Pseudoalignment tools as an efficient alternative to detect repeated transposable elements in scRNAseq data

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• dc.contributor.author Martínez de Villarreal, Jaime
• dc.contributor.author Kalisz, Mark
• dc.contributor.author Piedrafita, Gabriel
• dc.contributor.author Graña-Castro, Osvaldo
• dc.contributor.author Chondronasiou, Dafni
• dc.contributor.author Serrano, Manuel
• dc.contributor.author Real, Francisco X.
• dc.date.accessioned 2023-03-13T07:42:32Z
• dc.date.available 2023-03-13T07:42:32Z
• dc.date.issued 2023
• dc.description Includes supplementary material.
• dc.description.abstract Transposable elements (TE) have played a major role in configuring the structures of mammalian genomes through evolution. In normal conditions, the expression of these elements is repressed by different epigenetic regulation mechanisms such as DNA methylation, histone modification and regulation by small RNAs. TE re-activation is associated with stemness potential acquisition, regulation of innate immunity and disease, such as cancer. However, the vast majority of current knowledge in the field is based on bulk expression studies, and very little is known on cell-type- or state-specific expression of TE-derived transcripts. Therefore, cost-efficient single-cell-resolution TE expression analytical approaches are needed. We have implemented an analytical approach based on pseudoalignment to consensus sequences to incorporate TE expression information to scRNAseq data.
• dc.description.sponsorship This work was supported, in part, by Ministerio de Ciencia, Innovación y Universidades (Madrid, Spain) (co-funded by the ERDF-EU) [RTI2018-101071-B-I00]; Ministerio de Ciencia, Innovación y Universidades as a Centro de Excelencia Severo Ochoa SEV-2015-0510 to CNIO.
• dc.format.mimetype application/pdf
• dc.identifier.citation Martínez J, Kalisz M, Piedrafita G, Graña-Castro O, Chondronasiou D, Serrano M, et al. Pseudoalignment tools as an efficient alternative to detect repeated transposable elements in scRNAseq data. Bioinformatics. 2023 Jan;39(1):btac737. DOI: 10.1093/bioinformatics/btac737
• dc.identifier.doi http://dx.doi.org/10.1093/bioinformatics/btac737
• dc.identifier.issn 1367-4811
• dc.identifier.uri http://hdl.handle.net/10230/56176
• dc.language.iso eng
• dc.publisher Oxford University Press
• dc.relation.ispartof Bioinformatics. 2023 Jan;39(1):btac737
• dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/RTI2018-101071-B-I00
• dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/SEV-2015-0510
• dc.rights © The Author(s) 2022. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by/4.0/
• dc.subject.other Epigenètica
• dc.subject.other Expressió gènica
• dc.title Pseudoalignment tools as an efficient alternative to detect repeated transposable elements in scRNAseq data
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion