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Tuning methylation-dependent silencing dynamics by synthetic modulation of CpG density

Methylation of cytosines in CG dinucleotides (CpGs) within promoters has been shown to lead to gene silencing in mammals in natural contexts. Recently, engineered recruitment of methyltransferases (DNMTs) at specific loci was shown to be sufficient to silence synthetic and endogenous gene expression...

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Autores principales: Ma, Yitong, Budde, Mark W., Zhu, Junqin, Elowitz, Michael B.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10312471/
https://www.ncbi.nlm.nih.gov/pubmed/37398290
http://dx.doi.org/10.1101/2023.05.30.542205
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author Ma, Yitong
Budde, Mark W.
Zhu, Junqin
Elowitz, Michael B.
author_facet Ma, Yitong
Budde, Mark W.
Zhu, Junqin
Elowitz, Michael B.
author_sort Ma, Yitong
collection PubMed
description Methylation of cytosines in CG dinucleotides (CpGs) within promoters has been shown to lead to gene silencing in mammals in natural contexts. Recently, engineered recruitment of methyltransferases (DNMTs) at specific loci was shown to be sufficient to silence synthetic and endogenous gene expression through this mechanism. A critical parameter for DNA methylation-based silencing is the distribution of CpGs within the target promoter. However, how the number or density of CpGs in the target promoter affects the dynamics of silencing by DNMT recruitment has remained unclear. Here we constructed a library of promoters with systematically varying CpG content, and analyzed the rate of silencing in response to recruitment of DNMT. We observed a tight correlation between silencing rate and CpG content. Further, methylation-specific analysis revealed a constant accumulation rate of methylation at the promoter after DNMT recruitment. We identified a single CpG site between TATA box and transcription start site (TSS) that accounted for a substantial part of the difference in silencing rates between promoters with differing CpG content, indicating that certain residues play disproportionate roles in controlling silencing. Together, these results provide a library of promoters for synthetic epigenetic and gene regulation applications, as well as insights into the regulatory link between CpG content and silencing rate.
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spelling pubmed-103124712023-07-01 Tuning methylation-dependent silencing dynamics by synthetic modulation of CpG density Ma, Yitong Budde, Mark W. Zhu, Junqin Elowitz, Michael B. bioRxiv Article Methylation of cytosines in CG dinucleotides (CpGs) within promoters has been shown to lead to gene silencing in mammals in natural contexts. Recently, engineered recruitment of methyltransferases (DNMTs) at specific loci was shown to be sufficient to silence synthetic and endogenous gene expression through this mechanism. A critical parameter for DNA methylation-based silencing is the distribution of CpGs within the target promoter. However, how the number or density of CpGs in the target promoter affects the dynamics of silencing by DNMT recruitment has remained unclear. Here we constructed a library of promoters with systematically varying CpG content, and analyzed the rate of silencing in response to recruitment of DNMT. We observed a tight correlation between silencing rate and CpG content. Further, methylation-specific analysis revealed a constant accumulation rate of methylation at the promoter after DNMT recruitment. We identified a single CpG site between TATA box and transcription start site (TSS) that accounted for a substantial part of the difference in silencing rates between promoters with differing CpG content, indicating that certain residues play disproportionate roles in controlling silencing. Together, these results provide a library of promoters for synthetic epigenetic and gene regulation applications, as well as insights into the regulatory link between CpG content and silencing rate. Cold Spring Harbor Laboratory 2023-06-01 /pmc/articles/PMC10312471/ /pubmed/37398290 http://dx.doi.org/10.1101/2023.05.30.542205 Text en https://creativecommons.org/licenses/by-nc-nd/4.0/This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (https://creativecommons.org/licenses/by-nc-nd/4.0/) , which allows reusers to copy and distribute the material in any medium or format in unadapted form only, for noncommercial purposes only, and only so long as attribution is given to the creator.
spellingShingle Article
Ma, Yitong
Budde, Mark W.
Zhu, Junqin
Elowitz, Michael B.
Tuning methylation-dependent silencing dynamics by synthetic modulation of CpG density
title Tuning methylation-dependent silencing dynamics by synthetic modulation of CpG density
title_full Tuning methylation-dependent silencing dynamics by synthetic modulation of CpG density
title_fullStr Tuning methylation-dependent silencing dynamics by synthetic modulation of CpG density
title_full_unstemmed Tuning methylation-dependent silencing dynamics by synthetic modulation of CpG density
title_short Tuning methylation-dependent silencing dynamics by synthetic modulation of CpG density
title_sort tuning methylation-dependent silencing dynamics by synthetic modulation of cpg density
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10312471/
https://www.ncbi.nlm.nih.gov/pubmed/37398290
http://dx.doi.org/10.1101/2023.05.30.542205
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