Article (Scientific journals)
Identification of genes under dynamic post-transcriptional regulation from time-series epigenomic data
Becker, Julia Christina; Gerard, Déborah; Ginolhac, Aurélien et al.
2019In Epigenomics
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Keywords :
chromatin; microrna; linear regression
Abstract :
[en] Aim: Prediction of genes under dynamic post-transcriptional regulation from epigenomic data. Materials & methods: We used time-series profiles of chromatin immunoprecipitation-seq data of histone modifications from differentiation of mesenchymal progenitor cells toward adipocytes and osteoblasts to predict gene expression levels at five time points in both lineages and estimated the deviation of those predictions from the RNA-seq measured expression levels using linear regression. Results & conclusion: The genes with biggest changes in their estimated stability across the time series are enriched for noncoding RNAs and lineage-specific biological processes. Clustering mRNAs according to their stability dynamics allows identification of post-transcriptionally coregulated mRNAs and their shared regulators through sequence enrichment analysis. We identify miR-204 as an early induced adipogenic microRNA targeting Akr1c14 and Il1rl1.
Disciplines :
Biochemistry, biophysics & molecular biology
Author, co-author :
Becker, Julia Christina ;  University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Life Science Research Unit
Gerard, Déborah  ;  University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Computer Science and Communications Research Unit (CSC)
Ginolhac, Aurélien  ;  University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Life Science Research Unit
Sauter, Thomas ;  University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Life Science Research Unit
Sinkkonen, Lasse  ;  University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Life Science Research Unit
External co-authors :
no
Language :
English
Title :
Identification of genes under dynamic post-transcriptional regulation from time-series epigenomic data
Publication date :
02 May 2019
Journal title :
Epigenomics
ISSN :
1750-192X
Publisher :
Future Medicine, London, United Kingdom
Peer reviewed :
Peer Reviewed verified by ORBi
FnR Project :
FNR11191283 - Computational Models And Algorithms For Predicting Cell Reprogramming Determinants With High Efficiency And High Fidelity, 2015 (01/03/2017-15/07/2021) - Thomas Sauter
Funders :
FNR - Fonds National de la Recherche [LU]
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