Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
1
pubmed:dateCreated
2010-12-23
pubmed:abstractText
MOTIVATION: Many genes in the human genome produce a wide variety of transcript variants resulting from alternative exon splicing, differential promoter usage, or altered polyadenylation site utilization that may function differently in human cells. Here, we present a bioinformatics method for the systematic identification of human-specific novel transcript variants that might have arisen after the human-chimpanzee divergence. RESULTS: The procedure involved collecting genomic insertions that are unique to the human genome when compared with orthologous chimpanzee and rhesus macaque genomic regions, and that are expressed in the transcriptome as exons evidenced by mRNAs and/or expressed sequence tags (ESTs). Using this procedure, we identified 112 transcript variants that are specific to humans; 74 were associated with known genes and the remaining transcripts were located in unannotated genomic loci. The original source of inserts was mostly transposable elements including L1, Alu, SVA, and human endogenous retroviruses (HERVs). Interestingly, some non-repetitive genomic segments were also involved in the generation of novel transcript variants. Insert contributions to the transcripts included promoters, terminal exons and insertions in exons, splice donors and acceptors and complete exon cassettes. Comparison of personal genomes revealed that at least seven loci were polymorphic in humans. The exaptation of human-specific genomic inserts as novel transcript variants may have increased human gene versatility or affected gene regulation.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Jan
pubmed:issn
1367-4811
pubmed:author
pubmed:issnType
Electronic
pubmed:day
1
pubmed:volume
27
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
14-21
pubmed:meshHeading
pubmed-meshheading:21037245-Alternative Splicing, pubmed-meshheading:21037245-Animals, pubmed-meshheading:21037245-Base Sequence, pubmed-meshheading:21037245-DNA, pubmed-meshheading:21037245-DNA Transposable Elements, pubmed-meshheading:21037245-Evolution, Molecular, pubmed-meshheading:21037245-Exons, pubmed-meshheading:21037245-Expressed Sequence Tags, pubmed-meshheading:21037245-Genetic Variation, pubmed-meshheading:21037245-Genome, Human, pubmed-meshheading:21037245-Genomics, pubmed-meshheading:21037245-Humans, pubmed-meshheading:21037245-Molecular Sequence Data, pubmed-meshheading:21037245-Mutagenesis, Insertional, pubmed-meshheading:21037245-Pan troglodytes, pubmed-meshheading:21037245-Polyadenylation, pubmed-meshheading:21037245-Polymorphism, Genetic, pubmed-meshheading:21037245-Promoter Regions, Genetic, pubmed-meshheading:21037245-RNA, Messenger, pubmed-meshheading:21037245-RNA Splice Sites, pubmed-meshheading:21037245-Species Specificity, pubmed-meshheading:21037245-Transcription, Genetic
pubmed:year
2011
pubmed:articleTitle
Identification of human-specific transcript variants induced by DNA insertions in the human genome.
pubmed:affiliation
Department of Life Science (BK21 Program), Chung-Ang University, Seoul, Korea.
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't