Chromosome Evolution: The Junction of Mammalian Chromosomes in the Formation of Mouse Chromosome 10

Pletcher, Mathew T.; Roe, Bruce A.; Chen, Fang; Do, Trang; Do, Ahn; Malaj, Eda; Reeves, Roger H.

doi:10.1101/gr.146600

Cited by 27 publications

(17 citation statements)

References 21 publications

(27 reference statements)

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“…This difference was mainly accounted for by a lower fraction of repetitive elements in the mouse. Human unique sequence represented 1.04 Mb, versus 0.97 Mb in the mouse, consistent with the results in several other studies (Martindale et al 2000;Pletcher et al 2000). The relative paucity of repeats in the mouse genome might be explained in part by reduced transposition activity of repetitive elements in rodents (Casavant et al 2000).…”

Section: Discussionsupporting

confidence: 85%

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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Section: Discussionsupporting

confidence: 85%

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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“…Human SGLT3 was the first SGLT to be described as a sensor and not a transporter after extracellular glc resulted in cell depolarization without glc transport (4). While in humans there is only one gene that codes for one SGLT3 protein, in mouse (26) and rat there are two genes coding for the proteins SGLT3a and SGLT3b. The amino acid identities between hSGLT3 and mSGLT3a, and, between hSGLT3 and mSGLT3b, are 80% and 77%, respectively, while mSGLT3a and mSGLT3b are 75% identical.…”

Section: Discussionmentioning

confidence: 99%

“…In mouse, both genes, Slc5a4a and Slc5a4b, which code for mouse SGLT3a (mSGLT3a, gene ID: 64452) and mouse SGLT3b (mSGLT3b, gene ID: 64454), respectively, are found on chromosome 10 (26). In rat, these two genes are located on chromosome 20 (gene ID for rat type 3a: 294341 and for rat type 3b: 294342).…”

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confidence: 99%

Mouse SGLT3a generates proton-activated currents but does not transport sugar

Barcelona

Menegaz

Dı́ez-Sampedro

2012

American Journal of Physiology-Cell Physiology

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Sodium-glucose cotransporters (SGLTs) are secondary active transporters belonging to the SLC5 gene family. SGLT1, a well-characterized member of this family, electrogenically transports glucose and galactose. Human SGLT3 (hSGLT3), despite sharing a high amino acid identity with human SGLT1 (hSGLT1), does not transport sugar, although functions as a sugar sensor. In contrast to humans, two different genes in mice and rats code for two different SGLT3 proteins, SGLT3a and SGLT3b. We previously cloned and characterized mouse SGLT3b (mSGLT3b) and showed that, while it does transport sugar like SGLT1, it likely functions as a physiological sugar sensor like hSGLT3. In this study, we cloned mouse SGLT3a (mSGLT3a) and characterized it by expressing it in Xenopus laevis oocytes and performing electrophysiology and sugar transport assays. mSGLT3a did not transport sugar, and sugars did not induce currents at pH 7.4, though acidic pH induced inward currents that increased in the presence of sugar. Moreover, mutation of residue 457 from glutamate to glutamine resulted in a Na(+)-dependent transport of sugar that was inhibited by phlorizin. To corroborate our results in oocytes, we expressed and characterized mSGLT3a in mammalian cells and confirmed our findings. In addition, we cloned, expressed, and characterized rat SGLT3a in oocytes and found characteristics similar to mSGLT3a. In summary, acidic pH induces currents in mSGLT3a, and sugar-induced currents are increased at acidic pH, but wild-type SGLT3a does not transport sugar.

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“…Studies by Puttagunta et al (2000) and Pletcher et al (2000) on evolutionary breakpoints in mouse chromosome 10 showed an association with a region of very high (60%-70%) repeated sequence content and Dehal et al (2001) found a concentration of LINEs and LTR elements at evolutionary breakpoints. Consideration of the gross distribution of repeated elements, including simple repeats, and base composition in segment 5 (the breakpoint region) as a whole compared with the rest of the Del36H sequence, showed no apparent associations.…”

Section: Sites Of Evolutionary Rearrangementmentioning

confidence: 96%

Organization and Evolution of a Gene-Rich Region of the Mouse Genome: A 12.7-Mb Region Deleted in the Del(13)Svea36H Mouse

Mallon¹,

Wilming²,

Weekes³

et al. 2004

Genome Res.

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Del(13)Svea36H (Del36H) is a deletion of ∼20% of mouse chromosome 13 showing conserved synteny with human chromosome 6p22.1-6p22.3/6p25. The human region is lost in some deletion syndromes and is the site of several disease loci. Heterozygous Del36H mice show numerous phenotypes and may model aspects of human genetic disease. We describe 12.7 Mb of finished, annotated sequence from Del36H. Del36H has a higher gene density than the draft mouse genome, reflecting high local densities of three gene families (vomeronasal receptors, serpins, and prolactins) which are greatly expanded relative to human. Transposable elements are concentrated near these gene families. We therefore suggest that their neighborhoods are gene factories, regions of frequent recombination in which gene duplication is more frequent. The gene families show different proportions of pseudogenes, likely reflecting different strengths of purifying selection and/or gene conversion. They are also associated with relatively low simple sequence concentrations, which vary across the region with a periodicity of ∼5 Mb. Del36H contains numerous evolutionarily conserved regions (ECRs). Many lie in noncoding regions, are detectable in species as distant as Ciona intestinalis, and therefore are candidate regulatory sequences. This analysis will facilitate functional genomic analysis of Del36H and provides insights into mouse genome evolution.

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Chromosome Evolution: The Junction of Mammalian Chromosomes in the Formation of Mouse Chromosome 10

Cited by 27 publications

References 21 publications

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

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

Mouse SGLT3a generates proton-activated currents but does not transport sugar

Organization and Evolution of a Gene-Rich Region of the Mouse Genome: A 12.7-Mb Region Deleted in the Del(13)Svea36H Mouse

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