Literature DB >> 21916613

Genomic relationship between SINE retrotransposons, Pol III-Pol II transcription, and chromatin organization: the journey from junk to jewel.

Victoria V Lunyak1, Michelle Atallah.   

Abstract

A typical eukaryotic genome harbors a rich variety of repetitive elements. The most abundant are retrotransposons, mobile retroelements that utilize reverse transcriptase and an RNA intermediate to relocate to a new location within the cellular genomes. A vast majority of the repetitive mammalian genome content has originated from the retrotransposition of SINE (100-300 bp short interspersed nuclear elements that are derived from the structural 7SL RNA or tRNA), LINE (7kb long interspersed nuclear element), and LTR (2-3 kb long terminal repeats) transposable element superfamilies. Broadly labeled as "evolutionary junkyard" or "fossils", this enigmatic "dark matter" of the genome possesses many yet to be discovered properties.

Entities:  

Mesh：

Substances：

Year:  2011        PMID： 21916613      PMCID： PMC3660135          DOI： 10.1139/o11-046

Source DB:  PubMed          Journal:  Biochem Cell Biol        ISSN： 0829-8211            Impact factor:   3.626


  98 in total

1.  SINE retroposons can be used in vivo as nucleation centers for de novo methylation.

Authors:  P Arnaud; C Goubely; T Pélissier; J M Deragon
Journal:  Mol Cell Biol       Date:  2000-05       Impact factor: 4.272

Review 2.  Survey and summary: transcription by RNA polymerases I and III.

Authors:  M R Paule; R J White
Journal:  Nucleic Acids Res       Date:  2000-03-15       Impact factor: 16.971

3.  Initial sequencing and analysis of the human genome.

Authors:  E S Lander; L M Linton; B Birren; C Nusbaum; M C Zody; J Baldwin; K Devon; K Dewar; M Doyle; W FitzHugh; R Funke; D Gage; K Harris; A Heaford; J Howland; L Kann; J Lehoczky; R LeVine; P McEwan; K McKernan; J Meldrim; J P Mesirov; C Miranda; W Morris; J Naylor; C Raymond; M Rosetti; R Santos; A Sheridan; C Sougnez; Y Stange-Thomann; N Stojanovic; A Subramanian; D Wyman; J Rogers; J Sulston; R Ainscough; S Beck; D Bentley; J Burton; C Clee; N Carter; A Coulson; R Deadman; P Deloukas; A Dunham; I Dunham; R Durbin; L French; D Grafham; S Gregory; T Hubbard; S Humphray; A Hunt; M Jones; C Lloyd; A McMurray; L Matthews; S Mercer; S Milne; J C Mullikin; A Mungall; R Plumb; M Ross; R Shownkeen; S Sims; R H Waterston; R K Wilson; L W Hillier; J D McPherson; M A Marra; E R Mardis; L A Fulton; A T Chinwalla; K H Pepin; W R Gish; S L Chissoe; M C Wendl; K D Delehaunty; T L Miner; A Delehaunty; J B Kramer; L L Cook; R S Fulton; D L Johnson; P J Minx; S W Clifton; T Hawkins; E Branscomb; P Predki; P Richardson; S Wenning; T Slezak; N Doggett; J F Cheng; A Olsen; S Lucas; C Elkin; E Uberbacher; M Frazier; R A Gibbs; D M Muzny; S E Scherer; J B Bouck; E J Sodergren; K C Worley; C M Rives; J H Gorrell; M L Metzker; S L Naylor; R S Kucherlapati; D L Nelson; G M Weinstock; Y Sakaki; A Fujiyama; M Hattori; T Yada; A Toyoda; T Itoh; C Kawagoe; H Watanabe; Y Totoki; T Taylor; J Weissenbach; R Heilig; W Saurin; F Artiguenave; P Brottier; T Bruls; E Pelletier; C Robert; P Wincker; D R Smith; L Doucette-Stamm; M Rubenfield; K Weinstock; H M Lee; J Dubois; A Rosenthal; M Platzer; G Nyakatura; S Taudien; A Rump; H Yang; J Yu; J Wang; G Huang; J Gu; L Hood; L Rowen; A Madan; S Qin; R W Davis; N A Federspiel; A P Abola; M J Proctor; R M Myers; J Schmutz; M Dickson; J Grimwood; D R Cox; M V Olson; R Kaul; C Raymond; N Shimizu; K Kawasaki; S Minoshima; G A Evans; M Athanasiou; R Schultz; B A Roe; F Chen; H Pan; J Ramser; H Lehrach; R Reinhardt; W R McCombie; M de la Bastide; N Dedhia; H Blöcker; K Hornischer; G Nordsiek; R Agarwala; L Aravind; J A Bailey; A Bateman; S Batzoglou; E Birney; P Bork; D G Brown; C B Burge; L Cerutti; H C Chen; D Church; M Clamp; R R Copley; T Doerks; S R Eddy; E E Eichler; T S Furey; J Galagan; J G Gilbert; C Harmon; Y Hayashizaki; D Haussler; H Hermjakob; K Hokamp; W Jang; L S Johnson; T A Jones; S Kasif; A Kaspryzk; S Kennedy; W J Kent; P Kitts; E V Koonin; I Korf; D Kulp; D Lancet; T M Lowe; A McLysaght; T Mikkelsen; J V Moran; N Mulder; V J Pollara; C P Ponting; G Schuler; J Schultz; G Slater; A F Smit; E Stupka; J Szustakowki; D Thierry-Mieg; J Thierry-Mieg; L Wagner; J Wallis; R Wheeler; A Williams; Y I Wolf; K H Wolfe; S P Yang; R F Yeh; F Collins; M S Guyer; J Peterson; A Felsenfeld; K A Wetterstrand; A Patrinos; M J Morgan; P de Jong; J J Catanese; K Osoegawa; H Shizuya; S Choi; Y J Chen; J Szustakowki
Journal:  Nature       Date:  2001-02-15       Impact factor: 49.962

Review 4.  The RNA polymerase III transcription apparatus.

Authors:  E P Geiduschek; G A Kassavetis
Journal:  J Mol Biol       Date:  2001-06-29       Impact factor: 5.469

Review 5.  Condensin and cohesin complexity: the expanding repertoire of functions.

Authors:  Andrew J Wood; Aaron F Severson; Barbara J Meyer
Journal:  Nat Rev Genet       Date:  2010-05-05       Impact factor: 53.242

6.  Transposable B2 SINE elements can provide mobile RNA polymerase II promoters.

Authors:  O Ferrigno; T Virolle; Z Djabari; J P Ortonne; R J White; D Aberdam
Journal:  Nat Genet       Date:  2001-05       Impact factor: 38.330

Review 7.  Comparison of the RNA polymerase III transcription machinery in Schizosaccharomyces pombe, Saccharomyces cerevisiae and human.

Authors:  Y Huang; R J Maraia
Journal:  Nucleic Acids Res       Date:  2001-07-01       Impact factor: 16.971

Review 8.  Insulators and promoters: closer than we think.

Authors:  Jesse R Raab; Rohinton T Kamakaka
Journal:  Nat Rev Genet       Date:  2010-05-05       Impact factor: 53.242

9.  The transcription factor-like nuclear regulator (TFNR) contains a novel 55-amino-acid motif repeated nine times and maps closely to SMN1.

Authors:  A R Kelter; J Herchenbach; B Wirth
Journal:  Genomics       Date:  2000-12-15       Impact factor: 5.736

10.  Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells.

Authors:  Zarmik Moqtaderi; Jie Wang; Debasish Raha; Robert J White; Michael Snyder; Zhiping Weng; Kevin Struhl
Journal:  Nat Struct Mol Biol       Date:  2010-04-25       Impact factor: 15.369
View more
  9 in total

Review 1.  Epigenetics components of aging in the central nervous system.

Authors:  Yue-Qiang Zhao; I King Jordan; Victoria V Lunyak
Journal:  Neurotherapeutics       Date:  2013-10       Impact factor: 7.620

2.  Linkage disequilibrium and functional analysis of PRE1 insertion together with SNPs in the promoter region of IGFBP7 gene in different pig breeds.

Authors:  Qingyan Wu; Hao Yu; Wenzhen Wei; Yunyun Cheng; Shan Huang; Hongyu Shi; Songcai Liu; Jichao Xia; Hongyao Jia; Linlin Hao
Journal:  J Appl Genet       Date:  2018-03-25       Impact factor: 3.240

Review 3.  Chromatin insulators: linking genome organization to cellular function.

Authors:  Jennifer E Phillips-Cremins; Victor G Corces
Journal:  Mol Cell       Date:  2013-05-23       Impact factor: 17.970

Review 4.  TFIIIC bound DNA elements in nuclear organization and insulation.

Authors:  Jacob G Kirkland; Jesse R Raab; Rohinton T Kamakaka
Journal:  Biochim Biophys Acta       Date:  2012-09-21

5.  RNAs nonspecifically inhibit RNA polymerase II by preventing binding to the DNA template.

Authors:  Dave A Pai; Craig D Kaplan; Hye Kyong Kweon; Kenji Murakami; Philip C Andrews; David R Engelke
Journal:  RNA       Date:  2014-03-10       Impact factor: 4.942

6.  Identification of a recently active mammalian SINE derived from ribosomal RNA.

Authors:  Mark S Longo; Judy D Brown; Chu Zhang; Michael J O'Neill; Rachel J O'Neill
Journal:  Genome Biol Evol       Date:  2015-01-29       Impact factor: 3.416

7.  Growth signals employ CGGBP1 to suppress transcription of Alu-SINEs.

Authors:  Prasoon Agarwal; Stefan Enroth; Martin Teichmann; Helena Jernberg Wiklund; Arian Smit; Bengt Westermark; Umashankar Singh
Journal:  Cell Cycle       Date:  2016-06-17       Impact factor: 4.534

8.  Plant Regulomics Portal (PRP): a comprehensive integrated regulatory information and analysis portal for plant genomes.

Authors:  Ganesh Panzade; Indu Gangwar; Supriya Awasthi; Nitesh Sharma; Ravi Shankar
Journal:  Database (Oxford)       Date:  2019-01-01       Impact factor: 3.451

9.  The 3D folding of metazoan genomes correlates with the association of similar repetitive elements.

Authors:  Axel Cournac; Romain Koszul; Julien Mozziconacci
Journal:  Nucleic Acids Res       Date:  2015-11-24       Impact factor: 16.971
  9 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.