Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Mouse Transcriptome

ABSTRACT: Sequencing the transcriptome of DBAxC57BL/6J mice

ORGANISM(S): Mus musculus

SUBMITTER: David Adams

PROVIDER: E-MTAB-599 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Mouse genomic variation and its effect on phenotypes and gene regulation.

Keane Thomas M TM Goodstadt Leo L Danecek Petr P White Michael A MA Wong Kim K Yalcin Binnaz B Heger Andreas A Agam Avigail A Slater Guy G Goodson Martin M Furlotte Nicholas A NA Eskin Eleazar E Nellåker Christoffer C Whitley Helen H Cleak James J Janowitz Deborah D Hernandez-Pliego Polinka P Edwards Andrew A Belgard T Grant TG Oliver Peter L PL McIntyre Rebecca E RE Bhomra Amarjit A Nicod Jérôme J Gan Xiangchao X Yuan Wei W van der Weyden Louise L Steward Charles A CA Bala Sendu S Stalker Jim J Mott Richard R Durbin Richard R Jackson Ian J IJ Czechanski Anne A Guerra-Assunção José Afonso JA Donahue Leah Rae LR Reinholdt Laura G LG Payseur Bret A BA Ponting Chris P CP Birney Ewan E Flint Jonathan J Adams David J DJ

Nature 20110914 7364

We report genome sequences of 17 inbred strains of laboratory mice and identify almost ten times more variants than previously known. We use these genomes to explore the phylogenetic history of the laboratory mouse and to examine the functional consequences of allele-specific variation on transcript abundance, revealing that at least 12% of transcripts show a significant tissue-specific expression bias. By identifying candidate functional variants at 718 quantitative trait loci we show that the ...[more]

PMID: 21921910

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Project description:Combining dissimilar parents often leads to increased vigor in the hybrid offspring. “Heterosis” describes both this behavior and its underlying Mendelian and non-Mendelian interactions [1], although its molecular basis remains largely unknown. Recent comparisons of small RNA (sRNA) profiles from parents and their heterotic progeny identified correlations between interparental 24-nucleotide (24-nt) RNA variation and non-additive 24-nt RNA changes in the resulting hybrid [2,3]. 24-nt RNAs guide de novo cytosine methylation, and several proteins are required for their biogenesis, including a Snf2-like ATPase: required to maintain repression1 (RMR1) [4]. We found height variation between heterotic hybrids +/- RMR1 activity, implicating a role for RMR1 in heterosis. Based on the published correlations mentioned above [2,3], we hypothesized that RMR1-loss reduces parental sRNAs, altering their relative ratios and changing the sRNA profiles in the resulting hybrid from those of a standard hybrid (from +RMR1 parents). To probe this hypothesis, we profiled sRNAs from parents and hybrids +/- RMR1 function, limiting the parental diversity to only portions of chromosomes 6 and 9. Our analysis will address how RMR1 loss changes hybrid sRNAs in the presence and absence of underlying genetic variation and help to determine how this loss results in different phenotypic outcomes from heterotic crosses. 1. Shull (1948) Genetics 2. Groszmann et al (2011) PNAS 3. Barber et al (2012) PNAS 4. Hale et al (2007) PLoS Biology We used an interchange chromosome (T6-9 043-1) introgressed into B73 (~95% B73) to create a local region of genetic diversity when crossed as a female parent to 100% B73 individual. Small RNAs from immature cobs were sequenced from both of these parents and their resulting hybrid (2 samples each). Additionally, a similar cross where the T6-9 containing female parent lacked RMR1 activity (rmr1-1 / rmr1-1) was used to generate a counterpart hybrid whose small RNAs were also profiled (2 samples) from immature cobs. Finally, small RNAs from 2 immature cobs of an unrelated rmr1 heterozygote (again highly introgressed into B73) were sequenced as well.

Dataset Information

Mouse Transcriptome

Publications

Mouse genomic variation and its effect on phenotypes and gene regulation.

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