Transcription and splicing dynamics during early Drosophila development

Detalhes bibliográficos
Autor(a) principal: Prudêncio, Pedro
Data de Publicação: 2022
Outros Autores: Savisaar, Rosina, Rebelo, Kenny, Martinho, Rui Goncalo, Carmo-Fonseca, Maria
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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spelling 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
instname_str Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron_str RCAAP
institution RCAAP
reponame_str Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
collection Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
repository.name.fl_str_mv Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
repository.mail.fl_str_mv
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