[en] Long-noncoding RNA (lncRNA) interact with DNA, RNA and proteins to regulate the epigenome and fundamental biological processes. In the bovine genome, the nature and mechanisms of lncRNA interactions with specific chromatin regions are unexplored yet. Here, we aimed to unravel the chromatin interaction sites of the evolutionary conserved lncRNA TUG1 in the bovine genome using ChIRP-seq (chromatin isolation by RNA precipitation) in two popular bovine cell lines (MDBK, MAC-T) and liver tissue. About half of the genome-wide TUG1 chromatin occupancy in the genome (3225, 3587 and 3,977 interaction sites in MDBK, MAC-T and liver, respectively) was associated with protein-coding genes. Observation of numerous concordant TUG1 chromatin interaction sites between MDBK and MAC-T cells and liver tissue was consistent with the known ubiquitous expression of TUG1. Analysis of overlaps between ChIRP-seq peaks and ATAC-seq peaks in MDBK and MAC-T cells pinpointed TUG1 chromatin interaction sites relevant for modulating chromatin accessibility.
Disciplines :
Genetics & genetic processes
Author, co-author :
Weikard, Rosemarie; Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
Bhushan, Raghu; Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
Becker, Doreen; Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
Hadlich, Frieder; Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
Charlier, Carole ; Université de Liège - ULiège > Département de gestion vétérinaire des Ressources Animales (DRA)
Costa Monteiro Moreira, Gabriel ; Université de Liège - ULiège > Département de gestion vétérinaire des Ressources Animales (DRA)
Kuehn, Christa; Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany, Agricultural and Environmental Faculty, University of Rostock, Rostock, Germany, Friedrich Loeffler Institute, Greifswald-Riems, Germany. Electronic address: christa.kuehn@fli.de
Language :
English
Title :
Elucidating the landscape of genome-wide chromatin interaction sites of the lncRNA TUG1 in bovine cell lines and liver tissue.
H2020 - 815668 - BovReg - BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle
Funders :
EU - European Union DFG - German Research Foundation
Funding text :
This study was funded by the German Research Foundation (DFG grant numbers: KU 771/8-1 and WE 1786/5-1 ) and received funding from the European Union Horizon 2020 research and innovation program for the BovReg project (grant number 815668 ).The data generated and analysed in this study are included as figures and tables or included in supplementary tables as indicated appendix A. The liver RNA-seq data used in this study was already used in a previous study (Nolte et al. 2019) stored in the Functional Annotation of Animal Genomes (FAANG) database ( https://data.faang.org/dataset ) under project number PRJEB34570. The ATAC-seq datasets for MDBK and MAC-T cells are available from the FAANG data portal ( https://data.faang.org/home ) under the European Horizon 2020 project BovReg (Grant agreement ID 815668) and deposited under project number PRJEB51163. The ChIRP-seq datasets for MDBK, MAC-T and liver (BioSamples SAMEA119609839, SAMEA119609840, SAMEA119609841) are publicly available at ENA under project number PRJEB 96303.
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