Expanding the Chinese hamster ovary cell long noncoding RNA transcriptome using RNASeq.
Chinese hamster ovary
RNASeq
long noncoding RNA
next generation sequencing
temperature shift
transcriptomics
Journal
Biotechnology and bioengineering
ISSN: 1097-0290
Titre abrégé: Biotechnol Bioeng
Pays: United States
ID NLM: 7502021
Informations de publication
Date de publication:
10 2020
10 2020
Historique:
received:
03
12
2019
revised:
02
06
2020
accepted:
17
06
2020
pubmed:
20
6
2020
medline:
8
10
2021
entrez:
20
6
2020
Statut:
ppublish
Résumé
Our ability to study Chinese hamster ovary (CHO) cell biology has been revolutionised over the last decade following the development of next generation sequencing technology and publication of reference DNA sequences for CHO cells and the Chinese hamster. RNA sequencing has not only enabled the association of transcript expression with bioreactor conditions and desirable bioprocess phenotypes but played a key role in the characterisation of protein coding and small noncoding RNAs. The annotation of long noncoding RNAs, and therefore our understanding of their role in CHO cell biology, has been limited to date. In this manuscript, we use high-resolution RNASeq data to more than double the number of annotated lncRNA transcripts for the CHO K1 genome. In addition, the utilisation of strand-specific sequencing enabled the identification of more than 1,000 new antisense and divergent lncRNAs. The utility of monitoring lncRNA expression is demonstrated through an analysis of the transcriptomic response to a reduction of cell culture temperature and identification of simultaneous sense/antisense differential expression for the first time in CHO cells. To enable further studies of lncRNAs, the transcripts annotated in this study have been made available for the CHO cell biology community.
Substances chimiques
RNA, Long Noncoding
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
3224-3231Subventions
Organisme : H2020 Marie Sklodowska-Curie Actions
ID : 642663
Pays : International
Organisme : Science Foundation Ireland
ID : 13/SIRG/2084
Pays : Ireland
Organisme : Science Foundation Ireland
ID : 15/CDA/3259
Pays : Ireland
Informations de copyright
© 2020 Wiley Periodicals LLC.
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