High resolution temporal transcriptomics of mouse embryoid body development reveals complex expression dynamics of coding and noncoding loci.

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State: Public
Version: Final published version
Serval ID
serval:BIB_F6D84A4FC45D
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
High resolution temporal transcriptomics of mouse embryoid body development reveals complex expression dynamics of coding and noncoding loci.
Journal
Scientific reports
Author(s)
Gloss B.S., Signal B., Cheetham S.W., Gruhl F., Kaczorowski D.C., Perkins A.C., Dinger M.E.
ISSN
2045-2322 (Electronic)
ISSN-L
2045-2322
Publication state
Published
Issued date
27/07/2017
Peer-reviewed
Oui
Volume
7
Number
1
Pages
6731
Language
english
Notes
Publication types: Journal Article ; Research Support, Non-U.S. Gov't
Publication Status: epublish
Abstract
Cellular responses to stimuli are rapid and continuous and yet the vast majority of investigations of transcriptional responses during developmental transitions typically use long interval time courses; limiting the available interpretive power. Moreover, such experiments typically focus on protein-coding transcripts, ignoring the important impact of long noncoding RNAs. We therefore evaluated coding and noncoding expression dynamics at unprecedented temporal resolution (6-hourly) in differentiating mouse embryonic stem cells and report new insight into molecular processes and genome organization. We present a highly resolved differentiation cascade that exhibits coding and noncoding transcriptional alterations, transcription factor network interactions and alternative splicing events, little of which can be resolved by long-interval developmental time-courses. We describe novel short lived and cycling patterns of gene expression and dissect temporally ordered gene expression changes in response to transcription factors. We elucidate patterns in gene co-expression across the genome, describe asynchronous transcription at bidirectional promoters and functionally annotate known and novel regulatory lncRNAs. These findings highlight the complex and dynamic molecular events underlying mammalian differentiation that can only be observed though a temporally resolved time course.
Keywords
Alternative Splicing, Animals, Cell Differentiation, Chromosome Mapping, Embryoid Bodies/cytology, Embryoid Bodies/metabolism, Gene Expression Profiling, Gene Expression Regulation, Developmental, Mice, Molecular Sequence Annotation, Mouse Embryonic Stem Cells/cytology, Mouse Embryonic Stem Cells/metabolism, Open Reading Frames, Promoter Regions, Genetic, RNA, Long Noncoding/classification, RNA, Long Noncoding/genetics, RNA, Long Noncoding/metabolism, Time Factors, Transcription Factors/classification, Transcription Factors/genetics, Transcription Factors/metabolism, Transcriptome
Pubmed
Web of science
Open Access
Yes
Create date
08/08/2017 13:19
Last modification date
20/08/2019 17:23
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