The long and the short of RNA maps

BioEssays

Volumn 29, Issue 11, 2007, Pages 1077-1080

  Ponjavic, Jasmina ^a   Ponting, Chris P ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

RNA; TRANSFER RNA;

EXON; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE MAPPING; GENETIC TRANSCRIPTION; HUMAN; MOLECULAR EVOLUTION; NONHUMAN; PROMOTER REGION; REVIEW; RNA SEQUENCE;

ANIMALS; DOSAGE COMPENSATION, GENETIC; EVOLUTION, MOLECULAR; GENE EXPRESSION; GENE SILENCING; GENOME; GENOME, HUMAN; GENOMIC IMPRINTING; HUMANS; MAMMALS; MICRORNAS; MODELS, GENETIC; PROTEIN BIOSYNTHESIS; RNA; RNA, SMALL INTERFERING; RNA, SMALL NUCLEAR; RNA, SMALL NUCLEOLAR; RNA, UNTRANSLATED; SEQUENCE ANALYSIS, RNA; TRANSCRIPTION, GENETIC;

MAMMALIA;

EID: 35848970761     PISSN: 02659247     EISSN: None     Source Type: Journal    
DOI: 10.1002/bies.20669     Document Type: Review

References (15)

1. Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, et al. 2007. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316:1484-1488.
2. Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, et al. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420:520-562.
3. Lunter G, Ponting CP, Hein J. 2006. Genome-wide identification of human functional DNA using a neutral indel model. PLoS Comput Biol 2:e5.
4. Prasanth KV, Spector DL. 2007. Eukaryotic regulatory RNAs: an answer to the 'genome complexity' conundrum. Genes Dev 21:11-42.
5. Kapranov P, Willingham AT, Gingeras TR. 2007. Genome-wide transcription and the implications for genomic organization. Nat Rev Genet 8:413-423.
6. Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, et al. 2005. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 308:1149-1154.
7. Kampa D, Cheng J, Kapranov P, Yamanaka M, Brubaker S, et al. 2004. Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res 14:331-342.
8. Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, et al. 2007. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799-816.
9. Crowe ML, Wang XQ, Rothnagel JA. 2006. Evidence for conservation and selection of upstream open reading frames suggests probable encoding of bioactive peptides. BMC Genomics 7:16.
10. Guenther MG, Levine SS, Boyer LA, Jaenisch R, Young RA. 2007. A chromatin landmark and transcription initiation at most promoters in human cells. Cell 130:77-88.
11. Gribnau J, Diderich K, Pruzina S, Calzolari R, Fraser P. 2000. Intergenic transcription and developmental remodeling of chromatin subdomains in the human beta-globin locus. Mol Cell 5:377-386.
12. Schmitt S, Para R. 2004. Gene regulation: a reason for reading nonsense. Nature 429:510-511.
13. Ponjavic J, Ponting CP, Lunter G. 2007. Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs. Genome Res 17:556-565.
14. Wang J, Zhang J, Zheng H, Li J, Liu D, et al. 2004. Mouse transcriptome: neutral evolution of 'non-coding' complementary DNAs. Nature 431:1 p following 757; discussion following 757
15. Ponting CP, Lunter G. 2006. Signatures of adaptive evolution within human non-coding sequence. Hum Mol Genet 15 Spec No 2:R170-R175.