Advances in Approaches to Study Chromatin-Mediated Epigenetic Memory

Yuan Yao; Qing Wen; Tianjun Zhang; Chuanhe Yu; Kui Ming Chan; Haiyun Gan

doi:10.1021/acssynbio.1c00394

Advances in Approaches to Study Chromatin-Mediated Epigenetic Memory

Yuan Yao, Qing Wen, Tianjun Zhang, Chuanhe Yu, Kui Ming Chan, Haiyun Gan

Research output: Contribution to journal › Review article › peer-review

3 Scopus citations

Abstract

Chromatin structure contains critical epigenetic information in various forms, such as histone post-translational modifications (PTMs). The deposition of certain histone PTMs can remodel the chromatin structure, resulting in gene expression alteration. The epigenetic information carried by histone PTMs could be inherited by daughter cells to maintain the gene expression status. Recently, studies revealed that several conserved replisome proteins regulate the recycling of parental histones carrying epigenetic information in Saccharomyces cerevisiae. Hence, the proper recycling and deposition of parental histones onto newly synthesized DNA strands is presumed to be essential for epigenetic inheritance. Here, we first reviewed the fundamental mechanisms of epigenetic modification establishment and maintenance discovered within fungal models. Next, we discussed the functions of parental histone chaperones and the potential impacts of the parental histone recycling process on heterochromatin-mediated transcriptional silencing inheritance. Subsequently, we summarized novel synthetic biology approaches developed to analyze individual epigenetic components during epigenetic inheritance in fungal and mammalian systems. These newly emerged research paradigms enable us to dissect epigenetic systems in a bottom-up manner. Furthermore, we highlighted the approaches developed in this emerging field and discussed the potential applications of these engineered regulators to building synthetic epigenetic systems.

Original language	English (US)
Pages (from-to)	16-25
Number of pages	10
Journal	ACS Synthetic Biology
Volume	11
Issue number	1
DOIs	https://doi.org/10.1021/acssynbio.1c00394
State	Published - Jan 21 2022

Bibliographical note

Funding Information:
This work was supported by a grant from the National Key R&D Program of China (Grant No. 2019YFA0903803 for H.G.), the Major Program of National Natural Science Foundation of China (Grant No. 32090031 for H.G.), the Strategic Priority Research Program of the Chinese Academy of Science (No. XDPB18 for H.G.), the General program of National Natural Science Foundation of China (Grant No. 32070610 for H.G.), the Guangdong Province Fund for Distinguished Young Scholars (No. 21050001099 for H.G.), and National Natural Science Foundation of China (Grant No. 32101178 for Y.Y.; Grant No. 32000580 for Q.W.), and NIH Grant (R01GM130588 for C.Y.),

Funding Information:
The authors acknowledge the support from Guangdong Provincial Key Laboratory of Synthetic Genomics (2019B030301006) and Shenzhen Key Laboratory of Synthetic Genomics (ZDSYS201802061806209) for providing access permission to a database of scientific journals.

Publisher Copyright:
© 2021 American Chemical Society

Keywords

epigenetic inheritance
epigenome editing
fungi
heterochromatin
synthetic epigenetics

PubMed: MeSH publication types

Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1021/acssynbio.1c00394

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title = "Advances in Approaches to Study Chromatin-Mediated Epigenetic Memory",

abstract = "Chromatin structure contains critical epigenetic information in various forms, such as histone post-translational modifications (PTMs). The deposition of certain histone PTMs can remodel the chromatin structure, resulting in gene expression alteration. The epigenetic information carried by histone PTMs could be inherited by daughter cells to maintain the gene expression status. Recently, studies revealed that several conserved replisome proteins regulate the recycling of parental histones carrying epigenetic information in Saccharomyces cerevisiae. Hence, the proper recycling and deposition of parental histones onto newly synthesized DNA strands is presumed to be essential for epigenetic inheritance. Here, we first reviewed the fundamental mechanisms of epigenetic modification establishment and maintenance discovered within fungal models. Next, we discussed the functions of parental histone chaperones and the potential impacts of the parental histone recycling process on heterochromatin-mediated transcriptional silencing inheritance. Subsequently, we summarized novel synthetic biology approaches developed to analyze individual epigenetic components during epigenetic inheritance in fungal and mammalian systems. These newly emerged research paradigms enable us to dissect epigenetic systems in a bottom-up manner. Furthermore, we highlighted the approaches developed in this emerging field and discussed the potential applications of these engineered regulators to building synthetic epigenetic systems.",

keywords = "epigenetic inheritance, epigenome editing, fungi, heterochromatin, synthetic epigenetics",

author = "Yuan Yao and Qing Wen and Tianjun Zhang and Chuanhe Yu and Chan, {Kui Ming} and Haiyun Gan",

note = "Funding Information: This work was supported by a grant from the National Key R&D Program of China (Grant No. 2019YFA0903803 for H.G.), the Major Program of National Natural Science Foundation of China (Grant No. 32090031 for H.G.), the Strategic Priority Research Program of the Chinese Academy of Science (No. XDPB18 for H.G.), the General program of National Natural Science Foundation of China (Grant No. 32070610 for H.G.), the Guangdong Province Fund for Distinguished Young Scholars (No. 21050001099 for H.G.), and National Natural Science Foundation of China (Grant No. 32101178 for Y.Y.; Grant No. 32000580 for Q.W.), and NIH Grant (R01GM130588 for C.Y.), Funding Information: The authors acknowledge the support from Guangdong Provincial Key Laboratory of Synthetic Genomics (2019B030301006) and Shenzhen Key Laboratory of Synthetic Genomics (ZDSYS201802061806209) for providing access permission to a database of scientific journals. Publisher Copyright: {\textcopyright} 2021 American Chemical Society",

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doi = "10.1021/acssynbio.1c00394",

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T1 - Advances in Approaches to Study Chromatin-Mediated Epigenetic Memory

AU - Yao, Yuan

AU - Wen, Qing

AU - Zhang, Tianjun

AU - Yu, Chuanhe

AU - Chan, Kui Ming

AU - Gan, Haiyun

N1 - Funding Information: This work was supported by a grant from the National Key R&D Program of China (Grant No. 2019YFA0903803 for H.G.), the Major Program of National Natural Science Foundation of China (Grant No. 32090031 for H.G.), the Strategic Priority Research Program of the Chinese Academy of Science (No. XDPB18 for H.G.), the General program of National Natural Science Foundation of China (Grant No. 32070610 for H.G.), the Guangdong Province Fund for Distinguished Young Scholars (No. 21050001099 for H.G.), and National Natural Science Foundation of China (Grant No. 32101178 for Y.Y.; Grant No. 32000580 for Q.W.), and NIH Grant (R01GM130588 for C.Y.), Funding Information: The authors acknowledge the support from Guangdong Provincial Key Laboratory of Synthetic Genomics (2019B030301006) and Shenzhen Key Laboratory of Synthetic Genomics (ZDSYS201802061806209) for providing access permission to a database of scientific journals. Publisher Copyright: © 2021 American Chemical Society

PY - 2022/1/21

Y1 - 2022/1/21

N2 - Chromatin structure contains critical epigenetic information in various forms, such as histone post-translational modifications (PTMs). The deposition of certain histone PTMs can remodel the chromatin structure, resulting in gene expression alteration. The epigenetic information carried by histone PTMs could be inherited by daughter cells to maintain the gene expression status. Recently, studies revealed that several conserved replisome proteins regulate the recycling of parental histones carrying epigenetic information in Saccharomyces cerevisiae. Hence, the proper recycling and deposition of parental histones onto newly synthesized DNA strands is presumed to be essential for epigenetic inheritance. Here, we first reviewed the fundamental mechanisms of epigenetic modification establishment and maintenance discovered within fungal models. Next, we discussed the functions of parental histone chaperones and the potential impacts of the parental histone recycling process on heterochromatin-mediated transcriptional silencing inheritance. Subsequently, we summarized novel synthetic biology approaches developed to analyze individual epigenetic components during epigenetic inheritance in fungal and mammalian systems. These newly emerged research paradigms enable us to dissect epigenetic systems in a bottom-up manner. Furthermore, we highlighted the approaches developed in this emerging field and discussed the potential applications of these engineered regulators to building synthetic epigenetic systems.

AB - Chromatin structure contains critical epigenetic information in various forms, such as histone post-translational modifications (PTMs). The deposition of certain histone PTMs can remodel the chromatin structure, resulting in gene expression alteration. The epigenetic information carried by histone PTMs could be inherited by daughter cells to maintain the gene expression status. Recently, studies revealed that several conserved replisome proteins regulate the recycling of parental histones carrying epigenetic information in Saccharomyces cerevisiae. Hence, the proper recycling and deposition of parental histones onto newly synthesized DNA strands is presumed to be essential for epigenetic inheritance. Here, we first reviewed the fundamental mechanisms of epigenetic modification establishment and maintenance discovered within fungal models. Next, we discussed the functions of parental histone chaperones and the potential impacts of the parental histone recycling process on heterochromatin-mediated transcriptional silencing inheritance. Subsequently, we summarized novel synthetic biology approaches developed to analyze individual epigenetic components during epigenetic inheritance in fungal and mammalian systems. These newly emerged research paradigms enable us to dissect epigenetic systems in a bottom-up manner. Furthermore, we highlighted the approaches developed in this emerging field and discussed the potential applications of these engineered regulators to building synthetic epigenetic systems.

KW - epigenetic inheritance

KW - epigenome editing

KW - fungi

KW - heterochromatin

KW - synthetic epigenetics

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DO - 10.1021/acssynbio.1c00394

M3 - Review article

C2 - 34965084

AN - SCOPUS:85122723941

SN - 2161-5063

VL - 11

SP - 16

EP - 25

JO - ACS Synthetic Biology

JF - ACS Synthetic Biology

IS - 1

ER -

Advances in Approaches to Study Chromatin-Mediated Epigenetic Memory

Abstract

Bibliographical note

Keywords

PubMed: MeSH publication types

UN SDGs

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