publication . Article . 2016

Whole-genome expression analysis of mammalian-wide interspersed repeat elements in human cell lines

Davide Carnevali; Anastasia Conti; Matteo Pellegrini; Giorgio Dieci;
Open Access English
  • Published: 01 Dec 2016 Journal: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes, volume 24, issue 1, pages 59-69 (issn: 1340-2838, eissn: 1756-1663, Copyright policy)
  • Publisher: Oxford University Press
Abstract
Abstract With more than 500,000 copies, mammalian-wide interspersed repeats (MIRs), a sub-group of SINEs, represent ∼2.5% of the human genome and one of the most numerous family of potential targets for the RNA polymerase (Pol) III transcription machinery. Since MIR elements ceased to amplify ∼130 myr ago, previous studies primarily focused on their genomic impact, while the issue of their expression has not been extensively addressed. We applied a dedicated bioinformatic pipeline to ENCODE RNA-Seq datasets of seven human cell lines and, for the first time, we were able to define the Pol III-driven MIR transcriptome at single-locus resolution. While the majority...
Subjects
free text keywords: Full Papers, SINE, mammalian-wide interspersed repeats, RNA polymerase III, RNA-Seq, ENCODE, Interspersed repeat, Genetics, Human cell, Expression analysis, Genome, Biology
28 references, page 1 of 2

1 Jurka J.Zietkiewicz E.Labuda D.1995, Ubiquitous mammalian-wide interspersed repeats (MIRs) are molecular fossils from the mesozoic era,Nucleic Acids Res., 23, 170–5.7870583 [OpenAIRE] [PubMed]

2 Smit A.F.Riggs A.D.1995, MIRs are classic, tRNA-derived SINEs that amplified before the mammalian radiation,Nucleic Acids Res., 23, 98–102.7870595 [OpenAIRE] [PubMed]

3 Vassetzky N.S.Kramerov D.A.2013, SINEBase: a database and tool for SINE analysis, Nucleic Acids Res., 41, D83–9.23203982 [OpenAIRE] [PubMed]

4 Batzer M.A.Deininger P.L.2002, Alu repeats and human genomic diversity,Nat. Rev. Genet., 3, 370–9.11988762 [OpenAIRE] [PubMed]

5 Terai Y.Takahashi K.Okada N.1998, SINE cousins: the 3'-end tails of the two oldest and distantly related families of SINEs are descended from the 3' ends of LINEs with the same genealogical origin,Mol. Biol. Evol., 15, 1460–71.12572609 [OpenAIRE] [PubMed]

6 Gilbert N.Labuda D.1999, CORE-SINEs: eukaryotic short interspersed retroposing elements with common sequence motifs,Proc. Natl. Acad. Sci. USA, 96, 2869–74.10077603 [OpenAIRE] [PubMed]

7 Chalei M. B.Korotkov E. V.2001, Evolution of MIR Elements Located in the Coding Regions of Human Genome, Mol Biol (Mosk), 35, 1023–31.11771126 [OpenAIRE] [PubMed]

8 Sironi M.Menozzi G.Comi G.P., 2006, Gene function and expression level influence the insertion/fixation dynamics of distinct transposon families in mammalian introns, Genome Biol., 7, R120.17181857 [OpenAIRE] [PubMed]

9 Jjingo D.Conley A. B.Wang J.Marino-Ramirez L.Lunyak V.V.Jordan I.K.2014, Mammalian-wide interspersed repeat (MIR)-derived enhancers and the regulation o f human gene expression,Mob. DNA, 5, 14.25018785 [OpenAIRE] [PubMed]

10 Schramm L.Hernandez N.2002, Recruitment of RNA polymerase III to its target promoters,Genes Dev., 16, 2593–620.12381659 [OpenAIRE] [PubMed]

11 Canella D.Praz V.Reina J.H.Cousin P.Hernandez N.2010, Defining the RNA polymerase III transcriptome: Genome-wide localization of the RNA polymerase III transcription machinery in human cells,Genome Res., 20, 710–21.20413673 [OpenAIRE] [PubMed]

12 Oler A. J.Alla R. K.Roberts D.N., 2010, Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors,Nat. Struct. Mol. Biol., 17, 620–8.20418882 [OpenAIRE] [PubMed]

13 Carriere L.Graziani S.Alibert O., 2012, Genomic binding of Pol III transcription machinery and relationship with TFIIS transcription factor distribution in mouse embryonic stem cells,Nucleic Acids Res., 40, 270–83.21911356 [OpenAIRE] [PubMed]

14 Canella D.Bernasconi D.Gilardi F., 2012, A multiplicity of factors contributes to selective RNA polymerase III occupancy of a subset of RNA polymerase III genes in mouse liver,Genome Res., 22, 666–80.22287103 [OpenAIRE] [PubMed]

15 Wang J.Vicente-Garcia C.Seruggia D., 2015, MIR retrotransposon sequences provide insulators to the human genome,Proc. Natl. Acad. Sci. USA, 112, E4428–37.26216945 [OpenAIRE] [PubMed]

28 references, page 1 of 2
Abstract
Abstract With more than 500,000 copies, mammalian-wide interspersed repeats (MIRs), a sub-group of SINEs, represent ∼2.5% of the human genome and one of the most numerous family of potential targets for the RNA polymerase (Pol) III transcription machinery. Since MIR elements ceased to amplify ∼130 myr ago, previous studies primarily focused on their genomic impact, while the issue of their expression has not been extensively addressed. We applied a dedicated bioinformatic pipeline to ENCODE RNA-Seq datasets of seven human cell lines and, for the first time, we were able to define the Pol III-driven MIR transcriptome at single-locus resolution. While the majority...
Subjects
free text keywords: Full Papers, SINE, mammalian-wide interspersed repeats, RNA polymerase III, RNA-Seq, ENCODE, Interspersed repeat, Genetics, Human cell, Expression analysis, Genome, Biology
28 references, page 1 of 2

1 Jurka J.Zietkiewicz E.Labuda D.1995, Ubiquitous mammalian-wide interspersed repeats (MIRs) are molecular fossils from the mesozoic era,Nucleic Acids Res., 23, 170–5.7870583 [OpenAIRE] [PubMed]

2 Smit A.F.Riggs A.D.1995, MIRs are classic, tRNA-derived SINEs that amplified before the mammalian radiation,Nucleic Acids Res., 23, 98–102.7870595 [OpenAIRE] [PubMed]

3 Vassetzky N.S.Kramerov D.A.2013, SINEBase: a database and tool for SINE analysis, Nucleic Acids Res., 41, D83–9.23203982 [OpenAIRE] [PubMed]

4 Batzer M.A.Deininger P.L.2002, Alu repeats and human genomic diversity,Nat. Rev. Genet., 3, 370–9.11988762 [OpenAIRE] [PubMed]

5 Terai Y.Takahashi K.Okada N.1998, SINE cousins: the 3'-end tails of the two oldest and distantly related families of SINEs are descended from the 3' ends of LINEs with the same genealogical origin,Mol. Biol. Evol., 15, 1460–71.12572609 [OpenAIRE] [PubMed]

6 Gilbert N.Labuda D.1999, CORE-SINEs: eukaryotic short interspersed retroposing elements with common sequence motifs,Proc. Natl. Acad. Sci. USA, 96, 2869–74.10077603 [OpenAIRE] [PubMed]

7 Chalei M. B.Korotkov E. V.2001, Evolution of MIR Elements Located in the Coding Regions of Human Genome, Mol Biol (Mosk), 35, 1023–31.11771126 [OpenAIRE] [PubMed]

8 Sironi M.Menozzi G.Comi G.P., 2006, Gene function and expression level influence the insertion/fixation dynamics of distinct transposon families in mammalian introns, Genome Biol., 7, R120.17181857 [OpenAIRE] [PubMed]

9 Jjingo D.Conley A. B.Wang J.Marino-Ramirez L.Lunyak V.V.Jordan I.K.2014, Mammalian-wide interspersed repeat (MIR)-derived enhancers and the regulation o f human gene expression,Mob. DNA, 5, 14.25018785 [OpenAIRE] [PubMed]

10 Schramm L.Hernandez N.2002, Recruitment of RNA polymerase III to its target promoters,Genes Dev., 16, 2593–620.12381659 [OpenAIRE] [PubMed]

11 Canella D.Praz V.Reina J.H.Cousin P.Hernandez N.2010, Defining the RNA polymerase III transcriptome: Genome-wide localization of the RNA polymerase III transcription machinery in human cells,Genome Res., 20, 710–21.20413673 [OpenAIRE] [PubMed]

12 Oler A. J.Alla R. K.Roberts D.N., 2010, Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors,Nat. Struct. Mol. Biol., 17, 620–8.20418882 [OpenAIRE] [PubMed]

13 Carriere L.Graziani S.Alibert O., 2012, Genomic binding of Pol III transcription machinery and relationship with TFIIS transcription factor distribution in mouse embryonic stem cells,Nucleic Acids Res., 40, 270–83.21911356 [OpenAIRE] [PubMed]

14 Canella D.Bernasconi D.Gilardi F., 2012, A multiplicity of factors contributes to selective RNA polymerase III occupancy of a subset of RNA polymerase III genes in mouse liver,Genome Res., 22, 666–80.22287103 [OpenAIRE] [PubMed]

15 Wang J.Vicente-Garcia C.Seruggia D., 2015, MIR retrotransposon sequences provide insulators to the human genome,Proc. Natl. Acad. Sci. USA, 112, E4428–37.26216945 [OpenAIRE] [PubMed]

28 references, page 1 of 2
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publication . Article . 2016

Whole-genome expression analysis of mammalian-wide interspersed repeat elements in human cell lines

Davide Carnevali; Anastasia Conti; Matteo Pellegrini; Giorgio Dieci;