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Transcription of intragenic CpG islands influences spatiotemporal host gene pre-mRNA processing

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Transcription of intragenic CpG islands influences spatiotemporal host gene pre-mRNA processing. / Amante, Samuele; Montibus, Bertille; Cowley, Michael et al.

In: Nucleic Acids Research, Vol. 48, No. 15, 04.09.2020, p. 8349-8359.

Research output: Contribution to journalArticlepeer-review

Harvard

Amante, S, Montibus, B, Cowley, M, Barkas, N, Setiadi, J, Saadeh, H, Giemza, J, Contreras Castillo, S, Fleischanderl, K, Schulz, R & Oakey, R 2020, 'Transcription of intragenic CpG islands influences spatiotemporal host gene pre-mRNA processing', Nucleic Acids Research, vol. 48, no. 15, pp. 8349-8359. https://doi.org/10.1093/nar/gkaa556

APA

Amante, S., Montibus, B., Cowley, M., Barkas, N., Setiadi, J., Saadeh, H., Giemza, J., Contreras Castillo, S., Fleischanderl, K., Schulz, R., & Oakey, R. (2020). Transcription of intragenic CpG islands influences spatiotemporal host gene pre-mRNA processing. Nucleic Acids Research, 48(15), 8349-8359. https://doi.org/10.1093/nar/gkaa556

Vancouver

Amante S, Montibus B, Cowley M, Barkas N, Setiadi J, Saadeh H et al. Transcription of intragenic CpG islands influences spatiotemporal host gene pre-mRNA processing. Nucleic Acids Research. 2020 Sep 4;48(15):8349-8359. https://doi.org/10.1093/nar/gkaa556

Author

Amante, Samuele ; Montibus, Bertille ; Cowley, Michael et al. / Transcription of intragenic CpG islands influences spatiotemporal host gene pre-mRNA processing. In: Nucleic Acids Research. 2020 ; Vol. 48, No. 15. pp. 8349-8359.

Bibtex Download

@article{62c59be8c0934f32b48dea6058788207,
title = "Transcription of intragenic CpG islands influences spatiotemporal host gene pre-mRNA processing",
abstract = "Alternative splicing (AS) and alternative polyadenylation (APA) generate diverse transcripts in mammalian genomes during development and differentiation. Epigenetic marks such as trimethylation of histone H3 lysine 36 (H3K36me3) and DNA methylation play a role in generating transcriptome diversity. Intragenic CpG islands (iCGIs) and their corresponding host genes exhibit dynamic epigenetic and gene expression patterns during development and between different tissues. We hypothesise that iCGI-associated H3K36me3, DNA methylation and transcription can influence host gene AS and/or APA. We investigate H3K36me3 and find that this histone mark is not a major regulator of AS or APA in our model system. Genomewide, we identify over 4000 host genes that harbour an iCGI in the mammalian genome, including both previously annotated and novel iCGI/host gene pairs. The transcriptional activity of these iCGIs is tissue- and developmental stage-specific and, for the first time, we demonstrate that the premature termination of host gene transcripts upstream of iCGIs is closely correlated with the level of iCGI transcription in a DNA-methylation independent manner. These studies suggest that iCGI transcription, rather than H3K36me3 or DNA methylation, interfere with host gene transcription and pre-mRNA processing genomewide and contributes to the spatiotemporal diversification of both the transcriptome and proteome.",
author = "Samuele Amante and Bertille Montibus and Michael Cowley and Nikolas Barkas and Jessica Setiadi and Heba Saadeh and Joanna Giemza and {Contreras Castillo}, Stephania and Karin Fleischanderl and Reiner Schulz and Rebecca Oakey",
year = "2020",
month = sep,
day = "4",
doi = "10.1093/nar/gkaa556",
language = "English",
volume = "48",
pages = "8349--8359",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford Univerity Press; Oxford",
number = "15",

}

RIS (suitable for import to EndNote) Download

TY - JOUR

T1 - Transcription of intragenic CpG islands influences spatiotemporal host gene pre-mRNA processing

AU - Amante, Samuele

AU - Montibus, Bertille

AU - Cowley, Michael

AU - Barkas, Nikolas

AU - Setiadi, Jessica

AU - Saadeh, Heba

AU - Giemza, Joanna

AU - Contreras Castillo, Stephania

AU - Fleischanderl, Karin

AU - Schulz, Reiner

AU - Oakey, Rebecca

PY - 2020/9/4

Y1 - 2020/9/4

N2 - Alternative splicing (AS) and alternative polyadenylation (APA) generate diverse transcripts in mammalian genomes during development and differentiation. Epigenetic marks such as trimethylation of histone H3 lysine 36 (H3K36me3) and DNA methylation play a role in generating transcriptome diversity. Intragenic CpG islands (iCGIs) and their corresponding host genes exhibit dynamic epigenetic and gene expression patterns during development and between different tissues. We hypothesise that iCGI-associated H3K36me3, DNA methylation and transcription can influence host gene AS and/or APA. We investigate H3K36me3 and find that this histone mark is not a major regulator of AS or APA in our model system. Genomewide, we identify over 4000 host genes that harbour an iCGI in the mammalian genome, including both previously annotated and novel iCGI/host gene pairs. The transcriptional activity of these iCGIs is tissue- and developmental stage-specific and, for the first time, we demonstrate that the premature termination of host gene transcripts upstream of iCGIs is closely correlated with the level of iCGI transcription in a DNA-methylation independent manner. These studies suggest that iCGI transcription, rather than H3K36me3 or DNA methylation, interfere with host gene transcription and pre-mRNA processing genomewide and contributes to the spatiotemporal diversification of both the transcriptome and proteome.

AB - Alternative splicing (AS) and alternative polyadenylation (APA) generate diverse transcripts in mammalian genomes during development and differentiation. Epigenetic marks such as trimethylation of histone H3 lysine 36 (H3K36me3) and DNA methylation play a role in generating transcriptome diversity. Intragenic CpG islands (iCGIs) and their corresponding host genes exhibit dynamic epigenetic and gene expression patterns during development and between different tissues. We hypothesise that iCGI-associated H3K36me3, DNA methylation and transcription can influence host gene AS and/or APA. We investigate H3K36me3 and find that this histone mark is not a major regulator of AS or APA in our model system. Genomewide, we identify over 4000 host genes that harbour an iCGI in the mammalian genome, including both previously annotated and novel iCGI/host gene pairs. The transcriptional activity of these iCGIs is tissue- and developmental stage-specific and, for the first time, we demonstrate that the premature termination of host gene transcripts upstream of iCGIs is closely correlated with the level of iCGI transcription in a DNA-methylation independent manner. These studies suggest that iCGI transcription, rather than H3K36me3 or DNA methylation, interfere with host gene transcription and pre-mRNA processing genomewide and contributes to the spatiotemporal diversification of both the transcriptome and proteome.

UR - http://www.scopus.com/inward/record.url?scp=85090491754&partnerID=8YFLogxK

U2 - 10.1093/nar/gkaa556

DO - 10.1093/nar/gkaa556

M3 - Article

VL - 48

SP - 8349

EP - 8359

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - 15

ER -

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