{"data":{"id":"10.6084/m9.figshare.1288864.v3","type":"dois","attributes":{"doi":"10.6084/m9.figshare.1288864.v3","prefix":"10.6084","suffix":"m9.figshare.1288864.v3","identifiers":[],"alternateIdentifiers":[],"creators":[{"name":"Akhade, Vijay Suresh","nameType":"Personal","givenName":"Vijay Suresh","familyName":"Akhade","affiliation":[],"nameIdentifiers":[]},{"name":"Arun, Gayatri","nameType":"Personal","givenName":"Gayatri","familyName":"Arun","affiliation":[],"nameIdentifiers":[]},{"name":"Sainitin Donakonda","affiliation":[],"nameIdentifiers":[]},{"name":"Manchanahalli R Satyanarayana Rao","affiliation":[],"nameIdentifiers":[]}],"titles":[{"title":"Genome wide chromatin occupancy of \u003ci\u003emrhl\u003c/i\u003e RNA and its role in gene regulation in mouse spermatogonial cells"}],"publisher":"Taylor \u0026 Francis","container":{},"publicationYear":2015,"subjects":[{"subject":"Computational Biology"},{"subject":"110309 Infectious Diseases","subjectScheme":"FOR"},{"subject":"FOS: Health sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Health sciences","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"Hematology"},{"subject":"Cancer"},{"subject":"Developmental Biology"},{"subject":"Biological Sciences"},{"subject":"Immunology"},{"subject":"FOS: Clinical medicine","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Clinical medicine","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"Molecular Biology"},{"subject":"Genetics"},{"subject":"FOS: Biological sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Biological sciences","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"Cell Biology"},{"subject":"Biochemistry"},{"subject":"Biophysics"}],"contributors":[],"dates":[{"date":"2015-10-15","dateType":"Created"},{"date":"2016-01-19","dateType":"Updated"},{"date":"2015","dateType":"Issued"}],"language":null,"types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Dataset","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[{"relationType":"IsSupplementTo","relatedIdentifier":"10.1080/15476286.2014.996070","relatedIdentifierType":"DOI"},{"relationType":"IsIdenticalTo","relatedIdentifier":"10.6084/m9.figshare.1288864","relatedIdentifierType":"DOI"}],"relatedItems":[],"sizes":["291328 Bytes"],"formats":[],"version":null,"rightsList":[{"rights":"Creative Commons Attribution 4.0 International","rightsUri":"https://creativecommons.org/licenses/by/4.0/legalcode","schemeUri":"https://spdx.org/licenses/","rightsIdentifier":"cc-by-4.0","rightsIdentifierScheme":"SPDX"}],"descriptions":[{"description":"\u003ci\u003eMrhl\u003c/i\u003e RNA is a nuclear lncRNA encoded in the mouse genome and negatively regulates Wnt signaling in spermatogonial cells through p68/Ddx5 RNA helicase. \u003ci\u003eMrhl\u003c/i\u003e RNA is present in the chromatin fraction of mouse spermatogonial Gc1-Spg cells and genome wide chromatin occupancy of \u003ci\u003emrhl\u003c/i\u003e RNA by ChOP (Chromatin oligo affinity precipitation) technique identified 1370 statistically significant genomic loci. Among these, genes at 37 genomic loci also showed altered expression pattern upon \u003ci\u003emrhl\u003c/i\u003e RNA down regulation which are referred to as GRPAM (Genes Regulated by Physical Association of \u003ci\u003eMrhl\u003c/i\u003e RNA). p68 interacted with \u003ci\u003emrhl\u003c/i\u003e RNA in chromatin at these GRPAM loci. p68 silencing drastically reduced \u003ci\u003emrhl\u003c/i\u003e RNA occupancy at 27 GRPAM loci and also perturbed the expression of GRPAM suggesting a role for p68 mediated \u003ci\u003emrhl\u003c/i\u003e RNA occupancy in regulating GRPAM expression. Wnt3a ligand treatment of Gc1-Spg cells down regulated \u003ci\u003emrhl\u003c/i\u003e RNA expression and also perturbed expression of these 27 GRPAM genes that included genes regulating Wnt signaling pathway and spermatogenesis, one of them being Sox8, a developmentally important transcription factor. We also identified interacting proteins of \u003ci\u003emrhl\u003c/i\u003e RNA associated chromatin fraction which included Pc4, a chromatin organizer protein and hnRNP A/B and hnRNP A2/B1 which have been shown to be associated with lincRNA-Cox2 function in gene regulation. Our findings in the Gc1-Spg cell line also correlate with the results from analysis of mouse testicular tissue which further highlights the \u003ci\u003ein vivo\u003c/i\u003e physiological significance of \u003ci\u003emrhl\u003c/i\u003e RNA in the context of gene regulation during mammalian spermatogenesis.","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"xml":"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