabditis elegans

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