Human Chromosome 19 and Related Regions in Mouse: Conservative and Lineage-Specific Evolution-Reference-Cited by-同舟云学术

Human Chromosome 19 and Related Regions in Mouse: Conservative and Lineage-Specific Evolution

Published:2001-07-06 Issue:5527 Volume:293 Page:104-111
ISSN:0036-8075
Container-title:Science
language:en
Short-container-title:Science

Author:

Dehal Paramvir¹²³,Predki Paul¹²,Olsen Anne S.¹²,Kobayashi Art¹²,Folta Peg¹²,Lucas Susan¹²,Land Miriam¹⁴,Terry Astrid¹²,Ecale Zhou Carol L.¹²,Rash Sam¹²,Zhang Qing¹²,Gordon Laurie¹²,Kim Joomyeong¹²,Elkin Christopher¹⁵,Pollard Martin J.¹⁶,Richardson Paul¹²,Rokhsar Dan¹⁷,Uberbacher Ed¹⁴,Hawkins Trevor¹²,Branscomb Elbert¹²,Stubbs Lisa¹²

Affiliation:

1. DOE Joint Genome Institute, Walnut Creek, CA 94598, USA.

2. Genomics and

3. Department of Genetics, University of California Davis, Davis, CA 95616, USA.

4. Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.

5. Engineering Divisions, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA.

6. Engineering Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

7. Physics Department, University of California Berkeley, Berkeley, CA 94720, USA.

Abstract

To illuminate the function and evolutionary history of both genomes, we sequenced mouse DNA related to human chromosome 19. Comparative sequence alignments yielded confirmatory evidence for hypothetical genes and identified exons, regulatory elements, and candidate genes that were missed by other predictive methods. Chromosome-wide comparisons revealed a difference between single-copy HSA19 genes, which are overwhelmingly conserved in mouse, and genes residing in tandem familial clusters, which differ extensively in number, coding capacity, and organization between the two species. Finally, we sequenced breakpoints of all 15 evolutionary rearrangements, providing a view of the forces that drive chromosome evolution in mammals.

Publisher

American Association for the Advancement of Science (AAAS)

Subject

Multidisciplinary

Reference48 articles.

1. The Sequence of the Human Genome

2. The International Human Genome Sequencing Consortium Nature 409 860 (2001).

3. Kim J., et al., Genomics 74, 129 (2001);

4. . Human and mouse mapping data including sequencing tiling paths and homology links and GenBank assession numbers for all sequenced mouse and human clones are accessible at .

5. Mouse BAC DNA was isolated from overnight cultures with a commercially available kit (Qiagen catalog no. 12165). Purified DNA was fragmented with a GeneMachines Hydroshear end-repaired and size fractionated on agarose gels. Fragments in the 3- to 4-kb size range were excised eluted and blunt-end ligated to Sma I-linearized pUC-18. DNA from overnight cultures (180 μl) of these libraries was purified with an automated 96-well SPRI protocol (40). These templates were cycle-sequenced with both M13-fw and M13-rv primers with dye-terminator chemistry (AP Biotech catalog no. US81095). The resulting product was electrophoresed on MegaBACE 1000 capillary sequencers. Raw traces were preprocessed with Cimarron software version 2.1905 (AP Biotech) and base-called with Phred (41). Readlengths in libraries typically average 500 to 550 Phred>=20 bases. Individual sequence reads were assembled with Phrap () and contig order/orientation was established with the graphical user interface Finisher (available through William FitzHugh at will@genome.wi.mit.edu). All human and mouse clones were sequenced to a depth of at least 6× coverage. About 40% of the sequenced mouse BACs were assembled as fully ordered and oriented contigs; 50% were “partially ordered and oriented” or assembled into large contigs not all of which are fully ordered and oriented. The remaining 10% are presently available only as unordered draft sequence. Of the 22 Mb of HSA19 sequence that is presently in draft form 47% is completed as fully ordered and oriented contigs 27% is partially ordered and 26% remains in unordered draft contigs. Quality data statistics and sequence updates for each mouse and human clone are available at www.jgi.doe.gov.

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