Escape from X inactivation

Distèche, Christine M.; Filippova, Galina N.; Tsuchiya, Karen D.

doi:10.1159/000071572

Cited by 103 publications

(94 citation statements)

References 75 publications

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“…3) 61,68 . In mouse, we found that the LINE/L1 density is elevated in both the XCR (35%) and the XAR (32%), which is consistent with the observation that genes that escape inactivation on the human XAR are often inactivated in mouse 69 . As previously observed in human 68 , the LINE/L1 elevation in mouse is particularly dramatic among recent, lineage-specific subfamilies ( Supplementary Fig.…”

Section: Chromosome Inactivationsupporting

confidence: 89%

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences

Mikkelsen¹,

Wakefield²,

Aken³

et al. 2007

Nature

665

592

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We report a high-quality draft of the genome sequence of the grey, short-tailed opossum (Monodelphis domestica). As the first metatherian ('marsupial') species to be sequenced, the opossum provides a unique perspective on the organization and evolution of mammalian genomes. Distinctive features of the opossum chromosomes provide support for recent theories about genome evolution and function, including a strong influence of biased gene conversion on nucleotide sequence composition, and a relationship between chromosomal characteristics and X chromosome inactivation. Comparison of opossum and eutherian genomes also reveals a sharp difference in evolutionary innovation between protein-coding and non-coding functional elements. True innovation in protein-coding genes seems to be relatively rare, with lineage-specific differences being largely due to diversification and rapid turnover in gene families involved in environmental interactions. In contrast, about 20% of eutherian conserved non-coding elements (CNEs) are recent inventions that postdate the divergence of Eutheria and Metatheria. A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation.

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Section: Chromosome Inactivationsupporting

confidence: 89%

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences

Mikkelsen¹,

Wakefield²,

Aken³

et al. 2007

Nature

665

592

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show abstract

“…The analysis yielded three biologically informative sets. One consists of genes escaping X inactivation [merged from two sources (13,14) that largely overlap], discovering the expected enrichment in female cells. Two additional sets consist of genes enriched in reproductive tissues (testis and uterus), which is notable inasmuch as mRNA expression was measured in lymphoblastoid cells.…”

Section: Resultsmentioning

confidence: 99%

Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles

Subramanian

Tamayo

Mootha

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

43,087

304

38,314

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Although genomewide RNA expression analysis has become a routine tool in biomedical research, extracting biological insight from such information remains a major challenge. Here, we describe a powerful analytical method called Gene Set Enrichment Analysis (GSEA) for interpreting gene expression data. The method derives its power by focusing on gene sets, that is, groups of genes that share common biological function, chromosomal location, or regulation. We demonstrate how GSEA yields insights into several cancer-related data sets, including leukemia and lung cancer. Notably, where single-gene analysis finds little similarity between two independent studies of patient survival in lung cancer, GSEA reveals many biological pathways in common. The GSEA method is embodied in a freely available software package, together with an initial database of 1,325 biologically defined gene sets.

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“…These reactions include loss and restructuring of low-copy DNA sequences (Song et al, 1995;Feldman et al, 1997;Ozkan et al, 2001Ozkan et al, , 2002Shaked et al, 2001;Kashkush et al, 2002), activation of genes and retrotransposons (O'Neill et al, 2002;Kashkush et al, 2003), gene silencing (Chen and Pikaard, 1997a, b;Comai et al, 2000;Lee and Chen, 2001), and subfunctionalization of gene expression patterns (Adams et al, 2003(Adams et al, , 2004Samuel Yang et al, 2006;Hovav et al, 2008). These responses are closely paralleled in animals by inactivation (Lee and Jaenisch, 1997;Avner and Heard, 2001) and differential regulation of X-chromosome gene expression (Disteche et al, 2002;Parisi et al, 2003) and retroelement activation (O'Neill et al, 2002).…”

Section: Introductionmentioning

confidence: 99%