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Detecting haplotype-specific transcript variation in long reads with FLAIR2

BACKGROUND: RNA-Seq has brought forth significant discoveries regarding aberrations in RNA processing, implicating these RNA variants in a variety of diseases. Aberrant splicing and single nucleotide variants in RNA have been demonstrated to alter transcript stability, localization, and function. In...

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Autores principales: Tang, Alison D., Hrabeta-Robinson, Eva, Volden, Roger, Vollmers, Christopher, Brooks, Angela N.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10312636/
https://www.ncbi.nlm.nih.gov/pubmed/37398362
http://dx.doi.org/10.1101/2023.06.09.544396
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author Tang, Alison D.
Hrabeta-Robinson, Eva
Volden, Roger
Vollmers, Christopher
Brooks, Angela N.
author_facet Tang, Alison D.
Hrabeta-Robinson, Eva
Volden, Roger
Vollmers, Christopher
Brooks, Angela N.
author_sort Tang, Alison D.
collection PubMed
description BACKGROUND: RNA-Seq has brought forth significant discoveries regarding aberrations in RNA processing, implicating these RNA variants in a variety of diseases. Aberrant splicing and single nucleotide variants in RNA have been demonstrated to alter transcript stability, localization, and function. In particular, the upregulation of ADAR, an enzyme which mediates adenosine-to-inosine editing, has been previously linked to an increase in the invasiveness of lung ADC cells and associated with splicing regulation. Despite the functional importance of studying splicing and SNVs, short read RNA-Seq has limited the community’s ability to interrogate both forms of RNA variation simultaneously. RESULTS: We employed long-read technology to obtain full-length transcript sequences, elucidating cis-effects of variants on splicing changes at a single molecule level. We have developed a computational workflow that augments FLAIR, a tool that calls isoform models expressed in long-read data, to integrate RNA variant calls with the associated isoforms that bear them. We generated nanopore data with high sequence accuracy of H1975 lung adenocarcinoma cells with and without knockdown of ADAR. We applied our workflow to identify key inosine-isoform associations to help clarify the prominence of ADAR in tumorigenesis. CONCLUSIONS: Ultimately, we find that a long-read approach provides valuable insight toward characterizing the relationship between RNA variants and splicing patterns.
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spelling pubmed-103126362023-07-01 Detecting haplotype-specific transcript variation in long reads with FLAIR2 Tang, Alison D. Hrabeta-Robinson, Eva Volden, Roger Vollmers, Christopher Brooks, Angela N. bioRxiv Article BACKGROUND: RNA-Seq has brought forth significant discoveries regarding aberrations in RNA processing, implicating these RNA variants in a variety of diseases. Aberrant splicing and single nucleotide variants in RNA have been demonstrated to alter transcript stability, localization, and function. In particular, the upregulation of ADAR, an enzyme which mediates adenosine-to-inosine editing, has been previously linked to an increase in the invasiveness of lung ADC cells and associated with splicing regulation. Despite the functional importance of studying splicing and SNVs, short read RNA-Seq has limited the community’s ability to interrogate both forms of RNA variation simultaneously. RESULTS: We employed long-read technology to obtain full-length transcript sequences, elucidating cis-effects of variants on splicing changes at a single molecule level. We have developed a computational workflow that augments FLAIR, a tool that calls isoform models expressed in long-read data, to integrate RNA variant calls with the associated isoforms that bear them. We generated nanopore data with high sequence accuracy of H1975 lung adenocarcinoma cells with and without knockdown of ADAR. We applied our workflow to identify key inosine-isoform associations to help clarify the prominence of ADAR in tumorigenesis. CONCLUSIONS: Ultimately, we find that a long-read approach provides valuable insight toward characterizing the relationship between RNA variants and splicing patterns. Cold Spring Harbor Laboratory 2023-06-12 /pmc/articles/PMC10312636/ /pubmed/37398362 http://dx.doi.org/10.1101/2023.06.09.544396 Text en https://creativecommons.org/licenses/by/4.0/This work is licensed under a Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/) , which allows reusers to distribute, remix, adapt, and build upon the material in any medium or format, so long as attribution is given to the creator. The license allows for commercial use.
spellingShingle Article
Tang, Alison D.
Hrabeta-Robinson, Eva
Volden, Roger
Vollmers, Christopher
Brooks, Angela N.
Detecting haplotype-specific transcript variation in long reads with FLAIR2
title Detecting haplotype-specific transcript variation in long reads with FLAIR2
title_full Detecting haplotype-specific transcript variation in long reads with FLAIR2
title_fullStr Detecting haplotype-specific transcript variation in long reads with FLAIR2
title_full_unstemmed Detecting haplotype-specific transcript variation in long reads with FLAIR2
title_short Detecting haplotype-specific transcript variation in long reads with FLAIR2
title_sort detecting haplotype-specific transcript variation in long reads with flair2
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10312636/
https://www.ncbi.nlm.nih.gov/pubmed/37398362
http://dx.doi.org/10.1101/2023.06.09.544396
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