Epigenomes

17 pages, 1071 KiB

Open AccessEditor’s ChoiceReview

Chemical Inhibitors Targeting the Histone Lysine Demethylase Families with Potential for Drug Discovery

by Nando Dulal Das, Hideaki Niwa and Takashi Umehara

Epigenomes 2023, 7(1), 7; https://doi.org/10.3390/epigenomes7010007 - 11 Mar 2023

Cited by 8 | Viewed by 3887

The dynamic regulation of histone methylation and demethylation plays an important role in the regulation of gene expression. Aberrant expression of histone lysine demethylases has been implicated in various diseases including intractable cancers, and thus lysine demethylases serve as promising therapeutic targets. Recent [...] Read more.

The dynamic regulation of histone methylation and demethylation plays an important role in the regulation of gene expression. Aberrant expression of histone lysine demethylases has been implicated in various diseases including intractable cancers, and thus lysine demethylases serve as promising therapeutic targets. Recent studies in epigenomics and chemical biology have led to the development of a series of small-molecule demethylase inhibitors that are potent, specific, and have in vivo efficacy. In this review, we highlight emerging small-molecule inhibitors targeting the histone lysine demethylases and their progress toward drug discovery. Full article

(This article belongs to the Special Issue Epidrugs: Toward Understanding and Treating Diverse Diseases)

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16 pages, 2868 KiB

Open AccessEditor’s ChoiceReview

Nucleosome Structures Built from Highly Divergent Histones: Parasites and Giant DNA Viruses

by Shoko Sato, Mariko Dacher and Hitoshi Kurumizaka

Epigenomes 2022, 6(3), 22; https://doi.org/10.3390/epigenomes6030022 - 2 Aug 2022

Cited by 3 | Viewed by 4526

Abstract

In eukaryotes, genomic DNA is bound with histone proteins and packaged into chromatin. The nucleosome, a fundamental unit of chromatin, regulates the accessibility of DNA to enzymes involved in gene regulation. During the past few years, structural analyses of chromatin architectures have been [...] Read more.

In eukaryotes, genomic DNA is bound with histone proteins and packaged into chromatin. The nucleosome, a fundamental unit of chromatin, regulates the accessibility of DNA to enzymes involved in gene regulation. During the past few years, structural analyses of chromatin architectures have been limited to evolutionarily related organisms. The amino acid sequences of histone proteins are highly conserved from humans to yeasts, but are divergent in the deeply branching protozoan groups, including human parasites that are directly related to human health. Certain large DNA viruses, as well as archaeal organisms, contain distant homologs of eukaryotic histone proteins. The divergent sequences give rise to unique and distinct nucleosome architectures, although the fundamental principles of histone folding and DNA contact are highly conserved. In this article, we review the structures and biophysical properties of nucleosomes containing histones from the human parasites Giardia lamblia and Leishmania major, and histone-like proteins from the Marseilleviridae amoeba virus family. The presented data confirm the sharing of the overall DNA compaction system among evolutionally distant species and clarify the deviations from the species-specific nature of the nucleosome. Full article

(This article belongs to the Special Issue Chromatin Unlimited)

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13 pages, 2498 KiB

Open AccessEditor’s ChoiceReview

Making Mitotic Chromosomes in a Test Tube

by Keishi Shintomi

Epigenomes 2022, 6(3), 20; https://doi.org/10.3390/epigenomes6030020 - 20 Jul 2022

Cited by 2 | Viewed by 3535

Abstract

Mitotic chromosome assembly is an essential preparatory step for accurate transmission of the genome during cell division. During the past decades, biochemical approaches have uncovered the molecular basis of mitotic chromosomes. For example, by using cell-free assays of frog egg extracts, the condensin [...] Read more.

Mitotic chromosome assembly is an essential preparatory step for accurate transmission of the genome during cell division. During the past decades, biochemical approaches have uncovered the molecular basis of mitotic chromosomes. For example, by using cell-free assays of frog egg extracts, the condensin I complex central for the chromosome assembly process was first identified, and its functions have been intensively studied. A list of chromosome-associated proteins has been almost completed, and it is now possible to reconstitute structures resembling mitotic chromosomes with a limited number of purified factors. In this review, I introduce how far we have come in understanding the mechanism of chromosome assembly using cell-free assays and reconstitution assays, and I discuss their potential applications to solve open questions. Full article

(This article belongs to the Special Issue Chromatin Unlimited)

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32 pages, 871 KiB

Open AccessEditor’s ChoiceReview

The Transmission of Intergenerational Epigenetic Information by Sperm microRNAs

by Grace S. Lee and Colin C. Conine

Epigenomes 2022, 6(2), 12; https://doi.org/10.3390/epigenomes6020012 - 7 Apr 2022

Cited by 22 | Viewed by 6458

Abstract

Epigenetic information is transmitted from one generation to the next, modulating the phenotype of offspring non-genetically in organisms ranging from plants to mammals. For intergenerational non-genetic inheritance to occur, epigenetic information must accumulate in germ cells. The three main carriers of epigenetic information—histone [...] Read more.

Epigenetic information is transmitted from one generation to the next, modulating the phenotype of offspring non-genetically in organisms ranging from plants to mammals. For intergenerational non-genetic inheritance to occur, epigenetic information must accumulate in germ cells. The three main carriers of epigenetic information—histone post-translational modifications, DNA modifications, and RNAs—all exhibit dynamic patterns of regulation during germ cell development. For example, histone modifications and DNA methylation are extensively reprogrammed and often eliminated during germ cell maturation and after fertilization during embryogenesis. Consequently, much attention has been given to RNAs, specifically small regulatory RNAs, as carriers of inherited epigenetic information. In this review, we discuss examples in which microRNAs have been implicated as key players in transmitting paternal epigenetic information intergenerationally. Full article

(This article belongs to the Special Issue Transgenerational Epigenetic Inheritance)

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27 pages, 4243 KiB

Open AccessEditor’s ChoiceReview

Opportunities for Early Cancer Detection: The Rise of ctDNA Methylation-Based Pan-Cancer Screening Technologies

by Nicolas Constantin, Abu Ali Ibn Sina, Darren Korbie and Matt Trau

Epigenomes 2022, 6(1), 6; https://doi.org/10.3390/epigenomes6010006 - 4 Feb 2022

Cited by 18 | Viewed by 9606

Abstract

The efficiency of conventional screening programs to identify early-stage malignancies can be limited by the low number of cancers recommended for screening as well as the high cumulative false-positive rate, and associated iatrogenic burden, resulting from repeated multimodal testing. The opportunity to use [...] Read more.

The efficiency of conventional screening programs to identify early-stage malignancies can be limited by the low number of cancers recommended for screening as well as the high cumulative false-positive rate, and associated iatrogenic burden, resulting from repeated multimodal testing. The opportunity to use minimally invasive liquid biopsy testing to screen asymptomatic individuals at-risk for multiple cancers simultaneously could benefit from the aggregated diseases prevalence and a fixed specificity. Increasing both latter parameters is paramount to mediate high positive predictive value—a useful metric to evaluate a screening test accuracy and its potential harm-benefit. Thus, the use of a single test for multi-cancer early detection (stMCED) has emerged as an appealing strategy for increasing early cancer detection rate efficiency and benefit population health. A recent flurry of these stMCED technologies have been reported for clinical potential; however, their development is facing unique challenges to effectively improve clinical cost–benefit. One promising avenue is the analysis of circulating tumour DNA (ctDNA) for detecting DNA methylation biomarker fingerprints of malignancies—a hallmark of disease aetiology and progression holding the potential to be tissue- and cancer-type specific. Utilizing panels of epigenetic biomarkers could potentially help to detect earlier stages of malignancies as well as identify a tumour of origin from blood testing, useful information for follow-up clinical decision making and subsequent patient care improvement. Overall, this review collates the latest and most promising stMCED methodologies, summarizes their clinical performances, and discusses the specific requirements multi-cancer tests should meet to be successfully implemented into screening guidelines. Full article

(This article belongs to the Special Issue The Use of Epigenetic Biomarkers as Diagnostic and Therapeutic Options 2.0)

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11 pages, 707 KiB

Open AccessEditor’s ChoiceReview

Biochemical Principles in Prion-Based Inheritance

by Emily M. Dennis and David M. Garcia

Epigenomes 2022, 6(1), 4; https://doi.org/10.3390/epigenomes6010004 - 25 Jan 2022

Cited by 5 | Viewed by 5118

Abstract

Prions are proteins that can stably fold into alternative structures that frequently alter their activities. They can self-template their alternate structures and are inherited across cell divisions and generations. While they have been studied for more than four decades, their enigmatic nature has [...] Read more.

Prions are proteins that can stably fold into alternative structures that frequently alter their activities. They can self-template their alternate structures and are inherited across cell divisions and generations. While they have been studied for more than four decades, their enigmatic nature has limited their discovery. In the last decade, we have learned just how widespread they are in nature, the many beneficial phenotypes that they confer, while also learning more about their structures and modes of inheritance. Here, we provide a brief review of the biochemical principles of prion proteins, including their sequences, characteristics and structures, and what is known about how they self-template, citing examples from multiple organisms. Prion-based inheritance is the most understudied segment of epigenetics. Here, we lay a biochemical foundation and share a framework for how to define these molecules, as new examples are unearthed throughout nature. Full article

(This article belongs to the Special Issue Transgenerational Epigenetic Inheritance)

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11 pages, 651 KiB

Open AccessEditor’s ChoiceReview

The Regulation of Plant Vegetative Phase Transition and Rejuvenation: miRNAs, a Key Regulator

by Tajbir Raihan, Robert L. Geneve, Sharyn E. Perry and Carlos M. Rodriguez Lopez

Epigenomes 2021, 5(4), 24; https://doi.org/10.3390/epigenomes5040024 - 18 Oct 2021

Cited by 13 | Viewed by 5477

Abstract

In contrast to animals, adult organs in plants are not formed during embryogenesis but generated from meristematic cells as plants advance through development. Plant development involves a succession of different phenotypic stages and the transition between these stages is termed phase transition. Phase [...] Read more.

In contrast to animals, adult organs in plants are not formed during embryogenesis but generated from meristematic cells as plants advance through development. Plant development involves a succession of different phenotypic stages and the transition between these stages is termed phase transition. Phase transitions need to be tightly regulated and coordinated to ensure they occur under optimal seasonal, environmental conditions. Polycarpic perennials transition through vegetative stages and the mature, reproductive stage many times during their lifecycles and, in both perennial and annual species, environmental factors and culturing methods can reverse the otherwise unidirectional vector of plant development. Epigenetic factors regulating gene expression in response to internal cues and external (environmental) stimuli influencing the plant’s phenotype and development have been shown to control phase transitions. How developmental and environmental cues interact to epigenetically alter gene expression and influence these transitions is not well understood, and understanding this interaction is important considering the current climate change scenarios, since epigenetic maladaptation could have catastrophic consequences for perennial plants in natural and agricultural ecosystems. Here, we review studies focusing on the epigenetic regulators of the vegetative phase change and highlight how these mechanisms might act in exogenously induced plant rejuvenation and regrowth following stress. Full article

(This article belongs to the Special Issue Mechanisms of Plant Epigenome Dynamics)

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11 pages, 1328 KiB

Open AccessEditor’s ChoiceReview

Evolution of CG Methylation Maintenance Machinery in Plants

by Louis Tirot, Pauline E. Jullien and Mathieu Ingouff

Epigenomes 2021, 5(3), 19; https://doi.org/10.3390/epigenomes5030019 - 14 Sep 2021

Cited by 9 | Viewed by 4899

Abstract

Cytosine methylation is an epigenetic mark present in most eukaryotic genomes that contributes to the regulation of gene expression and the maintenance of genome stability. DNA methylation mostly occurs at CG sequences, where it is initially deposited by de novo DNA methyltransferases and [...] Read more.

Cytosine methylation is an epigenetic mark present in most eukaryotic genomes that contributes to the regulation of gene expression and the maintenance of genome stability. DNA methylation mostly occurs at CG sequences, where it is initially deposited by de novo DNA methyltransferases and propagated by maintenance DNA methyltransferases (DNMT) during DNA replication. In this review, we first summarize the mechanisms maintaining CG methylation in mammals that involve the DNA Methyltransferase 1 (DNMT1) enzyme and its cofactor, UHRF1 (Ubiquitin-like with PHD and RING Finger domain 1). We then discuss the evolutionary conservation and diversification of these two core factors in the plant kingdom and speculate on potential functions of novel homologues typically observed in land plants but not in mammals. Full article

(This article belongs to the Special Issue Mechanisms of Plant Epigenome Dynamics)

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16 pages, 1468 KiB

Open AccessEditor’s ChoiceReview

Deciphering Plant Chromatin Regulation via CRISPR/dCas9-Based Epigenome Engineering

by Annick Dubois and François Roudier

Epigenomes 2021, 5(3), 17; https://doi.org/10.3390/epigenomes5030017 - 24 Aug 2021

Cited by 10 | Viewed by 5130

Abstract

CRISPR-based epigenome editing uses dCas9 as a platform to recruit transcription or chromatin regulators at chosen loci. Despite recent and ongoing advances, the full potential of these approaches to studying chromatin functions in vivo remains challenging to exploit. In this review we discuss [...] Read more.

CRISPR-based epigenome editing uses dCas9 as a platform to recruit transcription or chromatin regulators at chosen loci. Despite recent and ongoing advances, the full potential of these approaches to studying chromatin functions in vivo remains challenging to exploit. In this review we discuss how recent progress in plants and animals provides new routes to investigate the function of chromatin regulators and address the complexity of associated regulations that are often interconnected. While efficient transcriptional engineering methodologies have been developed and can be used as tools to alter the chromatin state of a locus, examples of direct manipulation of chromatin regulators remain scarce in plants. These reports also reveal pitfalls and limitations of epigenome engineering approaches that are nevertheless informative as they are often associated with locus- and context-dependent features, which include DNA accessibility, initial chromatin and transcriptional state or cellular dynamics. Strategies implemented in different organisms to overcome and even take advantage of these limitations are highlighted, which will further improve our ability to establish the causality and hierarchy of chromatin dynamics on genome regulation. Full article

(This article belongs to the Special Issue Mechanisms of Plant Epigenome Dynamics)

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25 pages, 2035 KiB

Open AccessEditor’s ChoiceReview

Can Immune Suppression and Epigenome Regulation in Placenta Offer Novel Insights into Cancer Immune Evasion and Immunotherapy Resistance?

by Sultana Mehbuba Hossain, Chiemi F. Lynch-Sutherland, Aniruddha Chatterjee, Erin C. Macaulay and Michael R. Eccles

Epigenomes 2021, 5(3), 16; https://doi.org/10.3390/epigenomes5030016 - 25 Jul 2021

Cited by 5 | Viewed by 5732

Abstract

Cancer is the second leading cause of mortality and morbidity in the developed world. Cancer progression involves genetic and epigenetic alterations, accompanied by aggressive changes, such as increased immune evasion, onset of metastasis, and drug resistance. Similar to cancer, DNA hypomethylation, immune suppression, [...] Read more.

Cancer is the second leading cause of mortality and morbidity in the developed world. Cancer progression involves genetic and epigenetic alterations, accompanied by aggressive changes, such as increased immune evasion, onset of metastasis, and drug resistance. Similar to cancer, DNA hypomethylation, immune suppression, and invasive cell behaviours are also observed in the human placenta. Mechanisms that lead to the acquisition of invasive behaviour, immune evasion, and drug and immunotherapy resistance are presently under intense investigations to improve patient outcomes. Here, we review current knowledge regarding the similarities between immune suppression and epigenome regulation, including the expression of repetitive elements (REs), endogenous retroviruses (ERVs) and transposable elements (TEs) in cells of the placenta and in cancer, which are associated with changes in immune regulation and invasiveness. We explore whether immune suppression and epigenome regulation in placenta offers novel insights into immunotherapy resistance in cancer, and we also discuss the implications and the knowledge gaps relevant to these findings, which are rapidly being accrued in these quite disparate research fields. Finally, we discuss potential linkages between TE, ERV and RE activation and expression, regarding mechanisms of immune regulation in placenta and cancer. A greater understanding of the role of immune suppression and associated epigenome regulation in placenta could help to elucidate some comparable mechanisms operating in cancer, and identify potential new therapeutic targets for treating cancer. Full article

(This article belongs to the Special Issue Epigenetics and Immune Checkpoints)

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20 pages, 1310 KiB

Open AccessEditor’s ChoiceReview

The Contribution of Epigenetic Inheritance Processes on Age-Related Cognitive Decline and Alzheimer’s Disease

by Aina Bellver-Sanchis, Mercè Pallàs and Christian Griñán-Ferré

Epigenomes 2021, 5(2), 15; https://doi.org/10.3390/epigenomes5020015 - 18 Jun 2021

Cited by 14 | Viewed by 5169

Abstract

During the last years, epigenetic processes have emerged as important factors for many neurodegenerative diseases, such as Alzheimer’s disease (AD). These complex diseases seem to have a heritable component; however, genome-wide association studies failed to identify the genetic loci involved in the etiology. [...] Read more.

During the last years, epigenetic processes have emerged as important factors for many neurodegenerative diseases, such as Alzheimer’s disease (AD). These complex diseases seem to have a heritable component; however, genome-wide association studies failed to identify the genetic loci involved in the etiology. So, how can these changes be transmitted from one generation to the next? Answering this question would allow us to understand how the environment can affect human populations for multiple generations and explain the high prevalence of neurodegenerative diseases, such as AD. This review pays particular attention to the relationship among epigenetics, cognition, and neurodegeneration across generations, deepening the understanding of the relevance of heritability in neurodegenerative diseases. We highlight some recent examples of EI induced by experiences, focusing on their contribution of processes in learning and memory to point out new targets for therapeutic interventions. Here, we first describe the prominent role of epigenetic factors in memory processing. Then, we briefly discuss aspects of EI. Additionally, we summarize evidence of how epigenetic marks inherited by experience and/or environmental stimuli contribute to cognitive status offspring since better knowledge of EI can provide clues in the appearance and development of age-related cognitive decline and AD. Full article

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11 pages, 3932 KiB

Open AccessEditor’s ChoiceArticle

Thermal Stability Changes in Telomeric G-Quadruplex Structures Due to N⁶-Methyladenine Modification

by Ryohei Wada and Wataru Yoshida

Epigenomes 2021, 5(1), 5; https://doi.org/10.3390/epigenomes5010005 - 2 Feb 2021

Cited by 5 | Viewed by 4198

Abstract

N⁶-methyladenine modification (m⁶dA) has recently been identified in eukaryote genomic DNA. The methylation destabilizes the duplex structure when the adenine forms a Watson–Crick base pair, whereas the methylation on a terminal unpaired adenine stabilizes the duplex structure by increasing [...] Read more.

N⁶-methyladenine modification (m⁶dA) has recently been identified in eukaryote genomic DNA. The methylation destabilizes the duplex structure when the adenine forms a Watson–Crick base pair, whereas the methylation on a terminal unpaired adenine stabilizes the duplex structure by increasing the stacking interaction. In this study, the effects of m⁶dA modification on the thermal stability of four distinct telomeric G-quadruplex (G4) structures were investigated. The m⁶dA-modified telomeric oligonucleotide d[AGGG(TTAGGG)₃] that forms a basket-type G4 in Na⁺, d[(TTAGGG)₄TT] that forms a hybrid-type G4 in K⁺ (Form-2), d[AAAGGG(TTAGGG)₃AA] that forms a hybrid-type G4 in K⁺ (Form-1), and d[GGG(TTAGGG)₃T] that forms a basket-type G4 with two G-tetrads in K⁺ (Form-3) were analyzed. Circular dichroism melting analysis demonstrated that (1) A7- and A19-methylation destabilized the basket-type G4 structure that formed in Na⁺, whereas A13-methylation stabilized the structure; (2) A15-methylation stabilized the Form-2 G4 structure; (3) A15- and A21-methylations stabilized the Form-1 G4 structure; and (4) A12-methylation stabilized the Form-3 G4 structure. These results suggest that m⁶dA modifications may affect the thermal stability of human telomeric G4 structures in regulating the biological functions. Full article

(This article belongs to the Special Issue Recent Advances in Biological Methylation)

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22 pages, 1727 KiB

Open AccessEditor’s ChoiceReview

The Role of the PRMT5–SND1 Axis in Hepatocellular Carcinoma

by Tanner Wright, Yalong Wang and Mark T. Bedford

Epigenomes 2021, 5(1), 2; https://doi.org/10.3390/epigenomes5010002 - 5 Jan 2021

Cited by 10 | Viewed by 6045

Abstract

Arginine methylation is an essential post-translational modification (PTM) deposited by protein arginine methyltransferases (PRMTs) and recognized by Tudor domain-containing proteins. Of the nine mammalian PRMTs, PRMT5 is the primary enzyme responsible for the deposition of symmetric arginine methylation marks in cells. The staphylococcal [...] Read more.

Arginine methylation is an essential post-translational modification (PTM) deposited by protein arginine methyltransferases (PRMTs) and recognized by Tudor domain-containing proteins. Of the nine mammalian PRMTs, PRMT5 is the primary enzyme responsible for the deposition of symmetric arginine methylation marks in cells. The staphylococcal nuclease and Tudor domain-containing 1 (SND1) effector protein is a key reader of the marks deposited by PRMT5. Both PRMT5 and SND1 are broadly expressed and their deregulation is reported to be associated with a range of disease phenotypes, including cancer. Hepatocellular carcinoma (HCC) is an example of a cancer type that often displays elevated PRMT5 and SND1 levels, and there is evidence that hyperactivation of this axis is oncogenic. Importantly, this pathway can be tempered with small-molecule inhibitors that target PRMT5, offering a therapeutic node for cancer, such as HCC, that display high PRMT5–SND1 axis activity. Here we summarize the known activities of this writer–reader pair, with a focus on their biological roles in HCC. This will help establish a foundation for treating HCC with PRMT5 inhibitors and also identify potential biomarkers that could predict sensitivity to this type of therapy. Full article

(This article belongs to the Special Issue Recent Advances in Biological Methylation)

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