Expression of human snRNA genes from beginning to end

Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, UK.
Biochemical Society Transactions (Impact Factor: 3.19). 08/2008; 36(Pt 4):590-4. DOI: 10.1042/BST0360590
Source: PubMed


In addition to protein-coding genes, mammalian pol II (RNA polymerase II) transcribes independent genes for some non-coding RNAs, including the spliceosomal U1 and U2 snRNAs (small nuclear RNAs). snRNA genes differ from protein-coding genes in several key respects and some of the mechanisms involved in expression are gene-type-specific. For example, snRNA gene promoters contain an essential PSE (proximal sequence element) unique to these genes, the RNA-encoding regions contain no introns, elongation of transcription is P-TEFb (positive transcription elongation factor b)-independent and RNA 3'-end formation is directed by a 3'-box rather than a cleavage and polyadenylation signal. However, the CTD (C-terminal domain) of pol II closely couples transcription with RNA 5' and 3' processing in expression of both gene types. Recently, it was shown that snRNA promoter-specific recognition of the 3'-box RNA processing signal requires a novel phosphorylation mark on the pol II CTD. This new mark plays a critical role in the recruitment of the snRNA gene-specific RNA-processing complex, Integrator. These new findings provide the first example of a phosphorylation mark on the CTD heptapeptide that can be read in a gene-type-specific manner, reinforcing the notion of a CTD code. Here, we review the control of expression of snRNA genes from initiation to termination of transcription.

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Available from: Dawn O'Reilly, May 22, 2014
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    • "A key event in the splicing process is the recognition of the 5 splice site (5 ss) by U1 small nuclear RNA (U1 snRNA) that, within specific proteins , forms the U1 small nuclear ribonucleoparticle (snRNP) [Roca et al., 2013]. The U1 snRNA has a protruding 5 -tail that interacts by complementarity with donor splice sites, recruiting the spliceosome machinery on the exon and promoting the first step of the splicing reaction [Egloff et al., 2008; van der Feltz et al., 2012]. Recently, we have developed a novel strategy to correct exon skipping based on exon-specific U1 snRNAs (ExSpe U1s). "
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    ABSTRACT: The c.891C>T synonymous transition in SPINK5 induces exon 11 (E11) skipping and causes Netherton syndrome (NS). Using a specific RNA-protein interaction assay followed by mass spectrometry analysis along with silencing and over-expression of splicing factors, we showed that this mutation affects an exonic bi-functional splicing regulatory element (Bi-SRE) composed by two partially overlapping silencer and enhancer sequences, recognized by hnRNPA1 and Tra2β splicing factors, respectively. The C-to-T substitution concomitantly increases hnRNPA1 and weakens Tra2β binding sites, leading to pathological E11 skipping. In hybrid minigenes, Exon-specific U1 small nuclear RNAs (ExSpe U1s) that target by complementarity intronic sequences downstream of the donor splice site rescued the E11 skipping defect caused by the c.891C>T mutation. ExSpe U1 lentiviral-mediated transduction of primary NS keratinocytes from a patient bearing the mutation recovered the correct full-length SPINK5 mRNA and the corresponding functional LEKTI protein in a dose dependent manner. This study documents the reliability of a mutation-specific, ExSpe U1-based, splicing therapy for a relatively large subset of European NS patients. Usage of ExSpe U1 may represent a general approach for correction of splicing defects affecting skin disease genes. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
    Full-text · Article · Feb 2015 · Human Mutation
    • "Transcription of snRNA genes by RNAPII differs significantly from the transcription of most protein-coding genes (for recent reviews see Egloff et al., 2008; Jawdekar and Henry, 2008). However, the mechanism of snRNA transcription is still not understood in detail. "
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    ABSTRACT: Cajal bodies are nuclear structures involved in snRNP and snoRNP biogenesis, telomere maintenance and histone mRNA processing. Recently, the SUMO isopeptidase USPL1 was identified as a Cajal body component essential for cellular growth and Cajal body integrity. However, a cellular function for USPL1 is so far unknown. Here, we use RNAi mediated knockdown in human cells in combination with biochemical and fluorescence microscopy approaches to investigate the function of USPL1 and its relation to Cajal bodies. We demonstrate that the levels of RNAPII-transcribed snRNAs are reduced upon knockdown of USPL1 and that downstream processes such as snRNP assembly and pre-mRNA splicing are compromised. Importantly, we find that USPL1 associates directly with U snRNA loci and that it interacts and colocalizes with components of the Little Elongation Complex, which is involved in RNAPII-mediated snRNA transcription. Thus our data indicate that USPL1 plays a key role in the process of RNAPII-mediated snRNA transcription.
    No preview · Article · Jan 2014 · Journal of Cell Science
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    • "No significant differences occur over first exons, consistent with our previous observation that H3K36me3 levels are low in this region (6). As a control, we analyzed the human U6 snRNA gene set, which is transcribed by RNA polymerase III (39) and lacks enrichment for H3K36me3 (40). Lack of H3K36me3 marking in the U6 snRNA gene is consistent with the finding that in yeast, the H3K36 methyltransferase Set2 binds directly to the phosphorylated C-terminal domain of RNAPII (14,41,42), a structure that is absent from RNA polymerase III. "
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    ABSTRACT: Histone H3 of nucleosomes positioned on active genes is trimethylated at Lys36 (H3K36me3) by the SETD2 (also termed KMT3A/SET2 or HYPB) methyltransferase. Previous studies in yeast indicated that H3K36me3 prevents spurious intragenic transcription initiation through recruitment of a histone deacetylase complex, a mechanism that is not conserved in mammals. Here, we report that downregulation of SETD2 in human cells leads to intragenic transcription initiation in at least 11% of active genes. Reduction of SETD2 prevents normal loading of the FACT (FAcilitates Chromatin Transcription) complex subunits SPT16 and SSRP1, and decreases nucleosome occupancy in active genes. Moreover, co-immunoprecipitation experiments suggest that SPT16 is recruited to active chromatin templates, which contain H3K36me3-modified nucleosomes. Our results further show that within minutes after transcriptional activation, there is a SETD2-dependent reduction in gene body occupancy of histone H2B, but not of histone H3, suggesting that SETD2 coordinates FACT-mediated exchange of histone H2B during transcription-coupled nucleosome displacement. After inhibition of transcription, we observe a SETD2-dependent recruitment of FACT and increased histone H2B occupancy. These data suggest that SETD2 activity modulates FACT recruitment and nucleosome dynamics, thereby repressing cryptic transcription initiation.
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