{"data":{"id":"10.6084/m9.figshare.1263577.v1","type":"dois","attributes":{"doi":"10.6084/m9.figshare.1263577.v1","prefix":"10.6084","suffix":"m9.figshare.1263577.v1","identifiers":[],"alternateIdentifiers":[],"creators":[{"name":"Li, Yuli","givenName":"Yuli","familyName":"Li","affiliation":[],"nameIdentifiers":[]},{"name":"Wang, Xiliang","givenName":"Xiliang","familyName":"Wang","affiliation":[],"nameIdentifiers":[]},{"name":"Li, Cuiping","givenName":"Cuiping","familyName":"Li","affiliation":[],"nameIdentifiers":[]},{"name":"Hu, Songnian","givenName":"Songnian","familyName":"Hu","affiliation":[],"nameIdentifiers":[]},{"name":"Yu, Jun","givenName":"Jun","familyName":"Yu","affiliation":[],"nameIdentifiers":[]},{"name":"Song, Shuhui","givenName":"Shuhui","familyName":"Song","affiliation":[],"nameIdentifiers":[]}],"titles":[{"title":"Transcriptome-wide N\u003csup\u003e6\u003c/sup\u003e-methyladenosine profiling of rice callus and leaf reveals the presence of tissue-specific competitors involved in selective mRNA modification"}],"publisher":"Taylor \u0026 Francis","container":{},"publicationYear":2014,"subjects":[{"subject":"Computational Biology"},{"subject":"Plant Biology"},{"subject":"FOS: Biological sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"Infectious Diseases"},{"subject":"FOS: Health sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"Inorganic Chemistry"},{"subject":"FOS: Chemical sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"Developmental Biology"},{"subject":"Biological Sciences"},{"subject":"Social Science"},{"subject":"Molecular Biology"},{"subject":"Genetics"},{"subject":"Cell Biology"},{"subject":"Biochemistry"}],"contributors":[],"dates":[{"date":"2014-09-02","dateType":"Created"},{"date":"2023-07-29","dateType":"Updated"},{"date":"2014","dateType":"Issued"}],"language":null,"types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Dataset","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[{"relationType":"IsPreviousVersionOf","relatedIdentifier":"10.6084/m9.figshare.1263577","relatedIdentifierType":"DOI"},{"relationType":"IsSupplementTo","relatedIdentifier":"10.4161/rna.36281","relatedIdentifierType":"DOI"}],"relatedItems":[],"sizes":["5672918 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\u003eN\u003c/i\u003e\u003csup\u003e6\u003c/sup\u003e-methyladenosine (m\u003csup\u003e6\u003c/sup\u003eA) is the most prevalent internal modification present in mRNAs of all higher eukaryotes. With the development of MeRIP-seq technique, in-depth identification of mRNAs with m\u003csup\u003e6\u003c/sup\u003eA modification becomes feasible. Here we present a transcriptome-wide m\u003csup\u003e6\u003c/sup\u003eA modification profiling effort for rice transcriptomes of differentiated callus and leaf, which yields 8,138 and 14,253 m\u003csup\u003e6\u003c/sup\u003eA-modified genes, respectively. The m\u003csup\u003e6\u003c/sup\u003eA peak (m\u003csup\u003e6\u003c/sup\u003eA-modified nucleotide position on mRNAs) distribution exhibits preference toward both translation termination and initiation sites. The m\u003csup\u003e6\u003c/sup\u003eA peak enrichment is negatively correlated with gene expression and weakly positively correlated with certain gene features, such as exon length and number. By comparing m\u003csup\u003e6\u003c/sup\u003eA-modified genes between the two samples, we define 1,792 and 6,508 tissue-specific m\u003csup\u003e6\u003c/sup\u003eA-modified genes (TSMGs) in callus and leaf, respectively. Among which, 626 and 5,509 TSMGs are actively expressed in both tissues but are selectively m\u003csup\u003e6\u003c/sup\u003eA-modified (SMGs) only in one of the two tissues. Further analyses reveal characteristics of SMGs: (1) Most SMGs are differentially expressed between callus and leaf. (2) Two conserved RNA-binding motifs, predicted to be recognized by PUM and RNP4F, are significantly over-represented in SMGs. (3) GO enrichment analysis shows that SMGs in callus mainly participate in transcription regulator/factor activity whereas SMGs in leaf are mainly involved in plastid and thylakoid. Our results suggest the presence of tissue-specific competitors involved in SMGs. These findings provide a resource for plant RNA epitranscriptomic studies and further our knowledge on the function of RNA m\u003csup\u003e6\u003c/sup\u003eA modification.","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"xml":"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