{"data":{"id":"10.6084/m9.figshare.1288864.v1","type":"dois","attributes":{"doi":"10.6084/m9.figshare.1288864.v1","prefix":"10.6084","suffix":"m9.figshare.1288864.v1","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":2014,"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":"2014-10-03","dateType":"Created"},{"date":"2016-01-19","dateType":"Updated"},{"date":"2014","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":"IsPreviousVersionOf","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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