Transcription and splicing dynamics during early Drosophila development
Autor(a) principal: | |
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Data de Publicação: | 2022 |
Outros Autores: | , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | http://hdl.handle.net/10451/55079 |
Resumo: | © 2022 Prudêncio et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society. This article, published in RNA, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/. |
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Transcription and splicing dynamics during early Drosophila developmentDrosophila melanogaster embryoNET-seqTranscription terminationSplicing kinetics© 2022 Prudêncio et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society. This article, published in RNA, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.Widespread cotranscriptional splicing has been demonstrated from yeast to human. However, most studies to date addressing the kinetics of splicing relative to transcription used either Saccharomyces cerevisiae or metazoan cultured cell lines. Here, we adapted native elongating transcript sequencing technology (NET-seq) to measure cotranscriptional splicing dynamics during the early developmental stages of Drosophila melanogaster embryos. Our results reveal the position of RNA polymerase II (Pol II) when both canonical and recursive splicing occur. We found heterogeneity in splicing dynamics, with some RNAs spliced immediately after intron transcription, whereas for other transcripts no splicing was observed over the first 100 nt of the downstream exon. Introns that show splicing completion before Pol II has reached the end of the downstream exon are necessarily intron-defined. We studied the splicing dynamics of both nascent pre-mRNAs transcribed in the early embryo, which have few and short introns, as well as pre-mRNAs transcribed later in embryonic development, which contain multiple long introns. As expected, we found a relationship between the proportion of spliced reads and intron size. However, intron definition was observed at all intron sizes. We further observed that genes transcribed in the early embryo tend to be isolated in the genome whereas genes transcribed later are often overlapped by a neighboring convergent gene. In isolated genes, transcription termination occurred soon after the polyadenylation site, while in overlapped genes, Pol II persisted associated with the DNA template after cleavage and polyadenylation of the nascent transcript. Taken together, our data unravel novel dynamic features of Pol II transcription and splicing in the developing Drosophila embryo.This work was supported by funding to M.C.-F. (Fundação para a Ciência e Tecnologia, FCT/Ministério da Ciência, Tecnologia e Ensino Superior - Fundos do Orçamento de Estado [UIDB/50005/2020], and FCT/ FEDER/POR Lisboa 2020, Programa Operacional Regional de Lisboa PORTUGAL 2020, grant LISBOA-01-0145-FEDER-016394) and to R.G.M (FCT grant PTDC/BIA-BID/28441/2017). P.P. was a recipient of an FCT fellowship (SFRH/BD/109689/2015). R.S. was a recipient of an EMBO Long-Term Fellowship (EMBO ALTF 101-2019). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreements no. 842695 (Marie Skłodowska- Curie Actions) and no. 857119 (RiboMed)Cold Spring Harbor Laboratory PressRepositório da Universidade de LisboaPrudêncio, PedroSavisaar, RosinaRebelo, KennyMartinho, Rui GoncaloCarmo-Fonseca, Maria2022-11-11T16:48:24Z20222022-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10451/55079engRNA (2022) 28:139–1611355-838210.1261/rna.078933.1211469-9001info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-11-08T17:01:50Zoai:repositorio.ul.pt:10451/55079Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T22:05:47.018020Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
Transcription and splicing dynamics during early Drosophila development |
title |
Transcription and splicing dynamics during early Drosophila development |
spellingShingle |
Transcription and splicing dynamics during early Drosophila development Prudêncio, Pedro Drosophila melanogaster embryo NET-seq Transcription termination Splicing kinetics |
title_short |
Transcription and splicing dynamics during early Drosophila development |
title_full |
Transcription and splicing dynamics during early Drosophila development |
title_fullStr |
Transcription and splicing dynamics during early Drosophila development |
title_full_unstemmed |
Transcription and splicing dynamics during early Drosophila development |
title_sort |
Transcription and splicing dynamics during early Drosophila development |
author |
Prudêncio, Pedro |
author_facet |
Prudêncio, Pedro Savisaar, Rosina Rebelo, Kenny Martinho, Rui Goncalo Carmo-Fonseca, Maria |
author_role |
author |
author2 |
Savisaar, Rosina Rebelo, Kenny Martinho, Rui Goncalo Carmo-Fonseca, Maria |
author2_role |
author author author author |
dc.contributor.none.fl_str_mv |
Repositório da Universidade de Lisboa |
dc.contributor.author.fl_str_mv |
Prudêncio, Pedro Savisaar, Rosina Rebelo, Kenny Martinho, Rui Goncalo Carmo-Fonseca, Maria |
dc.subject.por.fl_str_mv |
Drosophila melanogaster embryo NET-seq Transcription termination Splicing kinetics |
topic |
Drosophila melanogaster embryo NET-seq Transcription termination Splicing kinetics |
description |
© 2022 Prudêncio et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society. This article, published in RNA, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/. |
publishDate |
2022 |
dc.date.none.fl_str_mv |
2022-11-11T16:48:24Z 2022 2022-01-01T00:00:00Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/10451/55079 |
url |
http://hdl.handle.net/10451/55079 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
RNA (2022) 28:139–161 1355-8382 10.1261/rna.078933.121 1469-9001 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.publisher.none.fl_str_mv |
Cold Spring Harbor Laboratory Press |
publisher.none.fl_str_mv |
Cold Spring Harbor Laboratory Press |
dc.source.none.fl_str_mv |
reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
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Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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RCAAP |
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RCAAP |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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1799134610052874240 |