Academic Journal

Locus-specific expression of transposable elements in single cells with CELLO-seq.

Bibliographic Details
Title: Locus-specific expression of transposable elements in single cells with CELLO-seq.
Authors: Berrens RV; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK. rebecca.berrens@gmail.com.; Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford, UK. rebecca.berrens@gmail.com., Yang A; European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK., Laumer CE; European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK., Lun ATL; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.; Genentech, South San Francisco, CA, USA., Bieberich F; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.; ETH Zürich, Basel, Switzerland., Law CT; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.; Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pok Fu Lam, Hong Kong., Lan G; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.; School of Biomedical Sciences,Stem Cell and Regenerative Consortium, Centre for PanorOmic Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pok Fu Lam, Hong Kong., Imaz M; Wellcome Sanger Institute, Cambridge, UK.; Division of Cardiovascular Medicine, University of Cambridge, Cambridge, UK., Bowness JS; Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford, UK., Brockdorff N; Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford, UK., Gaffney DJ; Wellcome Sanger Institute, Cambridge, UK.; Genomics Plc, Oxford, UK., Marioni JC; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK. marioni@ebi.ac.uk.; European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK. marioni@ebi.ac.uk.; Wellcome Sanger Institute, Cambridge, UK. marioni@ebi.ac.uk.
Source: Nature biotechnology [Nat Biotechnol] 2022 Apr; Vol. 40 (4), pp. 546-554. Date of Electronic Publication: 2021 Nov 15.
Publication Type: Journal Article; Research Support, Non-U.S. Gov't
Language: English
Journal Info: Publisher: Nature America Publishing Country of Publication: United States NLM ID: 9604648 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1546-1696 (Electronic) Linking ISSN: 10870156 NLM ISO Abbreviation: Nat Biotechnol Subsets: MEDLINE
Imprint Name(s): Publication: New York Ny : Nature America Publishing
Original Publication: New York, NY : Nature Pub. Co., [1996-
MeSH Terms: DNA Transposable Elements*/genetics , Induced Pluripotent Stem Cells*, Animals ; Humans ; Mice ; RNA
Abstract: Transposable elements (TEs) regulate diverse biological processes, from early development to cancer. Expression of young TEs is difficult to measure with next-generation, single-cell sequencing technologies because their highly repetitive nature means that short complementary DNA reads cannot be unambiguously mapped to a specific locus. Single CELl LOng-read RNA-sequencing (CELLO-seq) combines long-read single cell RNA-sequencing with computational analyses to measure TE expression at unique loci. We used CELLO-seq to assess the widespread expression of TEs in two-cell mouse blastomeres as well as in human induced pluripotent stem cells. Across both species, old and young TEs showed evidence of locus-specific expression with simulations demonstrating that only a small number of very young elements in the mouse could not be mapped back to the reference with high confidence. Exploring the relationship between the expression of individual elements and putative regulators revealed large heterogeneity, with TEs within a class showing different patterns of correlation and suggesting distinct regulatory mechanisms.
(© 2021. The Author(s), under exclusive licence to Springer Nature America, Inc.)
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Grant Information: United Kingdom WT_ Wellcome Trust; 213612 United Kingdom WT_ Wellcome Trust; A22231 United Kingdom CRUK_ Cancer Research UK; C9545/A29580 United Kingdom CRUK_ Cancer Research UK
Substance Nomenclature: 0 (DNA Transposable Elements)
63231-63-0 (RNA)
Entry Date(s): Date Created: 20211116 Date Completed: 20220414 Latest Revision: 20230804
Update Code: 20230804
PubMed Central ID: PMC7614850
DOI: 10.1038/s41587-021-01093-1
PMID: 34782740
Database: MEDLINE
Description
ISSN:1546-1696
DOI:10.1038/s41587-021-01093-1