Comparative Sequence Analysis of 634 kb of the Mouse Chromosome 16 Region of Conserved Synteny with the Human Velocardiofacial Syndrome Region on Chromosome 22q11.2

Lund, John E.; Chen, Feng; Hua, Axin; Roe, Bruce A.; Budarf, Marcia L.; Emanuel, Beverly S.; Reeves, Roger H.

doi:10.1006/geno.1999.6044

Cited by 46 publications

(31 citation statements)

References 23 publications

(34 reference statements)

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“…Multiple evolutionary breakpoints between the human and mouse genomes have been examined at the sequence level (Lund et al 2000;Dehal et al 2001;Puttagunta et al 2000). In many cases, these breakpoint sequences were found to be enriched for simple-sequence repeats and L1 repetitive elements or associated with clustered gene families, gene family expansions, and more limited gene duplications.…”

Section: Discussionmentioning

confidence: 99%

Pericentromeric Duplications in the Laboratory Mouse

et al. 2002

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Duplications have long been postulated to be an important mechanism by which genomes evolve. Interspecies genomic comparisons are one method by which the origin and molecular mechanism of duplications can be inferred. By comparative mapping in human, mouse, and rat, we previously found evidence for a recent chromosome-fission event that occurred in the mouse lineage. Cytogenetic mapping revealed that the genomic segments flanking the fission site appeared to be duplicated, with copies residing near the centromere of multiple mouse chromosomes. Here we report the mapping and sequencing of the regions of mouse chromosomes 5 and 6 involved in this chromosome-fission event as well as the results of comparative sequence analysis with the orthologous human and rat genomic regions. Our data indicate that the duplications associated with mouse chromosomes 5 and 6 are recent and that the resulting duplicated segments share significant sequence similarity with a series of regions near the centromeres of the mouse chromosomes previously identified by cytogenetic mapping. We also identified pericentromeric duplicated segments shared between mouse chromosomes 5 and 1. Finally, novel mouse satellite sequences as well as putative chimeric transcripts were found to be associated with the duplicated segments. Together, these findings demonstrate that pericentromeric duplications are not restricted to primates and may be a common mechanism for genome evolution in mammals.

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Section: Discussionmentioning

confidence: 99%

Pericentromeric Duplications in the Laboratory Mouse

et al. 2002

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“…1; Lund et al 2000;Mayor et al 2000). We adopted various conditions to search for significant sequence homology (conserved segments [CSs]) between the sequences (summarized in Table 4; for details, see Supplemental Fig.…”

Section: "Conserved Features" Sequence Mapmentioning

confidence: 99%

Comparative Genomic Sequence Analysis of the Human Chromosome 21 Down Syndrome Critical Region

Toyoda¹,

Noguchi²,

Taylor³

et al. 2002

Genome Res.

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Comprehensive knowledge of the gene content of human chromosome 21 (HSA21) is essential for understanding the etiology of Down syndrome (DS). Here we report the largest comparison of finished mouse and human sequence to date for a 1.35-Mb region of mouse chromosome 16 (MMU16) that corresponds to human chromosome 21q22.2. This includes a portion of the commonly described “DS critical region,” thought to contain a gene or genes whose dosage imbalance contributes to a number of phenotypes associated with DS. We used comparative sequence analysis to construct a DNA feature map of this region that includes all known genes, plus 144 conserved sequences ≥100 bp long that show ≥80% identity between mouse and human but do not match known exons. Twenty of these have matches to expressed sequence tag and cDNA databases, indicating that they may be transcribed sequences from chromosome 21. Eight putative CpG islands are found at conserved positions. Models for two human genes, DSCR4 and DSCR8, are not supported by conserved sequence, and close examination indicates that low-level transcripts from these loci are unlikely to encode proteins. Gene prediction programs give different results when used to analyze the well-conserved regions between mouse and human sequences. Our findings have implications for evolution and for modeling the genetic basis of DS in mice

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“…This criterion, although arbitrary, was used by Loots et al (2000). Other authors (e.g., Lund et al 2000;Mallon et al 2000) have adopted different thresholds. In our analysis, there were eight instances in which a cluster of nearby segments, each meeting this criterion, was merged and considered to be a single conserved region.…”

Section: Global Comparison Of the Mouse And Human Orthologous Imprintmentioning

confidence: 99%

Sequence and Comparative Analysis of the Mouse 1-Megabase Region Orthologous to the Human 11p15 Imprinted Domain

et al. 2000

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A major barrier to conceptual advances in understanding the mechanisms and regulation of imprinting of a genomic region is our relatively poor understanding of the overall organization of genes and of the potentially important cis-acting regulatory sequences that lie in the nonexonic segments that make up 97% of the genome. Interspecies sequence comparison offers an effective approach to identify sequence from conserved functional elements. In this article we describe the successful use of this approach in comparing a ∼1-Mb imprinted genomic domain on mouse chromosome 7 to its orthologous region on human 11p15.5. Within the region, we identified 112 exons of known genes as well as a novel gene identified uniquely in the mouse region, termed Msuit, that was found to be imprinted. In addition to these coding elements, we identified 33 CpG islands and 49 orthologous nonexonic, nonisland sequences that met our criteria as being conserved, and making up 4.1% of the total sequence. These conserved noncoding sequence elements were generally clustered near imprinted genes and the majority were between Igf2 and H19 or within Kvlqt1.

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Comparative Sequence Analysis of 634 kb of the Mouse Chromosome 16 Region of Conserved Synteny with the Human Velocardiofacial Syndrome Region on Chromosome 22q11.2

Cited by 46 publications

References 23 publications

Pericentromeric Duplications in the Laboratory Mouse

Pericentromeric Duplications in the Laboratory Mouse

Comparative Genomic Sequence Analysis of the Human Chromosome 21 Down Syndrome Critical Region

Sequence and Comparative Analysis of the Mouse 1-Megabase Region Orthologous to the Human 11p15 Imprinted Domain

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