title: Identification and dynamic changes of RNAs isolated from RALY-containing ribonucleoprotein complexes.
abstract: RALY is a member of the heterogeneous nuclear ribonucleoprotein family (hnRNP), a large family of RNA-binding proteins involved in many aspects of RNA metabolism. Although RALY interactome has been recently characterized, a comprehensive global analysis of RALY-associated RNAs is lacking and the biological function of RALY remains elusive. Here, we performed RIP-seq analysis to identify RALY interacting RNAs and assessed the role of RALY in gene expression. We demonstrate that RALY binds specific coding and non-coding RNAs and associates with translating mRNAs of mammalian cells. Among the identified transcripts, we focused on ANXA1 and H1FX mRNAs, encoding for Annexin A1 and for the linker variant of the histone H1X, respectively. Both proteins are differentially expressed by proliferating cells and are considered as markers for tumorigenesis. We demonstrate that cells lacking RALY expression exhibit changes in the levels of H1FX and ANXA1 mRNAs and proteins in an opposite manner. We also provide evidence for a direct binding of RALY to the U-rich elements present within the 3΄UTR of both transcripts. Thus, our results identify RALY as a poly-U binding protein and as a regulator of H1FX and ANXA1 in mammalian cells.
authors.affiliation: Laboratory of Molecular and Cellular Neurobiology, Centre for Integrative Biology, University of Trento, via Sommarive 9, 38123 Trento (TN), Italy.
authors.forename: Annalisa
authors.initials: A
authors.lastname: Rossi
authors.affiliation: Laboratory of Molecular and Cellular Neurobiology, Centre for Integrative Biology, University of Trento, via Sommarive 9, 38123 Trento (TN), Italy.
authors.forename: Albertomaria
authors.initials: A
authors.lastname: Moro
authors.affiliation: Laboratory of Translational Genomics, CIBIO - Centre for Integrative Biology, University of Trento, Italy.
authors.forename: Toma
authors.initials: T
authors.lastname: Tebaldi
authors.affiliation: Laboratory of Molecular and Cellular Neurobiology, Centre for Integrative Biology, University of Trento, via Sommarive 9, 38123 Trento (TN), Italy.
authors.forename: Nicola
authors.initials: N
authors.lastname: Cornella
authors.affiliation: Laboratory of Molecular and Cellular Neurobiology, Centre for Integrative Biology, University of Trento, via Sommarive 9, 38123 Trento (TN), Italy.
authors.forename: Lisa
authors.initials: L
authors.lastname: Gasperini
authors.affiliation: Laboratory of Biomolecular Sequence and Structure Analysis for Health, Fondazione Bruno Kessler, Via Sommarive 18, 38123 Povo (TN), Italy.
authors.forename: Lorenzo
authors.initials: L
authors.lastname: Lunelli
authors.affiliation: Laboratory of Translational Genomics, CIBIO - Centre for Integrative Biology, University of Trento, Italy.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Quattrone
authors.affiliation: Institute of Biophysics, CNR-Italian National Council for Research, via Sommarive 18, 38123 Trento (TN), Italy.
authors.forename: Gabriella
authors.initials: G
authors.lastname: Viero
authors.affiliation: Laboratory of Molecular and Cellular Neurobiology, Centre for Integrative Biology, University of Trento, via Sommarive 9, 38123 Trento (TN), Italy.
authors.forename: Paolo
authors.initials: P
authors.lastname: Macchi
mesh_terms: D020413:3' Untranslated Regions; D017305:Annexin A1 / Q000235:genetics / Q000378:metabolism; D063646:Carcinogenesis / Q000235:genetics / Q000378:metabolism; D002453:Cell Cycle; D015972:Gene Expression Regulation, Neoplastic; D057809:HEK293 Cells; D006367:HeLa Cells; D034482:Heterogeneous-Nuclear Ribonucleoprotein Group C / Q000502:physiology*; D006801:Humans; D019169:Jurkat Cells; D061986:MCF-7 Cells; D011132:Polyribosomes / Q000378:metabolism; D011485:Protein Binding; D012333:RNA, Messenger / Q000378:metabolism*
chemical_list: D020413:3' Untranslated Regions; D017305:Annexin A1; D034482:Heterogeneous-Nuclear Ribonucleoprotein Group C; C088730:RALY protein, human; D012333:RNA, Messenger