title: Mapping of chimpanzee full-length cDNAs onto the human genome unveils large potential divergence of the transcriptome.
abstract: The genetic basis of the phenotypic difference between human and chimpanzee is one of the most actively pursued issues in current genomics. Although the genomic divergence between the two species has been described, the transcriptomic divergence has not been well documented. Thus, we newly sequenced and analyzed chimpanzee full-length cDNAs (FLcDNAs) representing 87 protein-coding genes. The number of nucleotide substitutions and sites of insertions/deletions (indels) was counted as a measure of sequence divergence between the chimpanzee FLcDNAs and the human genome onto which the FLcDNAs were mapped. Difference in transcription start/termination sites (TSSs/TTSs) and alternative splicing (AS) exons was also counted as a measure of structural divergence between the chimpanzee FLcDNAs and their orthologous human transcripts (NCBI RefSeq). As a result, we found that transposons (Alu) and repetitive segments caused large indels, which strikingly increased the average amount of sequence divergence up to more than 2% in the 3'-UTRs. Moreover, 20 out of the 87 transcripts contained more than 10% structural divergence in length. In particular, two-thirds of the structural divergence was found in the 3'-UTRs, and variable transcription start sites were conspicuous in the 5'-UTRs. As both transcriptional and translational efficiency were supposed to be related to 5'- and 3'-UTR sequences, these results lead to the idea that the difference in gene regulation can be a major cause of the difference in phenotype between human and chimpanzee.
authors.affiliation: Japan Biological Information Research Center, Japan Biological Informatics Consortium: AIST Bio-IT Research Bldg. 7F, 2-42 Aomi, Koto-ku, Tokyo, 135-0064, Japan. sakate@prigen.org
authors.forename: Ryuichi
authors.initials: R
authors.lastname: Sakate
authors.forename: Yumiko
authors.initials: Y
authors.lastname: Suto
authors.forename: Tadashi
authors.initials: T
authors.lastname: Imanishi
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Tanoue
authors.forename: Munetomo
authors.initials: M
authors.lastname: Hida
authors.forename: Ikuo
authors.initials: I
authors.lastname: Hayasaka
authors.forename: Jun
authors.initials: J
authors.lastname: Kusuda
authors.forename: Takashi
authors.initials: T
authors.lastname: Gojobori
authors.forename: Katsuyuki
authors.initials: K
authors.lastname: Hashimoto
authors.forename: Momoki
authors.initials: M
authors.lastname: Hirai
mesh_terms: D020413:3' Untranslated Regions / Q000235:genetics; D020121:5' Untranslated Regions / Q000235:genetics; D020087:Alu Elements; D000818:Animals; D002874:Chromosome Mapping; D004251:DNA Transposable Elements / Q000235:genetics; D018076:DNA, Complementary / Q000235:genetics; D014644:Genetic Variation; D015894:Genome, Human / Q000235:genetics*; D006801:Humans; D002679:Pan troglodytes / Q000235:genetics*; D014158:Transcription, Genetic
chemical_list: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D004251:DNA Transposable Elements; D018076:DNA, Complementary