CUT&RUN identifies centromeric DNA regions of Rhodotorula toruloides IFO0880.

Autor:	Schultz JC; Department of Chemical and Biomolecular Engineering, U.S. Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA., Cao M; Department of Chemical and Biomolecular Engineering, U.S. Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA., Mejia A; Department of Chemical and Biomolecular Engineering, U.S. Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA., Zhao H; Department of Chemical and Biomolecular Engineering, U.S. Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.; Departments of Chemistry, Biochemistry, and Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
Jazyk:	angličtina
Zdroj:	FEMS yeast research [FEMS Yeast Res] 2022 Jan 11; Vol. 21 (8).
DOI:	10.1093/femsyr/foab066
Abstrakt:	Rhodotorula toruloides has been increasingly explored as a host for bioproduction of lipids, fatty acid derivatives and terpenoids. Various genetic tools have been developed, but neither a centromere nor an autonomously replicating sequence (ARS), both necessary elements for stable episomal plasmid maintenance, has yet been reported. In this study, cleavage under targets and release using nuclease (CUT&RUN), a method used for genome-wide mapping of DNA-protein interactions, was used to identify R. toruloides IFO0880 genomic regions associated with the centromeric histone H3 protein Cse4, a marker of centromeric DNA. Fifteen putative centromeres ranging from 8 to 19 kb in length were identified and analyzed, and four were tested for, but did not show, ARS activity. These centromeric sequences contained below average GC content, corresponded to transcriptional cold spots, were primarily nonrepetitive and shared some vestigial transposon-related sequences but otherwise did not show significant sequence conservation. Future efforts to identify an ARS in this yeast can utilize these centromeric DNA sequences to improve the stability of episomal plasmids derived from putative ARS elements. (© The Author(s) 2021. Published by Oxford University Press on behalf of FEMS.)
Databáze:	MEDLINE
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