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ReadZS detects cell type-specific and developmentally regulated RNA processing programs in single-cell RNA-seq
RNA processing, including splicing and alternative polyadenylation, is crucial to gene function and regulation, but methods to detect RNA processing from single-cell RNA sequencing data are limited by reliance on pre-existing annotations, peak calling heuristics, and collapsing measurements by cell...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9594907/ https://www.ncbi.nlm.nih.gov/pubmed/36284317 http://dx.doi.org/10.1186/s13059-022-02795-8 |
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author | Meyer, Elisabeth Chaung, Kaitlin Dehghannasiri, Roozbeh Salzman, Julia |
author_facet | Meyer, Elisabeth Chaung, Kaitlin Dehghannasiri, Roozbeh Salzman, Julia |
author_sort | Meyer, Elisabeth |
collection | PubMed |
description | RNA processing, including splicing and alternative polyadenylation, is crucial to gene function and regulation, but methods to detect RNA processing from single-cell RNA sequencing data are limited by reliance on pre-existing annotations, peak calling heuristics, and collapsing measurements by cell type. We introduce ReadZS, an annotation-free statistical approach to identify regulated RNA processing in single cells. ReadZS discovers cell type-specific RNA processing in human lung and conserved, developmentally regulated RNA processing in mammalian spermatogenesis—including global 3′ UTR shortening in human spermatogenesis. ReadZS also discovers global 3′ UTR lengthening in Arabidopsis development, highlighting the usefulness of this method in under-annotated transcriptomes. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-022-02795-8. |
format | Online Article Text |
id | pubmed-9594907 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-95949072022-10-26 ReadZS detects cell type-specific and developmentally regulated RNA processing programs in single-cell RNA-seq Meyer, Elisabeth Chaung, Kaitlin Dehghannasiri, Roozbeh Salzman, Julia Genome Biol Method RNA processing, including splicing and alternative polyadenylation, is crucial to gene function and regulation, but methods to detect RNA processing from single-cell RNA sequencing data are limited by reliance on pre-existing annotations, peak calling heuristics, and collapsing measurements by cell type. We introduce ReadZS, an annotation-free statistical approach to identify regulated RNA processing in single cells. ReadZS discovers cell type-specific RNA processing in human lung and conserved, developmentally regulated RNA processing in mammalian spermatogenesis—including global 3′ UTR shortening in human spermatogenesis. ReadZS also discovers global 3′ UTR lengthening in Arabidopsis development, highlighting the usefulness of this method in under-annotated transcriptomes. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-022-02795-8. BioMed Central 2022-10-25 /pmc/articles/PMC9594907/ /pubmed/36284317 http://dx.doi.org/10.1186/s13059-022-02795-8 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Method Meyer, Elisabeth Chaung, Kaitlin Dehghannasiri, Roozbeh Salzman, Julia ReadZS detects cell type-specific and developmentally regulated RNA processing programs in single-cell RNA-seq |
title | ReadZS detects cell type-specific and developmentally regulated RNA processing programs in single-cell RNA-seq |
title_full | ReadZS detects cell type-specific and developmentally regulated RNA processing programs in single-cell RNA-seq |
title_fullStr | ReadZS detects cell type-specific and developmentally regulated RNA processing programs in single-cell RNA-seq |
title_full_unstemmed | ReadZS detects cell type-specific and developmentally regulated RNA processing programs in single-cell RNA-seq |
title_short | ReadZS detects cell type-specific and developmentally regulated RNA processing programs in single-cell RNA-seq |
title_sort | readzs detects cell type-specific and developmentally regulated rna processing programs in single-cell rna-seq |
topic | Method |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9594907/ https://www.ncbi.nlm.nih.gov/pubmed/36284317 http://dx.doi.org/10.1186/s13059-022-02795-8 |
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