{"data":{"id":"10.6084/m9.figshare.c.2024765.v1","type":"dois","attributes":{"doi":"10.6084/m9.figshare.c.2024765.v1","prefix":"10.6084","suffix":"m9.figshare.c.2024765.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":2015,"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":"2015-12-05","dateType":"Created"},{"date":"2019-08-19","dateType":"Updated"},{"date":"2015","dateType":"Issued"}],"language":null,"types":{"ris":"GEN","bibtex":"misc","citeproc":"article","schemaOrg":"Collection","resourceType":"Collection","resourceTypeGeneral":"Collection"},"relatedIdentifiers":[{"relationType":"IsIdenticalTo","relatedIdentifier":"10.6084/m9.figshare.c.2024765","relatedIdentifierType":"DOI"}],"relatedItems":[],"sizes":[],"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 2 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 2 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 enlarge our knowledge on the function of RNA m\u003csup\u003e6\u003c/sup\u003eA modification.","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"xml":"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