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Literature DB >> 19429783

The function of non-coding RNAs in genomic imprinting.

Martha V Koerner¹, Florian M Pauler, Ru Huang, Denise P Barlow.

Abstract

Non-coding RNAs (ncRNAs) that regulate gene expression in cis or in trans are a shared feature of prokaryotic and eukaryotic genomes. In mammals, cis-acting functions are associated with macro ncRNAs, which can be several hundred thousand nucleotides long. Imprinted ncRNAs are well-studied macro ncRNAs that have cis-regulatory effects on multiple flanking genes. Recent advances indicate that they employ different downstream mechanisms to regulate gene expression in embryonic and placental tissues. A better understanding of these downstream mechanisms will help to improve our general understanding of the function of ncRNAs throughout the genome.

Entities: Chemical Disease Gene Mutation Species

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Year: 2009 PMID： 19429783 PMCID： PMC2847617 DOI： 10.1242/dev.030403

Source DB: PubMed Journal: Development ISSN： 0950-1991 Impact factor: 6.868

116 in total

1. Identification of tandemly-repeated C/D snoRNA genes at the imprinted human 14q32 domain reminiscent of those at the Prader-Willi/Angelman syndrome region.

Authors: Jérôme Cavaillé; Hervé Seitz; Martina Paulsen; Anne C Ferguson-Smith; Jean-Pierre Bachellerie
Journal: Hum Mol Genet Date: 2002-06-15 Impact factor: 6.150

2. Simian virus 40 late transcripts lacking excisable intervening sequences are defective in both stability in the nucleus and transport to the cytoplasm.

Authors: W S Ryu; J E Mertz
Journal: J Virol Date: 1989-10 Impact factor: 5.103

3. RNAi-mediated allelic trans-interaction at the imprinted Rtl1/Peg11 locus.

Authors: Erica Davis; Florian Caiment; Xavier Tordoir; Jérôme Cavaillé; Anne Ferguson-Smith; Noelle Cockett; Michel Georges; Carole Charlier
Journal: Curr Biol Date: 2005-04-26 Impact factor: 10.834

4. Novel imprinted transcripts from the Dlk1-Gtl2 intergenic region, Mico1 and Mico1os, show circadian oscillations.

Authors: Stéphane Labialle; Sylvie Croteau; Valérie Bélanger; Erin N McMurray; Xuan Ruan; Sanny Moussette; Maud Jonnaert; Jennifer V Schmidt; Nicolas Cermakian; Anna K Naumova
Journal: Epigenetics Date: 2008-11 Impact factor: 4.528

5. Multiple imprinted sense and antisense transcripts, differential methylation and tandem repeats in a putative imprinting control region upstream of mouse Igf2.

Authors: T Moore; M Constancia; M Zubair; B Bailleul; R Feil; H Sasaki; W Reik
Journal: Proc Natl Acad Sci U S A Date: 1997-11-11 Impact factor: 11.205

6. Promoter-driven splicing regulation in fission yeast.

Authors: Alberto Moldón; Jordi Malapeira; Natalia Gabrielli; Madelaine Gogol; Blanca Gómez-Escoda; Tsvetomira Ivanova; Chris Seidel; José Ayté
Journal: Nature Date: 2008-09-24 Impact factor: 49.962

7. Imprinted expression and methylation of the mouse H19 gene are conserved in extraembryonic lineages.

Authors: T L Davis; K D Tremblay; M S Bartolomei
Journal: Dev Genet Date: 1998

8. A mammalian microRNA expression atlas based on small RNA library sequencing.

Authors: Pablo Landgraf; Mirabela Rusu; Robert Sheridan; Alain Sewer; Nicola Iovino; Alexei Aravin; Sébastien Pfeffer; Amanda Rice; Alice O Kamphorst; Markus Landthaler; Carolina Lin; Nicholas D Socci; Leandro Hermida; Valerio Fulci; Sabina Chiaretti; Robin Foà; Julia Schliwka; Uta Fuchs; Astrid Novosel; Roman-Ulrich Müller; Bernhard Schermer; Ute Bissels; Jason Inman; Quang Phan; Minchen Chien; David B Weir; Ruchi Choksi; Gabriella De Vita; Daniela Frezzetti; Hans-Ingo Trompeter; Veit Hornung; Grace Teng; Gunther Hartmann; Miklos Palkovits; Roberto Di Lauro; Peter Wernet; Giuseppe Macino; Charles E Rogler; James W Nagle; Jingyue Ju; F Nina Papavasiliou; Thomas Benzing; Peter Lichter; Wayne Tam; Michael J Brownstein; Andreas Bosio; Arndt Borkhardt; James J Russo; Chris Sander; Mihaela Zavolan; Thomas Tuschl
Journal: Cell Date: 2007-06-29 Impact factor: 41.582

9. The transcriptional landscape of the mammalian genome.

Authors: P Carninci; T Kasukawa; S Katayama; J Gough; M C Frith; N Maeda; R Oyama; T Ravasi; B Lenhard; C Wells; R Kodzius; K Shimokawa; V B Bajic; S E Brenner; S Batalov; A R R Forrest; M Zavolan; M J Davis; L G Wilming; V Aidinis; J E Allen; A Ambesi-Impiombato; R Apweiler; R N Aturaliya; T L Bailey; M Bansal; L Baxter; K W Beisel; T Bersano; H Bono; A M Chalk; K P Chiu; V Choudhary; A Christoffels; D R Clutterbuck; M L Crowe; E Dalla; B P Dalrymple; B de Bono; G Della Gatta; D di Bernardo; T Down; P Engstrom; M Fagiolini; G Faulkner; C F Fletcher; T Fukushima; M Furuno; S Futaki; M Gariboldi; P Georgii-Hemming; T R Gingeras; T Gojobori; R E Green; S Gustincich; M Harbers; Y Hayashi; T K Hensch; N Hirokawa; D Hill; L Huminiecki; M Iacono; K Ikeo; A Iwama; T Ishikawa; M Jakt; A Kanapin; M Katoh; Y Kawasawa; J Kelso; H Kitamura; H Kitano; G Kollias; S P T Krishnan; A Kruger; S K Kummerfeld; I V Kurochkin; L F Lareau; D Lazarevic; L Lipovich; J Liu; S Liuni; S McWilliam; M Madan Babu; M Madera; L Marchionni; H Matsuda; S Matsuzawa; H Miki; F Mignone; S Miyake; K Morris; S Mottagui-Tabar; N Mulder; N Nakano; H Nakauchi; P Ng; R Nilsson; S Nishiguchi; S Nishikawa; F Nori; O Ohara; Y Okazaki; V Orlando; K C Pang; W J Pavan; G Pavesi; G Pesole; N Petrovsky; S Piazza; J Reed; J F Reid; B Z Ring; M Ringwald; B Rost; Y Ruan; S L Salzberg; A Sandelin; C Schneider; C Schönbach; K Sekiguchi; C A M Semple; S Seno; L Sessa; Y Sheng; Y Shibata; H Shimada; K Shimada; D Silva; B Sinclair; S Sperling; E Stupka; K Sugiura; R Sultana; Y Takenaka; K Taki; K Tammoja; S L Tan; S Tang; M S Taylor; J Tegner; S A Teichmann; H R Ueda; E van Nimwegen; R Verardo; C L Wei; K Yagi; H Yamanishi; E Zabarovsky; S Zhu; A Zimmer; W Hide; C Bult; S M Grimmond; R D Teasdale; E T Liu; V Brusic; J Quackenbush; C Wahlestedt; J S Mattick; D A Hume; C Kai; D Sasaki; Y Tomaru; S Fukuda; M Kanamori-Katayama; M Suzuki; J Aoki; T Arakawa; J Iida; K Imamura; M Itoh; T Kato; H Kawaji; N Kawagashira; T Kawashima; M Kojima; S Kondo; H Konno; K Nakano; N Ninomiya; T Nishio; M Okada; C Plessy; K Shibata; T Shiraki; S Suzuki; M Tagami; K Waki; A Watahiki; Y Okamura-Oho; H Suzuki; J Kawai; Y Hayashizaki
Journal: Science Date: 2005-09-02 Impact factor: 47.728

10. Epigenetic dynamics of the Kcnq1 imprinted domain in the early embryo.

Authors: Annabelle Lewis; Kelly Green; Claire Dawson; Lisa Redrup; Khanh D Huynh; Jeannie T Lee; Myriam Hemberger; Wolf Reik
Journal: Development Date: 2006-10-04 Impact factor: 6.868

101 in total

1. Zinc finger protein ZFP57 requires its co-factor to recruit DNA methyltransferases and maintains DNA methylation imprint in embryonic stem cells via its transcriptional repression domain.

Authors: Xiaopan Zuo; Jipo Sheng; Ho-Tak Lau; Carol M McDonald; Monica Andrade; Dana E Cullen; Fong T Bell; Michelina Iacovino; Michael Kyba; Guoliang Xu; Xiajun Li
Journal: J Biol Chem Date: 2011-12-05 Impact factor: 5.157

The function of non-coding RNAs in genomic imprinting.

1. Identification of tandemly-repeated C/D snoRNA genes at the imprinted human 14q32 domain reminiscent of those at the Prader-Willi/Angelman syndrome region.

2. Simian virus 40 late transcripts lacking excisable intervening sequences are defective in both stability in the nucleus and transport to the cytoplasm.

3. RNAi-mediated allelic trans-interaction at the imprinted Rtl1/Peg11 locus.

4. Novel imprinted transcripts from the Dlk1-Gtl2 intergenic region, Mico1 and Mico1os, show circadian oscillations.

5. Multiple imprinted sense and antisense transcripts, differential methylation and tandem repeats in a putative imprinting control region upstream of mouse Igf2.

6. Promoter-driven splicing regulation in fission yeast.

7. Imprinted expression and methylation of the mouse H19 gene are conserved in extraembryonic lineages.

8. A mammalian microRNA expression atlas based on small RNA library sequencing.

9. The transcriptional landscape of the mammalian genome.

10. Epigenetic dynamics of the Kcnq1 imprinted domain in the early embryo.

1. Zinc finger protein ZFP57 requires its co-factor to recruit DNA methyltransferases and maintains DNA methylation imprint in embryonic stem cells via its transcriptional repression domain.

2. Genomic landscape of human allele-specific DNA methylation.

3. Tissue-specific variation of Ube3a protein expression in rodents and in a mouse model of Angelman syndrome.

Review 4. Noncoding RNAs and enhancers: complications of a long-distance relationship.

Review 5. Imprinted and X-linked non-coding RNAs as potential regulators of human placental function.

Review 6. Maintenance of epigenetic information: a noncoding RNA perspective.

7. Genomic imprinting: employing and avoiding epigenetic processes.

8. A transcription switch toggled by noncoding RNAs.

9. Clustered transcripts that escape X inactivation at mouse XqD.

10. APeg3: regulation of Peg3 through an evolutionarily conserved ncRNA.