Transcriptional regulation of human small nuclear RNA genes

Jawdekar, Gauri W.; Henry, R. William

doi:10.1016/j.bbagrm.2008.04.001

Cited by 79 publications

(119 citation statements)

References 176 publications

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“…The U1-2 and U4-5 snRNA genes however display differences in the 59 region that harbors an upstream sequence element (USE) in vertebrates (Jawdekar and Henry 2008), an USE and a TATA-like box separated by 33-34 bp in A. thaliana (Waibel and Filipowicz 1990) or by 18 bp in P. tetraurelia (see Fig. 2) and T. thermophila (Supplemental Fig.…”

Section: Purifying Selection and Snrnasmentioning

confidence: 99%

Genome-wide evolutionary analysis of the noncoding RNA genes and noncoding DNA of Paramecium tetraurelia

Chen¹,

Zhou²,

Liao³

et al. 2009

RNA

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The compact genome of the unicellular eukaryote Paramecium tetraurelia contains noncoding DNA (ncDNA) distributed into >39,000 intergenic sequences and >90,000 introns of 390 base pairs (bp) and 25 bp on average, respectively. Here we analyzed the molecular features of the ncRNA genes, introns, and intergenic sequences of this genome. We mainly used computational programs and comparative genomics possible because the P. tetraurelia genome had formed throughout whole-genome duplications (WGDs). We characterized 417 5S rRNA, snRNA, snoRNA, SRP RNA, and tRNA putative genes, 415 of which map within intergenic sequences, and two, within introns. The evolution of these ncRNA genes appears to have mainly involved purifying selection and gene deletion. We then compared the introns that interrupt the protein-coding gene duplicates arisen from the recent WGD and identified a population of a few thousands of introns having evolved under most stringent constraints (>95% of identity). We also showed that low nucleotide substitution levels characterize the 50 and 80-115 base pairs flanking, respectively, the stop and start codons of the protein-coding genes. Lower substitution levels mark the base pairs flanking the highly transcribed genes, or the start codons of the genes of the sets with a high number of WGD-related sequences. Finally, adjacent to protein-coding genes, we characterized 32 DNA motifs able to encode stable and evolutionary conserved RNA secondary structures and defining putative expression controlling elements. Fourteen DNA motifs with similar properties map distant from protein-coding genes and may encode regulatory ncRNAs.

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Section: Purifying Selection and Snrnasmentioning

confidence: 99%

Genome-wide evolutionary analysis of the noncoding RNA genes and noncoding DNA of Paramecium tetraurelia

Chen¹,

Zhou²,

Liao³

et al. 2009

RNA

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“…Nevertheless, gene duplications have led to new protein functions, as for BRF1 and BRF2, which recognize different subsets of promoters (Schramm et al 2000;Geiduschek and Kassavetis 2001;Schramm and Hernandez 2002;Jawdekar and Henry 2008;Carriere et al 2012), or RNA polymerases IV and V, which appeared in plants through several gene duplications and are specifically involved in noncoding RNA-mediated gene silencing processes (Haag and Pikaard 2011), as well as to transcription units with new regulation potentials, of which the POLR3G/ POLR3GL duplication is an example.…”

Section: Polr3g and Polr3gl-rna Polymerase III Target Genesmentioning

confidence: 99%

“…In yeast, TFIIIB consists of three subunits, the TATA box binding protein Spt15 (Tbp), the SANT domain protein Bdp1, and the TFIIB-related factor Brf1. In mammalian cells, two forms of TFIIIB exist, BRF1-TFIIIB and BRF2-TFIIIB, in which BRF1 is replaced by another TFIIB-related factor, BRF2 (Geiduschek and Kassavetis 2001;Schramm and Hernandez 2002;Jawdekar and Henry 2008). The trimeric POLR3C (RPC3)-POLR3F (RPC6)-POLR3G (RPC7) complex plays a role in transcription initiation complex formation (Thuillier et al 1995;Brun et al 1997;Wang and Roeder 1997), at least in part through direct contacts with TFIIIB: The yeast homolog of human POLR3F, Rpc34, has been shown to associate with Brf1 (Werner et al 1993), and human POLR3F with both BRF1 and TBP (Wang and Roeder 1997).…”

mentioning

confidence: 99%

Gene duplication and neofunctionalization: POLR3G and POLR3GL

et al. 2013

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RNA polymerase III (Pol III) occurs in two versions, one containing the POLR3G subunit and the other the closely related POLR3GL subunit. It is not clear whether these two Pol III forms have the same function, in particular whether they recognize the same target genes. We show that the POLR3G and POLR3GL genes arose from a DNA-based gene duplication, probably in a common ancestor of vertebrates. POLR3G-as well as POLR3GL-containing Pol III are present in cultured cell lines and in normal mouse liver, although the relative amounts of the two forms vary, with the POLR3G-containing Pol III relatively more abundant in dividing cells. Genome-wide chromatin immunoprecipitations followed by high-throughput sequencing (ChIP-seq) reveal that both forms of Pol III occupy the same target genes, in very constant proportions within one cell line, suggesting that the two forms of Pol III have a similar function with regard to specificity for target genes. In contrast, the POLR3G promoter-not the POLR3GL promoter-binds the transcription factor MYC, as do all other promoters of genes encoding Pol III subunits. Thus, the POLR3G/POLR3GL duplication did not lead to neo-functionalization of the gene product (at least with regard to target gene specificity) but rather to neo-functionalization of the transcription units, which acquired different mechanisms of regulation, thus likely affording greater regulation potential to the cell.

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“…We found BDP1, SNAPC2, and POLR3D peaks on RNU6 (U6-8) and RNU6 (U6-9) (Supplemental Table S6, rows 2, 3), and POLR3D and SNAPC2 on RNU6 (U6-2) (Supplemental Table S6, row 4). RNU6 (U6-1), an snRNA gene that has been intensively studied (for review, see Hernandez 2001;Jawdekar and Henry 2008), had surprisingly only a POLR3D peak (peak score 138), and so did RNU6 (U6-7) (peak score 16) (see below; Supplemental Table S7, rows 3, 4). This suggests that three RNU6 snRNA genes are highly transcribed in IMR90hTert cells, with a fourth one (U6-1) transcribed at a lower level and a fifth one (U6-7) transcribed at a very low level.…”

Section: Snapc2 Occupancy Marks Type 3 Pol III Genesmentioning

confidence: 99%

Defining the RNA polymerase III transcriptome: Genome-wide localization of the RNA polymerase III transcription machinery in human cells

Canella

Praz²,

Reina³

et al. 2010

Genome Res.

167

203

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Our view of the RNA polymerase III (Pol III) transcription machinery in mammalian cells arises mostly from studies of the RN5S (5S) gene, the Ad2 VAI gene, and the RNU6 (U6) gene, as paradigms for genes with type 1, 2, and 3 promoters. Recruitment of Pol III onto these genes requires prior binding of well-characterized transcription factors. Technical limitations in dealing with repeated genomic units, typically found at mammalian Pol III genes, have so far hampered genome-wide studies of the Pol III transcription machinery and transcriptome. We have localized, genome-wide, Pol III and some of its transcription factors. Our results reveal broad usage of the known Pol III transcription machinery and define a minimal Pol III transcriptome in dividing IMR90hTert fibroblasts. This transcriptome consists of some 500 actively transcribed genes including a few dozen candidate novel genes, of which we confirmed nine as Pol III transcription units by additional methods. It does not contain any of the microRNA genes previously described as transcribed by Pol III, but reveals two other microRNA genes, MIR886 (hsa-mir-886) and MIR1975 (RNY5, hY5, hsa-mir-1975), which are genuine Pol III transcription units.

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Transcriptional regulation of human small nuclear RNA genes

Cited by 79 publications

References 176 publications

Genome-wide evolutionary analysis of the noncoding RNA genes and noncoding DNA of Paramecium tetraurelia

Genome-wide evolutionary analysis of the noncoding RNA genes and noncoding DNA of Paramecium tetraurelia

Gene duplication and neofunctionalization: POLR3G and POLR3GL

Defining the RNA polymerase III transcriptome: Genome-wide localization of the RNA polymerase III transcription machinery in human cells

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