{"data":{"id":"10.6084/m9.figshare.1632156","type":"dois","attributes":{"doi":"10.6084/m9.figshare.1632156","prefix":"10.6084","suffix":"m9.figshare.1632156","identifiers":[],"alternateIdentifiers":[],"creators":[{"name":"Redko, Yulia","nameType":"Personal","givenName":"Yulia","familyName":"Redko","affiliation":[],"nameIdentifiers":[]},{"name":"Eloïse Galtier","affiliation":[],"nameIdentifiers":[]},{"name":"Arnion, Hélène","nameType":"Personal","givenName":"Hélène","familyName":"Arnion","affiliation":[],"nameIdentifiers":[]},{"name":"Darfeuille, Fabien","nameType":"Personal","givenName":"Fabien","familyName":"Darfeuille","affiliation":[],"nameIdentifiers":[]},{"name":"Sismeiro, Odile","nameType":"Personal","givenName":"Odile","familyName":"Sismeiro","affiliation":[],"nameIdentifiers":[]},{"name":"Jean-Yves Coppée","affiliation":[],"nameIdentifiers":[]},{"name":"Médigue, Claudine","nameType":"Personal","givenName":"Claudine","familyName":"Médigue","affiliation":[],"nameIdentifiers":[]},{"name":"Weiman, Marion","nameType":"Personal","givenName":"Marion","familyName":"Weiman","affiliation":[],"nameIdentifiers":[]},{"name":"Cruveiller, Stéphane","nameType":"Personal","givenName":"Stéphane","familyName":"Cruveiller","affiliation":[],"nameIdentifiers":[]},{"name":"Reuse, Hilde De","nameType":"Personal","givenName":"Hilde De","familyName":"Reuse","affiliation":[],"nameIdentifiers":[]}],"titles":[{"title":"RNase J depletion leads to massive changes in mRNA abundance in \u003ci\u003eHelicobacter pylori\u003c/i\u003e"}],"publisher":"Taylor \u0026 Francis","container":{},"publicationYear":2016,"subjects":[{"subject":"Biochemistry"},{"subject":"Space Science"},{"subject":"Microbiology"},{"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":"Genetics"},{"subject":"Molecular Biology"},{"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":"69999 Biological Sciences not elsewhere classified","subjectScheme":"FOR"},{"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":"60506 Virology","subjectScheme":"FOR"},{"subject":"Computational Biology"}],"contributors":[],"dates":[{"date":"2016-01-05","dateType":"Created"},{"date":"2016-03-17","dateType":"Updated"},{"date":"2016","dateType":"Issued"}],"language":null,"types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Dataset","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[{"relationType":"IsSupplementTo","relatedIdentifier":"10.1080/15476286.2015.1132141","relatedIdentifierType":"DOI"}],"relatedItems":[],"sizes":["1030084 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":"Degradation of RNA as an intermediate message between genes and corresponding proteins is important for rapid attenuation of gene expression and maintenance of cellular homeostasis. This process is controlled by ribonucleases that have different target specificities. In the bacterial pathogen \u003ci\u003eHelicobacter pylori\u003c/i\u003e, an exo- and endoribonuclease RNase J is essential for growth. To explore the role of RNase J in \u003ci\u003eH. pylori\u003c/i\u003e, we identified its putative targets at a global scale using next generation RNA sequencing. We found that strong depletion for RNase J led to a massive increase in the steady-state levels of non-rRNAs. mRNAs and RNAs antisense to open reading frames were most affected with over 80% increased more than 2-fold. Non-coding RNAs expressed in the intergenic regions were much less affected by RNase J depletion. Northern blotting of selected messenger and non-coding RNAs validated these results. Globally, our data suggest that RNase J of \u003ci\u003eH. pylori\u003c/i\u003e is a major RNase involved in degradation of most cellular RNAs.","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"xml":"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