Development of a ribosome profiling protocol to study translation in Kluyveromyces marxianus

Fenton, Darren; Kiniry, Stephen J.; Yordanova, Martina M.; Baranov, Pavel V.; Morrissey, John P.

Development of a ribosome profiling protocol to study translation in Kluyveromyces marxianus

dc.contributor.author	Fenton, Darren	en
dc.contributor.author	Kiniry, Stephen J.	en
dc.contributor.author	Yordanova, Martina M.	en
dc.contributor.author	Baranov, Pavel V.	en
dc.contributor.author	Morrissey, John P.	en
dc.contributor.funder	Horizon 2020 Framework Programme	en
dc.contributor.funder	Science Foundation Ireland	en
dc.contributor.funder	Health Research Board	en
dc.contributor.funder	Wellcome Trust	en
dc.date.accessioned	2024-09-05T14:54:14Z
dc.date.available	2024-09-05T14:54:14Z
dc.date.issued	2022	en
dc.description.abstract	Kluyveromyces marxianus is an interesting and important yeast because of particular traits such as thermotolerance and rapid growth, and for applications in food and industrial biotechnology. For both understanding its biology and developing bioprocesses, it is important to understand how K. marxianus responds and adapts to changing environments. For this, a full suite of omics tools to measure and compare global patterns of gene expression and protein synthesis is needed. We report here the development of a ribosome profiling method for K. marxianus, which allows codon resolution of translation on a genome-wide scale by deep sequencing of ribosome locations on mRNAs. To aid in the analysis and sharing of ribosome profiling data, we added the K. marxianus genome as well as transcriptome and ribosome profiling data to the publicly accessible GWIPS-viz and Trips-Viz browsers. Users are able to upload custom ribosome profiling and RNA-Seq data to both browsers, therefore allowing easy analysis and sharing of data. We also provide a set of step-by-step protocols for the experimental and bioinformatic methods that we developed.	en
dc.description.status	Peer reviewed	en
dc.description.version	Published Version	en
dc.format.mimetype	application/pdf	en
dc.identifier.articleid	foac024	en
dc.identifier.citation	Fenton, D.A., Kiniry, S.J., Yordanova, M.M., Baranov, P.V. and Morrissey, J.P. (2022) ‘Development of a ribosome profiling protocol to study translation in Kluyveromyces marxianus’, FEMS Yeast Research, 22(1), foac024 (9pp). doi: 10.1093/femsyr/foac024	en
dc.identifier.doi	10.1093/femsyr/foac024	en
dc.identifier.eissn	1567-1364	en
dc.identifier.endpage	9	en
dc.identifier.issn	1567-1356	en
dc.identifier.issued	1	en
dc.identifier.journaltitle	FEMS Yeast Research	en
dc.identifier.startpage	1	en
dc.identifier.uri	https://hdl.handle.net/10468/16304
dc.identifier.volume	22	en
dc.language.iso	en	en
dc.publisher	Oxford University Press	en
dc.relation.project	info:eu-repo/grantAgreement/EC/H2020::RIA/720824/EU/Model-Based Construction And Optimisation Of Versatile Chassis Yeast Strains For Production Of Valuable Lipid And Aromatic Compounds/CHASSY	en
dc.relation.project	info:eu-repo/grantAgreement/WT/Molecular Basis of Cell Function/210692//Molecular memory in human AMD1 gene: mechanisms and functions./	en
dc.rights	© TheAuthor(s) 2022. Published by Oxford University Press on behalf of FEMS. This is an Open Access article distributed under the terms of the Creative CommonsAttribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com	en
dc.rights.uri	https://creativecommons.org/licenses/by-nc/4.0/	en
dc.subject	Nonconventional yeast (NCY)	en
dc.subject	Ribo-Seq	en
dc.subject	RNA-Seq	en
dc.subject	Transcriptome visualization	en
dc.subject	Global analysis	en
dc.subject	Industrial biotechnology	en
dc.title	Development of a ribosome profiling protocol to study translation in Kluyveromyces marxianus	en
dc.type	Article (peer-reviewed)	en