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PMID: 17386095 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription.

Genome biology ·Vol. 8 ·No. 3 ·2007-00-00 ·Pages R43

Nakaya HI, Amaral PP, Louro R, Lopes A, Fachel AA, Moreira YB, El-Jundi TA, da Silva AM, Reis EM, Verjovski-Almeida S

Abstract

RNAs transcribed from intronic regions of genes are involved in a number of processes related to post-transcriptional control of gene expression. However, the complement of human genes in which introns are transcribed, and the number of intronic transcriptional units and their tissue expression patterns are not known. A survey of mRNA and EST public databases revealed more than 55,000 totally intronic noncoding (TIN) RNAs transcribed from the introns of 74% of all unique RefSeq genes. Guided by this information, we designed an oligoarray platform containing sense and antisense probes for each of 7,135 randomly selected TIN transcripts plus the corresponding protein-coding genes. We identified exonic and intronic tissue-specific expression signatures for human liver, prostate and kidney. The most highly expressed antisense TIN RNAs were transcribed from introns of protein-coding genes significantly enriched (p = 0.002 to 0.022) in the 'Regulation of transcription' Gene Ontology category. RNA polymerase II inhibition resulted in increased expression of a fraction of intronic RNAs in cell cultures, suggesting that other RNA polymerases may be involved in their biosynthesis. Members of a subset of intronic and protein-coding signatures transcribed from the same genomic loci have correlated expression patterns, suggesting that intronic RNAs regulate the abundance or the pattern of exon usage in protein-coding messages. We have identified diverse intronic RNA expression patterns, pointing to distinct regulatory roles. This gene-oriented approach, using a combined intron-exon oligoarray, should permit further comparative analysis of intronic transcription under various physiological and pathological conditions, thus advancing current knowledge about the biological functions of these noncoding RNAs.

MeSH Terms
Gene Expression Regulation/genetics Genes Genome, Human Genomics/methods Humans Introns RNA, Untranslated Tissue Distribution Transcription, Genetic
Chemicals
RNA, Untranslated
Authors & Affiliations
10 authors, click to expand affiliations / ORCID
Nakaya Helder I
Departamento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, São Paulo, SP, Brazil. [email protected]
Amaral Paulo P
Louro Rodrigo
Lopes André
Fachel Angela A
Moreira Yuri B
El-Jundi Tarik A
da Silva Aline M
Reis Eduardo M
Verjovski-Almeida Sergio
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Article Info
Journal
Genome biology
Abbr.
Genome Biol
ISSN
1474-760X
DOI
10.1186/gb-2007-8-3-r43
Email
[email protected]
Published
2007-00-00
Pages
R43
Language
English
Region
England
NLM ID
100960660
PMCID
PMC1868932
Subset
IM
Databases
GEO
GSE5452, GSE5453
External Links
PubMed source DOI: 10.1186/gb-2007-8-3-r43 PMC Full Text View journal details
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