國家衛生研究院 NHRI:Item 3990099045/1726
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    题名: Human-specific insertions and deletions inferred from mammalian genome sequences
    作者: Chen, FC;Chen, CJ;Li, WH;Chuang, TJ
    贡献者: Division of Biostatistics and Bioinformatics
    摘要: It has been suggested that insertions and deletions (indels) have contributed to the sequence divergence between the human and chimpanzee genomes more than do nucleotide changes (3% vs. 1.2%). However, although there have been studies of large indels between the two genomes, no systematic analysis of small indels (i.e., indels <= 100 bp) has been published. In this study, we first estimated that the false- positive rate of small indels inferred from human - chimpanzee pairwise sequence alignments is quite high, suggesting that the chimpanzee genome draft is not sufficiently accurate for our purpose. We have therefore inferred only human-specific indels using multiple sequence alignments of mammalian genomes. We identified > 840,000 "small" indels, which affect > 7000 UCSC-annotated human genes (> 11,000 transcripts). These indels, however, amount to only similar to 0.21% sequence change in the human lineage for the regions compared, whereas in pseudogenes indels contribute to a sequence divergence of 1.40%, suggesting that most of the indels that occurred in genic regions have been eliminated. Functional analysis reveals that the genes whose coding exons have been affected by human-specific indels are enriched in transcription and translation regulatory activities but are underrepresented in catalytic and transporter activities, cellular and physiological processes, and extracellular region/matrix. This functional bias suggests that human-specific indels might have contributed to human unique traits by causing changes at the RNA and protein level.
    关键词: Biochemistry & Molecular Biology;Biotechnology & Applied Microbiology;Genetics & Heredity
    日期: 2007-01
    關聯: Genome Research. 2007 Jan;17(1):16-22.
    Link to: http://dx.doi.org/10.1101/gr.5429606
    JIF/Ranking 2023: http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=NHRI&SrcApp=NHRI_IR&KeyISSN=1088-9051&DestApp=IC2JCR
    Cited Times(WOS): https://www.webofscience.com/wos/woscc/full-record/WOS:000243191400003
    Cited Times(Scopus): http://www.scopus.com/inward/record.url?partnerID=HzOxMe3b&scp=33846027485
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