A Chinese hamster transcription start site atlas that enables targeted editing of CHO cells.
Journal
NAR genomics and bioinformatics
ISSN: 2631-9268
Titre abrégé: NAR Genom Bioinform
Pays: England
ID NLM: 101756213
Informations de publication
Date de publication:
Sep 2021
Sep 2021
Historique:
received:
15
01
2021
revised:
29
04
2021
accepted:
14
06
2021
entrez:
16
7
2021
pubmed:
17
7
2021
medline:
17
7
2021
Statut:
epublish
Résumé
Chinese hamster ovary (CHO) cells are widely used for producing biopharmaceuticals, and engineering gene expression in CHO is key to improving drug quality and affordability. However, engineering gene expression or activating silent genes requires accurate annotation of the underlying regulatory elements and transcription start sites (TSSs). Unfortunately, most TSSs in the published Chinese hamster genome sequence were computationally predicted and are frequently inaccurate. Here, we use nascent transcription start site sequencing methods to revise TSS annotations for 15 308 Chinese hamster genes and 3034 non-coding RNAs based on experimental data from CHO-K1 cells and 10 hamster tissues. We further capture tens of thousands of putative transcribed enhancer regions with this method. Our revised TSSs improves upon the RefSeq annotation by revealing core sequence features of gene regulation such as the TATA box and the Initiator and, as exemplified by targeting the glycosyltransferase gene
Identifiants
pubmed: 34268494
doi: 10.1093/nargab/lqab061
pii: lqab061
pmc: PMC8276764
doi:
Types de publication
Journal Article
Langues
eng
Pagination
lqab061Subventions
Organisme : NIGMS NIH HHS
ID : K99 GM135515
Pays : United States
Organisme : NIGMS NIH HHS
ID : R00 GM135515
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM134366
Pays : United States
Organisme : NIDA NIH HHS
ID : U01 DA051972
Pays : United States
Informations de copyright
© The Author(s) 2021. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics.
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