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

Nakaya, Hidehiko; Amaral, Paulo; Louro, Rodrigo; Lopes, Antonio Sérgio de Santis Andrade; Fachel, Angela Aguirres; Moreira, Yuri B; El-Jundi, Tarik; Silva, da; Reis, Eduardo M.; Verjovski-Almeida, Sérgio

doi:10.1186/gb-2007-8-3-r43

Cited by 209 publications

(242 citation statements)

References 67 publications

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“…In general, it is not unusual for large introns, such as intron 2 of the PRKCB1 gene, which spans approximately 150 kb, to produce totally intronic noncoding RNAs, especially frequent among members of the Gene Ontology 'Regulation of transcription' gene category. 51 Alternatively, single base pair changes can indeed affect gene expression by creating or deleting an intronic response element, enhancer or repressor, 52 as recently demonstrated for a single base pair change causing the loss of an Sp1 response element in the MET gene promoter. 4 Regardless of the underlying mechanism, the association of PRKCB1 'risk' alleles with a blunted adaptive downregulation of gene expression seemingly fits with several converging lines of evidence.…”

Section: Discussionmentioning

confidence: 99%

Involvement of the PRKCB1 gene in autistic disorder: significant genetic association and reduced neocortical gene expression

et al. 2008

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Protein kinase C enzymes play an important role in signal transduction, regulation of gene expression and control of cell division and differentiation. The fsI and bII isoenzymes result from the alternative splicing of the PKCb gene (PRKCB1), previously found to be associated with autism. We performed a family-based association study in 229 simplex and 5 multiplex families, and a postmortem study of PRKCB1 gene expression in temporocortical gray matter (BA41/42) of 11 autistic patients and controls. PRKCB1 gene haplotypes are significantly associated with autism (P < 0.05) and have the autistic endophenotype of enhanced oligopeptiduria (P < 0.05). Temporocortical PRKCB1 gene expression was reduced on average by 35 and 31% for the PRKCB1-1 and PRKCB1-2 isoforms (P < 0.01 and < 0.05, respectively) according to qPCR. Protein amounts measured for the PKCbII isoform were similarly decreased by 35% (P = 0.05). Decreased gene expression characterized patients carrying the 'normal' PRKCB1 alleles, whereas patients homozygous for the autism-associated alleles displayed mRNA levels comparable to those of controls. Whole genome expression analysis unveiled a partial disruption in the coordinated expression of PKCb-driven genes, including several cytokines. These results confirm the association between autism and PRKCB1 gene variants, point toward PKCb roles in altered epithelial permeability, demonstrate a significant downregulation of brain PRKCB1 gene expression in autism and suggest that it could represent a compensatory adjustment aimed at limiting an ongoing dysreactive immune process. Altogether, these data underscore potential PKCb roles in autism pathogenesis and spur interest in the identification and functional characterization of PRKCB1 gene variants conferring autism vulnerability.

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Section: Discussionmentioning

confidence: 99%

Involvement of the PRKCB1 gene in autistic disorder: significant genetic association and reduced neocortical gene expression

et al. 2008

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“…59,60 Recently, pancreatic ductal adenocarcinoma (PDAC) was studied to identify the gene expression profiles of lncRNAs correlated with pancreatic cancer and metastasis. [61][62][63] A subset of intronic lncRNAs (PPP3CB, MAP3K14, and DAPK1 loci) expressed in pancreatic tissues was identified; the abundance of these lncRNAs was correlated with PDAC metastasis and were enriched in genes associated with the MAPK pathway. 64,65 Nevertheless, further studies will be necessary to reveal the possible biological functions and molecular mechanisms of these lncRNAs in PDAC tumorigenesis and/or progression, and these intronic lncRNAs might be novel candidate biomarkers of pancreatic tumors.…”

Section: Malat1 H19 and Ccat2-wnt/b-catenin Pathwaymentioning

confidence: 99%

Long non-coding RNAs in cancer invasion and metastasis

Shen

Pan

2015

Modern Pathology

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Recent large-scale transcriptome analyses have revealed that the human genome contains more than just protein-coding genes. Indeed, a large number of transcripts, including long non-coding RNAs (lncRNAs), lack protein-coding capacity, and increasing evidence suggests that lncRNAs could have a critical role in the regulation of diverse cellular processes, such as stem cell pluripotency, development, cell growth and apoptosis, and cancer invasion and/or metastasis. Furthermore, the aberrant expression of several lncRNAs is closely linked to cancer invasion and/or metastasis. Although the underlying molecular mechanisms by which lncRNAs regulate cancer invasion and/or metastasis are not clearly understood, recent studies have revealed that aberrant lncRNAs expression affects the progression of cancer. In this review, we highlight recent findings regarding the roles of lncRNAs in cancer invasion and/or metastasis.

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“…Tens of thousands of totally and partially intronic transcripts (TINs and PINs) have been reported in the human and mouse transcriptomes [5,6,7], many of which are unspliced. A large fraction of these comprises unspliced long anti-sense intronic RNAs [8,9].…”

Section: Introductionmentioning

confidence: 99%

Hidden treasures in unspliced EST data

Engelhardt

Stadler

2012

Theory Biosci.

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Abstract. Several classes of exclusively -or at least predominantly -unspliced non-coding RNAs have been described in the last years, including totally and partially intronic transcripts and long intergenic RNAs. Functionally, they appear to be involved in regulating gene expression, at least in part by associating with the chromatin. Here we systematically analyze the distribution of unspliced ESTs in the human genome. Most appear in clusters overlapping or in the close vicinity of annotated RefSeq genes. Partially Intronic (PIN) unspliced ESTs show complex patterns of overlap with the intron/exon structure of the RefSeq gene. Distinctive patterns of CAGE tags indicate that a large class of unspliced EST clusters forms long extensions of 3'UTRs, at least several hundreds of which probably appear also as independent uaRNAs.

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

Abstract: An analysis of the expression of 7,135 human totally intronic noncoding RNA transcripts plus the corresponding protein-coding genes using oligonucleotide arrays has identified diverse intronic RNA expression patterns, pointing to distinct regulatory roles.

Cited by 209 publications

References 67 publications

Involvement of the PRKCB1 gene in autistic disorder: significant genetic association and reduced neocortical gene expression

Involvement of the PRKCB1 gene in autistic disorder: significant genetic association and reduced neocortical gene expression

Long non-coding RNAs in cancer invasion and metastasis

Hidden treasures in unspliced EST data

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