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Literature DB >> 19920851

The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs.

Abstract

Over the past few years, techniques have been developed that have allowed the study of transcriptomes without bias from previous genome annotations, which has led to the discovery of a plethora of unexpected RNAs that have no obvious coding capacities. There are many different kinds of products that are generated by this pervasive transcription; this Review focuses on small non-coding RNAs (ncRNAs) that have been found to be associated with promoters in eukaryotes from animals to yeast. After comparing the different classes of such ncRNAs described in various studies, the Review discusses how the models proposed for their origins and their possible functions challenge previous views of the basic transcription process and its regulation.

Entities: Species

Mesh：

Substances：
RNA, Untranslated

Year: 2009 PMID： 19920851 DOI： 10.1038/nrg2683

Source DB: PubMed Journal: Nat Rev Genet ISSN： 1471-0056 Impact factor: 53.242

78 in total

1. Transcription termination and nuclear degradation of cryptic unstable transcripts: a role for the nrd1-nab3 pathway in genome surveillance.

Authors: Marilyne Thiebaut; Elena Kisseleva-Romanova; Mathieu Rougemaille; Jocelyne Boulay; Domenico Libri
Journal: Mol Cell Date: 2006-09-15 Impact factor: 17.970

2. The cotranscriptional assembly of snoRNPs controls the biosynthesis of H/ACA snoRNAs in Saccharomyces cerevisiae.

Authors: Monica Ballarino; Mariangela Morlando; Francesca Pagano; Alessandro Fatica; Irene Bozzoni
Journal: Mol Cell Biol Date: 2005-07 Impact factor: 4.272

Review 3. Genome-wide transcription and the implications for genomic organization.

Authors: Philipp Kapranov; Aarron T Willingham; Thomas R Gingeras
Journal: Nat Rev Genet Date: 2007-05-08 Impact factor: 53.242

Review 4. Poised RNA polymerase II gives pause for thought.

Authors: Thanasis Margaritis; Frank C P Holstege
Journal: Cell Date: 2008-05-16 Impact factor: 41.582

5. A high-resolution atlas of nucleosome occupancy in yeast.

Authors: William Lee; Desiree Tillo; Nicolas Bray; Randall H Morse; Ronald W Davis; Timothy R Hughes; Corey Nislow
Journal: Nat Genet Date: 2007-09-16 Impact factor: 38.330

6. Novel low abundance and transient RNAs in yeast revealed by tiling microarrays and ultra high-throughput sequencing are not conserved across closely related yeast species.

Authors: Albert Lee; Kasper Daniel Hansen; James Bullard; Sandrine Dudoit; Gavin Sherlock
Journal: PLoS Genet Date: 2008-12-19 Impact factor: 5.917

Review 7. Beyond expression profiling: next generation uses of high density oligonucleotide arrays.

Authors: Philipp Kapranov; Victor I Sementchenko; Thomas R Gingeras
Journal: Brief Funct Genomic Proteomic Date: 2003-04

Review 8. RNA-Seq: a revolutionary tool for transcriptomics.

Authors: Zhong Wang; Mark Gerstein; Michael Snyder
Journal: Nat Rev Genet Date: 2009-01 Impact factor: 53.242

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. The Nrd1-Nab3-Sen1 termination complex interacts with the Ser5-phosphorylated RNA polymerase II C-terminal domain.

Authors: Lidia Vasiljeva; Minkyu Kim; Hannes Mutschler; Stephen Buratowski; Anton Meinhart
Journal: Nat Struct Mol Biol Date: 2008-07-27 Impact factor: 15.369

215 in total

1. Premature terminator analysis sheds light on a hidden world of bacterial transcriptional attenuation.

Authors: Magali Naville; Daniel Gautheret
Journal: Genome Biol Date: 2010-09-29 Impact factor: 13.583

2. The yeast RPL9B gene is regulated by modulation between two modes of transcription termination.

Authors: Rajani Kanth Gudipati; Helen Neil; Frank Feuerbach; Christophe Malabat; Alain Jacquier
Journal: EMBO J Date: 2012-04-13 Impact factor: 11.598

Review 3. Metazoan promoters: emerging characteristics and insights into transcriptional regulation.

Authors: Boris Lenhard; Albin Sandelin; Piero Carninci
Journal: Nat Rev Genet Date: 2012-03-06 Impact factor: 53.242

4. "Hypothesis for the modern RNA world": a pervasive non-coding RNA-based genetic regulation is a prerequisite for the emergence of multicellular complexity.

Authors: Irma Lozada-Chávez; Peter F Stadler; Sonja J Prohaska
Journal: Orig Life Evol Biosph Date: 2012-02-10 Impact factor: 1.950

5. RNAspace.org: An integrated environment for the prediction, annotation, and analysis of ncRNA.

Authors: Marie-Josée Cros; Antoine de Monte; Jérôme Mariette; Philippe Bardou; Benjamin Grenier-Boley; Daniel Gautheret; Hélène Touzet; Christine Gaspin
Journal: RNA Date: 2011-09-23 Impact factor: 4.942

6. Small RNAs: A novel class.

Authors: Meera Swami
Journal: Nat Rev Genet Date: 2010-09 Impact factor: 53.242

7. Transcriptomics: Throwing light on dark matter.

Authors: Louisa Flintoft
Journal: Nat Rev Genet Date: 2010-07 Impact factor: 53.242

Review 8. Next-generation sequencing techniques for eukaryotic microorganisms: sequencing-based solutions to biological problems.

Authors: Minou Nowrousian
Journal: Eukaryot Cell Date: 2010-07-02

Review 9. RNAs: regulators of bacterial virulence.

Authors: Jonas Gripenland; Sakura Netterling; Edmund Loh; Teresa Tiensuu; Alejandro Toledo-Arana; Jörgen Johansson
Journal: Nat Rev Microbiol Date: 2010-12 Impact factor: 60.633

10. In vivo SELEX reveals novel sequence and structural determinants of Nrd1-Nab3-Sen1-dependent transcription termination.

Authors: Odil Porrua; Fruzsina Hobor; Jocelyne Boulay; Karel Kubicek; Yves D'Aubenton-Carafa; Rajani Kanth Gudipati; Richard Stefl; Domenico Libri
Journal: EMBO J Date: 2012-08-28 Impact factor: 11.598