Article
Microbiology
Samuel S. Porter, Jennifer C. Liddle, Kristen Browne, Diana Pastrana, Benjamin A. Garcia, Christopher B. Buck, Matthew D. Weitzman, Alison A. McBride
Summary: Papillomaviruses package their genomes with host histones into virions, with specific histone modifications being acquired late in infection that benefit viral replication and gene expression. The viral minichromosome is enriched in posttranslational modifications associated with active chromatin, potentially aiding in evasion of detection and promoting early infection stages.
Article
Multidisciplinary Sciences
Kenneth Wu, Namrita Dhillon, Kelvin Du, Rohinton T. Kamakaka
Summary: Gene silencing in budding yeast is maintained by unacetylated nucleosomes and requires 50% to 75% acetylation for activation. The Sir4 gene is a key component in maintaining gene silencing, with even a two-fold reduction in acetyltransferases potentially leading to transcriptional silence.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Biochemistry & Molecular Biology
Lucia Lopez-Gil, Amparo Pascual-Ahuir, Markus Proft
Summary: This scientific review highlights the central importance of genomic instability in the aging process and explores the cellular and molecular changes associated with aging, as well as the genetic and epigenetic alterations that contribute to genomic instability.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Cell Biology
Paul B. Talbert, Steven Henikoff
Summary: Eukaryotic nucleosomes are organized by histones, with common histones deposited during S-phase and histone variants available throughout the cell cycle. Variants alter nucleosome structure and function, playing specialized roles in DNA repair, chromosome segregation, and transcriptional regulation.
JOURNAL OF CELL SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Dustin C. Woods, Francisco Rodriguez-Ropero, Jeff Wereszczynski
Summary: Linker histones play a crucial role in regulating chromatin structure and dynamics through their binding to nucleosomes. They increase chromatin compaction and internal stiffness, leading to stronger long-range correlations within the fiber and potential propagation of epigenetic signals. The removal of linker histones destabilizes chromatin structure and results in decreased compaction and stiffness.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Microbiology
Suffian Azizan, Shamista A. Selvarajah, Jingyi Tang, Myriam D. Jeninga, Danae Schulz, Kapil Pareek, Tamara Herr, Karen P. Day, Tania F. De Koning-Ward, Michaela Petter, Michael F. Duffy
Summary: The alternative histones Pf H2A.Z and Pf H2B.Z in Plasmodium falciparum are enriched in intergenic euchromatin and play critical roles in gene expression and chromatin structure. The acetylated forms of these histones are dynamically associated with gene expression at promoters and are antagonized by histone deacetylases at heterochromatin boundaries. These findings suggest that acetylated Pf H2A.Z and Pf H2B.Z contribute to the maintenance of chromatin structure and enable rapid adaptation to altered host environments.
Article
Biochemistry & Molecular Biology
Jose-Luis Garcia-Gimenez, Concepcion Garces, Carlos Roma-Mateo, Federico Pallardo
Summary: Epigenetic regulation of gene expression plays a crucial role in cellular response to environmental changes, but cellular imbalance can lead to pathological conditions. Oxidative stress and free radicals can influence histone modifications, affecting gene expression.
FREE RADICAL BIOLOGY AND MEDICINE
(2021)
Review
Cell Biology
Maria Luiza S. Mello
Summary: Valproic acid/sodium valproate can affect chromatin remodeling by inducing histone acetylation and altering gene expression, ultimately modulating gene expression levels.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Multidisciplinary Sciences
Hitoshi Kurumizaka
Summary: In eukaryotic cells, genomic DNA is organized into chromatin, which plays a critical role in regulating gene expression and nuclear functions. Aberrant chromatin structures can lead to various health issues. The nucleosome, as the basic repeating unit of chromatin, is highly conserved yet structurally versatile. Studying nucleosomes helps to elucidate higher-order chromatin architecture.
PROCEEDINGS OF THE JAPAN ACADEMY SERIES B-PHYSICAL AND BIOLOGICAL SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Celine Duc, Christophe Thiriet
Summary: The review focuses on the remodeling of chromatin during DNA replication in the S-phase, including the eviction of nucleosomes and the assembly of newly synthesized histones. The recycling of parental histones and the nuclear import of histones are also discussed in relation to epigenetic inheritance.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Entomology
Jean-Michel Gibert, Frederique Peronnet
Summary: Drosophila melanogaster has played a crucial role in epigenetics, studying changes in gene function inherited through mitosis or meiosis that are not due to changes in the DNA sequence. By analyzing simple phenotypes, such as bristle position or cuticle pigmentation, identification of mutated genes led to the discovery of major chromatin regulators that are often conserved in distantly related organisms.
Review
Cell Biology
Faith M. Joseph, Nicolas L. Young
Summary: Post-translational modifications (PTMs) of histones play a key role in DNA-based processes and contribute to cell differentiation and gene function by adding an extra layer of regulation. Variations in histone sequences within each family of histones expand the chromatin repertoire and provide further mechanisms for regulation and signaling. However, much remains unknown about variant-specific PTMs and their role in regulating chromatin due to limited technologies and appropriate reagents.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Shane M. Ginnard, Alyssa E. Winkler, Carlos Mellado Fritz, Tatum Bluhm, Ray Kemmer, Marisa Gilliam, Nick Butkevich, Sara Abdrabbo, Kaitlyn Bricker, Justin Feiler, Isaak Miller, Jenna Zoerman, Zeineb El-Mohri, Panida Khuansanguan, Madyson Basch, Timothy Petzold, Matthew Kostoff, Sean Konopka, Brendon Kociba, Thomas Gillis, Deborah L. Heyl, Raymond C. Trievel, Brittany N. Albaugh
Summary: UHRF1 and UHRF2 are multidomain epigenetic proteins that play critical roles in histone modifications and DNA methylation, with differences in histone binding mechanisms. UHRF2's TTD has higher affinity to H3 tail compared to PHD, while PHD has weaker interaction, providing potential avenues for selectively targeting histone binding interactions.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2022)
Article
Plant Sciences
Xi Wu, Jiena Xu, Xingnan Meng, Xue Fang, Minghui Xia, Jing Zhang, Shuqing Cao, Tingting Fan
Summary: HIS1-3 and WRKY1 oppositely modulate salt tolerance in Arabidopsis by transcriptionally regulating SOS genes, with HIS1-3 inhibiting their expression and enhancing salt tolerance, while WRKY1 inducing their expression and increasing salt sensitivity.
Review
Medicine, Research & Experimental
Raja Amir Hassan Kuchay, Asima Hassan, Yaser Rafiq Mir
Summary: Epigenetics plays a crucial role in gene expression regulation and also has an impact on eye development and progression of ocular disorders.
CURRENT MOLECULAR MEDICINE
(2023)
Article
Biochemistry & Molecular Biology
Hongwei Lei, Aaron D. DenDekker, Guobing Li, Zhiguo Zhang, Liang Sha, Matthew A. Schaller, Steven L. Kunkel, Liangyou Rui, Kaixiong Tao, Yali Dou
Summary: MOF plays a crucial role in adult liver function, with its deletion leading to acute liver injury resembling human steatohepatitis. The coordinated changes and reciprocal signaling between hepatocytes and Kupffer cells are essential for the liver injury induced by Mof deletion. The characteristic changes in metabolic gene programs induced by Mof deletion bear similarity to the molecular signature of human steatohepatitis.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Michael A. Willcockson, Sean E. Healton, Cary N. Weiss, Boris A. Bartholdy, Yair Botbol, Laxmi N. Mishra, Dhruv S. Sidhwani, Tommy J. Wilson, Hugo B. Pinto, Maxim I. Maron, Karin A. Skalina, Laura Norwood Toro, Jie Zhao, Chul-Hwan Lee, Harry Hou, Nevin Yusufova, Cem Meydan, Adewola Osunsade, Yael David, Ethel Cesarman, Ari M. Melnick, Simone Sidoli, Benjamin A. Garcia, Winfried Edelmann, Fernando Macian, Arthur I. Skoultchi
Summary: Histone H1 functions as a critical regulator of gene silencing by controlling chromatin compaction, genome organization, and histone methylation. Experimental evidence using a conditional triple-knockout mouse strain demonstrates that H1 plays a key role in regulating the activity of chromatin domains.
Article
Multidisciplinary Sciences
Young-Tae Lee, Alex Ayoub, Sang-Ho Park, Liang Sha, Jing Xu, Fengbiao Mao, Wei Zheng, Yang Zhang, Uhn-Soo Cho, Yali Dou
Summary: This study demonstrates how the intrinsically disordered regions of ASH2L and DPY30 restrict the rotational dynamics of MLL1 on the nucleosome core particle, leading to more efficient enzyme-substrate engagement and higher H3K4 trimethylation activity.
NATURE COMMUNICATIONS
(2021)
Review
Hematology
Justin C. Wheat, Ulrich Steidl
Summary: Non-genetic heterogeneity, or gene expression stochasticity, is an important source of variability in biological systems. Recent advancements in single-molecule technologies have shown that transcription dynamics and transcript number fluctuations play a significant role in generating cell-to-cell variability, impacting tissue homeostasis and disease. Studies on the pathophysiology of stem cell-derived malignancies like leukemia may benefit from reevaluation using insights from single-molecule, biophysical, and systems research to progress novel therapies.
Review
Biochemistry & Molecular Biology
Luke T. Marr, Prasoon Jaya, Laxmi N. Mishra, Jeffrey J. Hayes
Summary: The article reviews decades of research efforts on defining the genome-wide chromatin landscape, from initial experiments showing discontinuities in chromatin structure related to gene activation to extensions using deep sequencing methods to elucidate general features of chromatin related to gene states. It also discusses chromatin conformational capture methods to identify patterns in long-range interactions between genomic loci.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2022)
Article
Biochemistry & Molecular Biology
Alex Ayoub, Sang Ho Park, Young-Tae Lee, Uhn-Soo Cho, Yali Dou
Summary: The study demonstrates that the MLL1 core complex exhibits high rotational dynamics when bound to nucleosome core particles, which can be exploited for locus-specific regulation of H3K4 methylation in higher eukaryotes.
Editorial Material
Hematology
Justin C. Wheat, Ulrich Steidl
Summary: In this study, new insights are provided on how trisomy 21 and truncating mutations in the Gata1 transcription factor collaborate to generate acute megakaryoblastic leukemia (AMKL).
Article
Biochemical Research Methods
Fanfan Hao, Laxmi N. Mishra, Prasoon Jaya, Richard Jones, Jeffrey J. Hayes
Summary: Linker histones (H1s) are important for stabilizing chromatin structure and regulating transcription. The C-terminal domain (CTD) of H1 is involved in binding to chromatin and condensing upon nucleosome binding. Phosphorylation is a common modification in H1, but its specific effects and locations are unclear. Mass spectrometry techniques were used to identify phosphorylation sites in the CTD of linker histone Xenopus H1.0 and investigate its effects on chromatin structure.
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Article
Biochemistry & Molecular Biology
Prakriti Kalra, Huda Zahid, Alex Ayoub, Yali Dou, William C. K. Pomerantz
Summary: The N-terminal bromodomain of the BET protein BRD4 interacts with double-stranded DNA in a binding pocket overlapping with the acetylated histone binding site. This binding mechanism is distinct from other similar proteins and contributes to the regulation of gene expression by BRD4.
Review
Biochemistry & Molecular Biology
Zi Yang, Robert Zepeda, Yali Dou
Summary: The MLL/KMT2 family enzymes are frequently mutated in human cancers and congenital diseases. They deposit the majority of histone 3 lysine 4 (H3K4) mono-, di-, or tri-methylation in mammals and are tightly associated with gene activation. Recent studies have provided in-depth understanding of their interaction with the nucleosome core particle (NCP) and the regulation of their methylation activities for H3K4.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2023)
Editorial Material
Cell Biology
Xue Qing David Wang, Yali Dou
Summary: A new study has found that MENIN, together with KMT2A/B methyltransferase complexes, plays an unorthodox role in repressing bivalent genes.
NATURE CELL BIOLOGY
(2023)
Editorial Material
Cell Biology
Rui Yi, Yali Dou
Summary: A study uncovers that Pioneer transcription factors can bind closed chromatin regions, modify local accessibility, and activate target genes. The SOX9 transcription factor drives cell fate switching by activating hair follicle cell enhancers, while simultaneously repressing epidermal enhancers through sequestration of epigenetic factors.
NATURE CELL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Dongmei Wang, Haimin Li, Navdeep S. Chandel, Yali Dou, Rui Yi
Summary: This study reveals the important roles of MOF and H4K16ac in controlling cellular function and regulating mammalian tissue development. Conditional deletion of Mof in the skin causes severe defects in the self-renewal of basal epithelial progenitors, epidermal differentiation, and hair follicle growth, resulting in barrier defects and perinatal lethality. The study also highlights the essential functions of MOF-regulated genes in mitochondria and cilia.
NATURE COMMUNICATIONS
(2023)