DNA sequence and comparative analysis of chimpanzee chromosome 22

Watanabe, Hidemi; Fujiyama, Asao; Hattori, Masahira; Taylor, Todd D.; Toyoda, Atsushi; Kuroki, Yoshio; Noguchi, Hideki; Benkahla, Alia; Lehrach, Hans; Sudbrak, Ralf; Kube, Michael; Tænzer, Simone; Galgóczy, Petra; Platzer, Matthias; Scharfe, Maren; Nordsiek, Gabriele; Blöcker, Helmut; Hellmann, Ines; Khaitovich, Philipp; Pääbo, Svante; Reinhardt, Richard; Zheng, Hongkun; Zhang, X.-L.; Zhu, Genfeng; Wang, B.-F.; Fu, Gang; Ren, S.-X.; Zhao, Guoping; Chen, Z.; Lee, Y.-S.; Cheong, Jieun; Choi, Sun-Hye; Wu, Kevin; Liu, T.-T.; Hsiao, Keh-Lin; Tsai, Shih Feng; Kim, C.-G.; Oota, Satoshi; Kitano, Takashi; Kohara, Yuji; Saitou, Naruya; Park, H.-S.; Wang, S.-Y.; Yaspo, Marie Laure; Sakaki, Yoshiyuki

doi:10.1038/nature02564

Cited by 209 publications

(70 citation statements)

References 46 publications

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“…identical Alu repeats (<0.01) in human as compared to chimpanzee, consistent with previous observations Hedges et al 2004;Watanabe et al 2004; The Chimpanzee Sequencing and Analysis Consortium 2005). Similar K-plots were obtained for Alu elements derived from finished primate genomic sequences (data not shown).…”

Section: Pairwise Sequence Divergence Distributionsupporting

confidence: 80%

Comparative analysis of Alu repeats in primate genomes

Liu¹,

Alkan²,

Lu³

et al. 2009

Genome Res.

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Using bacteria artificial chromosome (BAC) end sequences (16.9 Mb) and high-quality alignments of genomic sequences (17.4 Mb), we performed a global assessment of the divergence distributions, phylogenies, and consensus sequences for Alu elements in primates including lemur, marmoset, macaque, baboon, and chimpanzee as compared to human. We found that in lemurs, Alu elements show a broader and more symmetric sequence divergence distribution, suggesting a steady rate of Alu retrotransposition activity among prosimians. In contrast, Alu elements in anthropoids show a skewed distribution shifted toward more ancient elements with continual declining rates in recent Alu activity along the hominoid lineage of evolution. Using an integrated approach combining mutation profile and insertion/deletion analyses, we identified nine novel lineage-specific Alu subfamilies in lemur (seven), marmoset (one), and baboon/macaque (one) containing multiple diagnostic mutations distinct from their human counterparts-Alu J, S, and Y subfamilies, respectively. Among these primates, we show that that the lemur has the lowest density of Alu repeats (55 repeats/Mb), while marmoset has the greatest abundance (188 repeats/Mb). We estimate that ;70% of lemur and 16% of marmoset Alu elements belong to lineage-specific subfamilies. Our analysis has provided an evolutionary framework for further classification and refinement of the Alu repeat phylogeny. The differences in the distribution and rates of Alu activity have played an important role in subtly reshaping the structure of primate genomes. The functional consequences of these changes among the diverse primate lineages over such short periods of evolutionary time are an important area of future investigation.

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Section: Pairwise Sequence Divergence Distributionsupporting

confidence: 80%

Comparative analysis of Alu repeats in primate genomes

Liu¹,

Alkan²,

Lu³

et al. 2009

Genome Res.

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“…5). Only 2 of the 231 genes recently analyzed on chimpanzee chromosome 22 have a K a /K s value greater than 2.79 (observed for the 5¢ half of AHI1); 15 of the 231 genes have a K a /K s value greater than 1.26 (for fulllength AHI1) 22 . Accelerated evolution of AHI1 in the human lineage could indicate either the action of directional selection or relaxed functional constraint.…”

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confidence: 94%

Abnormal cerebellar development and axonal decussation due to mutations in AHI1 in Joubert syndrome

et al. 2004

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“…6F) further revealed a string of nine identical nucleotides that includes the HNF-1 binding site and the overlapping sequence suggested to be a Cdx binding site (6). This same sequence is also present in the chimpanzee ortholog located in chromosome 22 (19). In the SIF3 and LTR sequences, the HNF-1/Cdx binding sequence is found in the sense orientation, whereas in both the Ϫ614 to Ϫ572 fragment and in the chimpanzee ortholog, this element is present in the antisense orientation.…”

Section: Characterization Of the Promoter-driving Expression Of Type mentioning

confidence: 90%

Comparative Analysis of Retroviral and Native Promoters Driving Expression of β1,3-Galactosyltransferase β3Gal-T5 in Human and Mouse Tissues

Mare¹,

Trinchera

2007

Journal of Biological Chemistry

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␤1,3-Galactosyltransferase ␤3Gal-T5 is highly expressed in the colons of humans and certain primates due to a retroviral long terminal repeat (LTR) acting as a strong promoter. Because this promoter is inactive in other human tissues or mice, we attempted to understand how adoption of a retrotransposon allowed the gene to acquire tissue-specific expression. We identified three novel 5 -UTRs of ␤3Gal-T5 mRNA, types A, B, and C, and found widespread expression of the type A transcript at much lower levels than the LTR transcript, the expression of which is restricted to organs of the gastrointestinal tract. Expression of the type C 5 -UTR transcript was mostly restricted to the ileum, where it was expressed at high levels. We cloned the 5 -flanking regions of both types A and B 5 -UTRs, found deletion constructs functionally active as promoters, and identified CCAAT-binding factor (CBF) and hepatocyte nuclear factor 1 (HNF-1) as the principal nuclear factors controlling the promoters of types A and B 5 -UTR transcripts, respectively. The CCAAT-binding factor binding site and the entire downstream sequence driving the expression of type A transcripts in humans are structurally and functionally conserved in mice, where they constitute a unique ␤3Gal-T5 promoter that appears to be the ancestral promoter of the gene. The HNF-1 binding motif of the second human promoter is identical to the HNF-1/Cdx binding motif of the LTR promoter but is in the antisense orientation, resulting in much lower binding affinity and promoter strength. These data may explain the successful insertion of the transposon during evolution.␤1,3-Galactosyltransferase 5 (␤3Gal-T5) 3 is a late-acting glycosyltransferase responsible for the synthesis of type 1 chain carbohydrates, including Lewis antigens, in human epithelial cells (1, 2). ␤3Gal-T5 is highly expressed in human colon mucosa, down-regulated in colon cancers (3), and large amounts of its reaction products are found in the bile and small intestine (4, 5). In some colon cancer cells, the first exon (exon 1) in the 5Ј-UTR of the ␤3Gal-T5 transcript is under the control of a promoter located ϳ150 bp upstream and regulated primarily by the transcription factors HNF-1 and Cdx (6). Interestingly, the entire exon 1, as well as the HNF-1/Cdx binding motif, belongs to a retroviral long terminal repeat (LTR) sequence that is the dominant promoter for the ␤3Gal-T5 gene in the colon but is inactive in other tissues where ␤3Gal-T5 is expressed (7).Transposable elements within eukaryotic genomes from plants (8) to mammals (9) greatly affect gene expression both at the protein (10) and regulatory sequence (11) levels. The most common transposable elements in the human genome are of retroviral origin (retroelements). Retroelements often directly donate transcriptional regulatory signals that may be either excluded from some genes or taken up by others. The former group probably includes highly conserved genes with basic functions, whereas the latter likely includes gene classes that have recently expan...

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DNA sequence and comparative analysis of chimpanzee chromosome 22

Cited by 209 publications

References 46 publications

Comparative analysis of Alu repeats in primate genomes

Comparative analysis of Alu repeats in primate genomes

Abnormal cerebellar development and axonal decussation due to mutations in AHI1 in Joubert syndrome

Comparative Analysis of Retroviral and Native Promoters Driving Expression of β1,3-Galactosyltransferase β3Gal-T5 in Human and Mouse Tissues

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