Eintrag weiter verarbeiten
Cell-type-specific analysis of alternative polyadenylation using single-cell transcriptomics data
Gespeichert in:
| Zeitschriftentitel: | Nucleic Acids Research |
|---|---|
| Personen und Körperschaften: | , |
| In: | Nucleic Acids Research, 47, 2019, 19, S. 10027-10039 |
| Format: | E-Article |
| Sprache: | Englisch |
| veröffentlicht: |
Oxford University Press (OUP)
|
| Schlagwörter: |
| author_facet |
Shulman, Eldad David Elkon, Ran Shulman, Eldad David Elkon, Ran |
|---|---|
| author |
Shulman, Eldad David Elkon, Ran |
| spellingShingle |
Shulman, Eldad David Elkon, Ran Nucleic Acids Research Cell-type-specific analysis of alternative polyadenylation using single-cell transcriptomics data Genetics |
| author_sort |
shulman, eldad david |
| spelling |
Shulman, Eldad David Elkon, Ran 0305-1048 1362-4962 Oxford University Press (OUP) Genetics http://dx.doi.org/10.1093/nar/gkz781 <jats:title>Abstract</jats:title><jats:p>Alternative polyadenylation (APA) is emerging as an important layer of gene regulation because the majority of mammalian protein-coding genes contain multiple polyadenylation (pA) sites in their 3′ UTR. By alteration of 3′ UTR length, APA can considerably affect post-transcriptional gene regulation. Yet, our understanding of APA remains rudimentary. Novel single-cell RNA sequencing (scRNA-seq) techniques allow molecular characterization of different cell types to an unprecedented degree. Notably, the most popular scRNA-seq protocols specifically sequence the 3′ end of transcripts. Building on this property, we implemented a method for analysing patterns of APA regulation from such data. Analyzing multiple datasets from diverse tissues, we identified widespread modulation of APA in different cell types resulting in global 3′ UTR shortening/lengthening and enhanced cleavage at intronic pA sites. Our results provide a proof-of-concept demonstration that the huge volume of scRNA-seq data that accumulates in the public domain offers a unique resource for the exploration of APA based on a very broad collection of cell types and biological conditions.</jats:p> Cell-type-specific analysis of alternative polyadenylation using single-cell transcriptomics data Nucleic Acids Research |
| doi_str_mv |
10.1093/nar/gkz781 |
| facet_avail |
Online Free |
| finc_class_facet |
Biologie |
| format |
ElectronicArticle |
| fullrecord |
blob:ai-49-aHR0cDovL2R4LmRvaS5vcmcvMTAuMTA5My9uYXIvZ2t6Nzgx |
| id |
ai-49-aHR0cDovL2R4LmRvaS5vcmcvMTAuMTA5My9uYXIvZ2t6Nzgx |
| institution |
DE-L229 DE-D275 DE-Bn3 DE-Brt1 DE-Zwi2 DE-D161 DE-Gla1 DE-Zi4 DE-15 DE-Pl11 DE-Rs1 DE-105 DE-14 DE-Ch1 |
| imprint |
Oxford University Press (OUP), 2019 |
| imprint_str_mv |
Oxford University Press (OUP), 2019 |
| issn |
0305-1048 1362-4962 |
| issn_str_mv |
0305-1048 1362-4962 |
| language |
English |
| mega_collection |
Oxford University Press (OUP) (CrossRef) |
| match_str |
shulman2019celltypespecificanalysisofalternativepolyadenylationusingsinglecelltranscriptomicsdata |
| publishDateSort |
2019 |
| publisher |
Oxford University Press (OUP) |
| recordtype |
ai |
| record_format |
ai |
| series |
Nucleic Acids Research |
| source_id |
49 |
| title |
Cell-type-specific analysis of alternative polyadenylation using single-cell transcriptomics data |
| title_unstemmed |
Cell-type-specific analysis of alternative polyadenylation using single-cell transcriptomics data |
| title_full |
Cell-type-specific analysis of alternative polyadenylation using single-cell transcriptomics data |
| title_fullStr |
Cell-type-specific analysis of alternative polyadenylation using single-cell transcriptomics data |
| title_full_unstemmed |
Cell-type-specific analysis of alternative polyadenylation using single-cell transcriptomics data |
| title_short |
Cell-type-specific analysis of alternative polyadenylation using single-cell transcriptomics data |
| title_sort |
cell-type-specific analysis of alternative polyadenylation using single-cell transcriptomics data |
| topic |
Genetics |
| url |
http://dx.doi.org/10.1093/nar/gkz781 |
| publishDate |
2019 |
| physical |
10027-10039 |
| description |
<jats:title>Abstract</jats:title><jats:p>Alternative polyadenylation (APA) is emerging as an important layer of gene regulation because the majority of mammalian protein-coding genes contain multiple polyadenylation (pA) sites in their 3′ UTR. By alteration of 3′ UTR length, APA can considerably affect post-transcriptional gene regulation. Yet, our understanding of APA remains rudimentary. Novel single-cell RNA sequencing (scRNA-seq) techniques allow molecular characterization of different cell types to an unprecedented degree. Notably, the most popular scRNA-seq protocols specifically sequence the 3′ end of transcripts. Building on this property, we implemented a method for analysing patterns of APA regulation from such data. Analyzing multiple datasets from diverse tissues, we identified widespread modulation of APA in different cell types resulting in global 3′ UTR shortening/lengthening and enhanced cleavage at intronic pA sites. Our results provide a proof-of-concept demonstration that the huge volume of scRNA-seq data that accumulates in the public domain offers a unique resource for the exploration of APA based on a very broad collection of cell types and biological conditions.</jats:p> |
| container_issue |
19 |
| container_start_page |
10027 |
| container_title |
Nucleic Acids Research |
| container_volume |
47 |
| format_de105 |
Article, E-Article |
| format_de14 |
Article, E-Article |
| format_de15 |
Article, E-Article |
| format_de520 |
Article, E-Article |
| format_de540 |
Article, E-Article |
| format_dech1 |
Article, E-Article |
| format_ded117 |
Article, E-Article |
| format_degla1 |
E-Article |
| format_del152 |
Buch |
| format_del189 |
Article, E-Article |
| format_dezi4 |
Article |
| format_dezwi2 |
Article, E-Article |
| format_finc |
Article, E-Article |
| format_nrw |
Article, E-Article |
| _version_ |
1792346216163442689 |
| geogr_code |
not assigned |
| last_indexed |
2024-03-01T17:35:33.859Z |
| geogr_code_person |
not assigned |
| openURL |
url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fvufind.svn.sourceforge.net%3Agenerator&rft.title=Cell-type-specific+analysis+of+alternative+polyadenylation+using+single-cell+transcriptomics+data&rft.date=2019-11-04&genre=article&issn=1362-4962&volume=47&issue=19&spage=10027&epage=10039&pages=10027-10039&jtitle=Nucleic+Acids+Research&atitle=Cell-type-specific+analysis+of+alternative+polyadenylation+using+single-cell+transcriptomics+data&aulast=Elkon&aufirst=Ran&rft_id=info%3Adoi%2F10.1093%2Fnar%2Fgkz781&rft.language%5B0%5D=eng |
| SOLR | |
| _version_ | 1792346216163442689 |
| author | Shulman, Eldad David, Elkon, Ran |
| author_facet | Shulman, Eldad David, Elkon, Ran, Shulman, Eldad David, Elkon, Ran |
| author_sort | shulman, eldad david |
| container_issue | 19 |
| container_start_page | 10027 |
| container_title | Nucleic Acids Research |
| container_volume | 47 |
| description | <jats:title>Abstract</jats:title><jats:p>Alternative polyadenylation (APA) is emerging as an important layer of gene regulation because the majority of mammalian protein-coding genes contain multiple polyadenylation (pA) sites in their 3′ UTR. By alteration of 3′ UTR length, APA can considerably affect post-transcriptional gene regulation. Yet, our understanding of APA remains rudimentary. Novel single-cell RNA sequencing (scRNA-seq) techniques allow molecular characterization of different cell types to an unprecedented degree. Notably, the most popular scRNA-seq protocols specifically sequence the 3′ end of transcripts. Building on this property, we implemented a method for analysing patterns of APA regulation from such data. Analyzing multiple datasets from diverse tissues, we identified widespread modulation of APA in different cell types resulting in global 3′ UTR shortening/lengthening and enhanced cleavage at intronic pA sites. Our results provide a proof-of-concept demonstration that the huge volume of scRNA-seq data that accumulates in the public domain offers a unique resource for the exploration of APA based on a very broad collection of cell types and biological conditions.</jats:p> |
| doi_str_mv | 10.1093/nar/gkz781 |
| facet_avail | Online, Free |
| finc_class_facet | Biologie |
| format | ElectronicArticle |
| format_de105 | Article, E-Article |
| format_de14 | Article, E-Article |
| format_de15 | Article, E-Article |
| format_de520 | Article, E-Article |
| format_de540 | Article, E-Article |
| format_dech1 | Article, E-Article |
| format_ded117 | Article, E-Article |
| format_degla1 | E-Article |
| format_del152 | Buch |
| format_del189 | Article, E-Article |
| format_dezi4 | Article |
| format_dezwi2 | Article, E-Article |
| format_finc | Article, E-Article |
| format_nrw | Article, E-Article |
| geogr_code | not assigned |
| geogr_code_person | not assigned |
| id | ai-49-aHR0cDovL2R4LmRvaS5vcmcvMTAuMTA5My9uYXIvZ2t6Nzgx |
| imprint | Oxford University Press (OUP), 2019 |
| imprint_str_mv | Oxford University Press (OUP), 2019 |
| institution | DE-L229, DE-D275, DE-Bn3, DE-Brt1, DE-Zwi2, DE-D161, DE-Gla1, DE-Zi4, DE-15, DE-Pl11, DE-Rs1, DE-105, DE-14, DE-Ch1 |
| issn | 0305-1048, 1362-4962 |
| issn_str_mv | 0305-1048, 1362-4962 |
| language | English |
| last_indexed | 2024-03-01T17:35:33.859Z |
| match_str | shulman2019celltypespecificanalysisofalternativepolyadenylationusingsinglecelltranscriptomicsdata |
| mega_collection | Oxford University Press (OUP) (CrossRef) |
| physical | 10027-10039 |
| publishDate | 2019 |
| publishDateSort | 2019 |
| publisher | Oxford University Press (OUP) |
| record_format | ai |
| recordtype | ai |
| series | Nucleic Acids Research |
| source_id | 49 |
| spelling | Shulman, Eldad David Elkon, Ran 0305-1048 1362-4962 Oxford University Press (OUP) Genetics http://dx.doi.org/10.1093/nar/gkz781 <jats:title>Abstract</jats:title><jats:p>Alternative polyadenylation (APA) is emerging as an important layer of gene regulation because the majority of mammalian protein-coding genes contain multiple polyadenylation (pA) sites in their 3′ UTR. By alteration of 3′ UTR length, APA can considerably affect post-transcriptional gene regulation. Yet, our understanding of APA remains rudimentary. Novel single-cell RNA sequencing (scRNA-seq) techniques allow molecular characterization of different cell types to an unprecedented degree. Notably, the most popular scRNA-seq protocols specifically sequence the 3′ end of transcripts. Building on this property, we implemented a method for analysing patterns of APA regulation from such data. Analyzing multiple datasets from diverse tissues, we identified widespread modulation of APA in different cell types resulting in global 3′ UTR shortening/lengthening and enhanced cleavage at intronic pA sites. Our results provide a proof-of-concept demonstration that the huge volume of scRNA-seq data that accumulates in the public domain offers a unique resource for the exploration of APA based on a very broad collection of cell types and biological conditions.</jats:p> Cell-type-specific analysis of alternative polyadenylation using single-cell transcriptomics data Nucleic Acids Research |
| spellingShingle | Shulman, Eldad David, Elkon, Ran, Nucleic Acids Research, Cell-type-specific analysis of alternative polyadenylation using single-cell transcriptomics data, Genetics |
| title | Cell-type-specific analysis of alternative polyadenylation using single-cell transcriptomics data |
| title_full | Cell-type-specific analysis of alternative polyadenylation using single-cell transcriptomics data |
| title_fullStr | Cell-type-specific analysis of alternative polyadenylation using single-cell transcriptomics data |
| title_full_unstemmed | Cell-type-specific analysis of alternative polyadenylation using single-cell transcriptomics data |
| title_short | Cell-type-specific analysis of alternative polyadenylation using single-cell transcriptomics data |
| title_sort | cell-type-specific analysis of alternative polyadenylation using single-cell transcriptomics data |
| title_unstemmed | Cell-type-specific analysis of alternative polyadenylation using single-cell transcriptomics data |
| topic | Genetics |
| url | http://dx.doi.org/10.1093/nar/gkz781 |