Unveiling co-transcriptional splicing kinetics using novel nascent transcriptomic techniques

Bibliographic Details
Main Author: Monteiro, Ana Pereira de Brito Líbano
Publication Date: 2023
Format: Master thesis
Language: eng
Source: Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
Download full: http://hdl.handle.net/10451/59248
Summary: Tese de mestrado, Bioinformática e Biologia Computacional, 2023, Universidade de Lisboa, Faculdade de Ciências
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spelling Unveiling co-transcriptional splicing kinetics using novel nascent transcriptomic techniquesSplicing co-transcricionalmammalian native elongation transcript sequencing (mNET-seq)carboxyl terminal domain da polymerase II (Pol II CTD)inibição da transcriçãofosforilação da Tirosina 1Teses de mestrado - 2023Departamento de InformáticaTese de mestrado, Bioinformática e Biologia Computacional, 2023, Universidade de Lisboa, Faculdade de CiênciasMost RNA splicing – the excision of non-coding regions within precursor messenger RNA (mRNA) molecules – happens at the nascent moment, when the multiprotein complex RNA Polymerase II (Pol II) is synthesizing the new RNA molecules. Post-translational phosphorylations on the C-terminal domain (CTD) of the biggest Pol II subunit have been indicated as an inducer of different transcriptional and processivity moments. However, how a temporary inhibition of transcription influences these dynamics is still largely unexplored. In this study, a temporary transcription inhibition was promoted in Hela cells with the reversible drug 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB). To analyse co-transcriptional splicing, it was employed the mammalian native elongation transcript sequencing (mNET-seq) technique, that isolates the latest transcribed nucleotides from nascent pre-mRNAs, in a Pol II CTD-specific manner. The results of this work showed that there was a decrease of co-transcriptional splicing after treating cells with DRB. 47% of exons before DRB had splicing intermediates peaks – indicative of splicing first reaction – but only ~10% had these peaks 30 minutes after washing DRB. Splicing ratio distribution also shifted towards 0 after DRB treatment. It was also detected an increase of CTD Tyrosine 1 phosphorylation (Y1P) during and after the treatment. The absence of spliceosome components in Y1P elongation complex and the low levels of splicing signals in nascent RNA from Pol II Y1P suggest that this phosphorylation might not be associate with co-transcriptional splicing. This could explain the decrease observed after transcription restart. The association of CTD Serine 5 phosphorylation with splicing, discovered in previous studies, was also identified in these analyses, and barely affected by the DRB treatment. To conclude, these results suggest that higher Y1P levels inhibit co-transcription splicing, although further experiments are necessary to discriminate its effect from the influence of S5P.Fonseca, Maria CarmoCouto, Francisco José MoreiraRepositório da Universidade de LisboaMonteiro, Ana Pereira de Brito Líbano202320232026-02-13T00:00:00Z2023-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/masterThesisapplication/pdfhttp://hdl.handle.net/10451/59248TID:203485629enginfo:eu-repo/semantics/embargoedAccessreponame:Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)instname:FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologiainstacron:RCAAP2025-03-17T15:01:09Zoai:repositorio.ulisboa.pt:10451/59248Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireinfo@rcaap.ptopendoar:https://opendoar.ac.uk/repository/71602025-05-29T03:31:44.620794Repositórios Científicos de Acesso Aberto de Portugal (RCAAP) - FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologiafalse
dc.title.none.fl_str_mv Unveiling co-transcriptional splicing kinetics using novel nascent transcriptomic techniques
title Unveiling co-transcriptional splicing kinetics using novel nascent transcriptomic techniques
spellingShingle Unveiling co-transcriptional splicing kinetics using novel nascent transcriptomic techniques
Monteiro, Ana Pereira de Brito Líbano
Splicing co-transcricional
mammalian native elongation transcript sequencing (mNET-seq)
carboxyl terminal domain da polymerase II (Pol II CTD)
inibição da transcrição
fosforilação da Tirosina 1
Teses de mestrado - 2023
Departamento de Informática
title_short Unveiling co-transcriptional splicing kinetics using novel nascent transcriptomic techniques
title_full Unveiling co-transcriptional splicing kinetics using novel nascent transcriptomic techniques
title_fullStr Unveiling co-transcriptional splicing kinetics using novel nascent transcriptomic techniques
title_full_unstemmed Unveiling co-transcriptional splicing kinetics using novel nascent transcriptomic techniques
title_sort Unveiling co-transcriptional splicing kinetics using novel nascent transcriptomic techniques
author Monteiro, Ana Pereira de Brito Líbano
author_facet Monteiro, Ana Pereira de Brito Líbano
author_role author
dc.contributor.none.fl_str_mv Fonseca, Maria Carmo
Couto, Francisco José Moreira
Repositório da Universidade de Lisboa
dc.contributor.author.fl_str_mv Monteiro, Ana Pereira de Brito Líbano
dc.subject.por.fl_str_mv Splicing co-transcricional
mammalian native elongation transcript sequencing (mNET-seq)
carboxyl terminal domain da polymerase II (Pol II CTD)
inibição da transcrição
fosforilação da Tirosina 1
Teses de mestrado - 2023
Departamento de Informática
topic Splicing co-transcricional
mammalian native elongation transcript sequencing (mNET-seq)
carboxyl terminal domain da polymerase II (Pol II CTD)
inibição da transcrição
fosforilação da Tirosina 1
Teses de mestrado - 2023
Departamento de Informática
description Tese de mestrado, Bioinformática e Biologia Computacional, 2023, Universidade de Lisboa, Faculdade de Ciências
publishDate 2023
dc.date.none.fl_str_mv 2023
2023
2023-01-01T00:00:00Z
2026-02-13T00:00:00Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/masterThesis
format masterThesis
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://hdl.handle.net/10451/59248
TID:203485629
url http://hdl.handle.net/10451/59248
identifier_str_mv TID:203485629
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/embargoedAccess
eu_rights_str_mv embargoedAccess
dc.format.none.fl_str_mv application/pdf
dc.source.none.fl_str_mv reponame:Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
instname:FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologia
instacron:RCAAP
instname_str FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologia
instacron_str RCAAP
institution RCAAP
reponame_str Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
collection Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
repository.name.fl_str_mv Repositórios Científicos de Acesso Aberto de Portugal (RCAAP) - FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologia
repository.mail.fl_str_mv info@rcaap.pt
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