Article
Biochemistry & Molecular Biology
Parviz Seifpanahi Shabane, Alexey Onufriev
Summary: The study explores the conformational changes of the H4 tail under different charged states. As the charge of the H4 tail is gradually neutralized, its structure transitions from a random coil to a more compact and stable form. Based on ensemble similarity, K -> M is proposed as a possible alternative to the commonly used K -> Q substitution.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Biology
Xiaowei Xu, Xu Hua, Kyle Brown, Xiaojun Ren, Zhiguo Zhang
Summary: Mcm2 plays an important role in the differentiation of mouse embryonic stem cells by manipulating chromatin landscapes at bivalent chromatin domains.
Article
Biology
Calvin Jon A. Leonen, Miho Shimada, Caroline E. Weller, Tomoyoshi Nakadai, Peter L. Hsu, Elizabeth L. Tyson, Arpit Mishra, Patrick M. M. Shelton, Martin Sadilek, R. David Hawkins, Ning Zheng, Robert G. Roeder, Champak Chatterjee
Summary: Post-translational modification of histones by the small ubiquitin-like modifier protein SUMO plays a key role in gene silencing, centromeric localization, and DNA repair in eukaryotes. The study demonstrated that H4K12su inhibits acetylation of H4 tail and methylation of H3K4 associated with transcription activation, as well as transcription mediated by RNA polymerase II. Cell-based assays confirmed the negative crosstalk between histone sumoylation and acetylation/methylation in human cells.
Article
Multidisciplinary Sciences
Mark Boltengagen, Anke Samel-Pommerencke, David Fechtig, Ann E. Ehrenhofer-Murray
Summary: The acetylation of H4 lysine 16 in yeast regulates gene silencing by inhibiting the binding of heterochromatin complex SIR to chromatin. The SAS-I complex is a major provider of H4 K16Ac in yeast, and its absence leads to improper gene silencing. Replication disrupts histone marks, with H4 K16Ac appearing immediately and being influenced by transcription levels. Additionally, the acetyltransferases Esa1 and Sas2 redundantly regulate H4 K16Ac levels in yeast cells.
Article
Biology
Christine E. Cucinotta, Rachel H. Dell, Keean Ca Braceros, Toshio Tsukiyama
Summary: This study found that there is robust transcription activity within the first few minutes of quiescence exit. The chromatin-remodeling enzyme RSC is already bound to genes induced upon quiescence exit. Depletion of RSC results in severe defects during quiescence exit, including a global decrease in Pol II loading and aberrant transcription initiation.
Article
Biochemistry & Molecular Biology
Anagh Ray, Preeti Khan, Ronita Nag Chaudhuri
Summary: The study highlights the importance of lysine acetylation in maintaining chromatin structure and function, specifically focusing on the role of H4K16 acetylation in regulating the expression of constitutive genes. Deacetylation of H4K16 is associated with hypoacetylation of H4K12 and H3K9, along with hyperacetylation of H3K56, creating a chromatin landscape conducive for transcription of constitutive genes.
Article
Biochemistry & Molecular Biology
Chuizheng Kong, Guangyao Zhao, Lifeng Gao, Xiuying Kong, Daowen Wang, Xu Liu, Jizeng Jia
Summary: In this study, the association between transposons (TEs), chromatin states, and chromatin accessibility in Aegilops tauschii was analyzed. It was found that TEs contributed to the diverse distribution of chromatin states and affected the chromatin state and openness of potential regulatory elements. Some TE superfamilies carried active/open chromatin regions. Furthermore, the accessibility shaped by TEs was associated with the histone mark H3K9ac. These findings highlight the role of TEs in shaping the epigenetic landscape and regulating gene expression in Aegilops tauschii.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biotechnology & Applied Microbiology
Nando D. Das, Jen-Chien Chang, Chung-Chau Hon, S. Thomas Kelly, Shinsuke Ito, Marina Lizio, Bogumil Kaczkowski, Hisami Watanabe, Keisuke Katsushima, Atsushi Natsume, Haruhiko Koseki, Yutaka Kondo, Aki Minoda, Takashi Umehara
Summary: This study found that H4K5acK8ac and H3K27ac signals have some overlap in binding to the super-enhancer transcription factor BRD4 at higher levels, but they also have distinct specificities, especially in glioblastoma stem-like cell lines. Deletion of H4K5acK8ac-preferred super-enhancers associated with MYCN and NFIC resulted in a reduction in stem-like properties.
Review
Endocrinology & Metabolism
Xiaoqiang Sun, Liu Wang, S. M. Bukola Obayomi, Zong Wei
Summary: Epigenetic signatures play a crucial role in defining beta cell identity during development and maintaining function in homeostatic states, but they are disrupted during the progression of T2DM.
FRONTIERS IN ENDOCRINOLOGY
(2021)
Review
Plant Sciences
Rocio Nunez-Vazquez, Benedicte Desvoyes, Crisanto Gutierrez
Summary: Plants have developed various mechanisms to adapt to abiotic stresses, which involve transcriptional regulation and chromatin modifications. Understanding and manipulating these regulatory networks are crucial for enhancing crop resilience and performance against stress.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Reproductive Biology
Naiara Z. Saraiva, Clara S. Oliveira, Nathalia N. C. Almeida, Marivaldo R. Figueiro, Carolina C. R. Quintao, Joaquim M. Garcia
Summary: This study investigated the epigenetic changes resulting from the use of histone deacetylase inhibitors in the maturation of bovine oocytes and subsequent embryo development. The results showed that the treatment with histone deacetylase inhibitors promoted the development of bovine oocytes and had a positive impact on embryo development.
Article
Biochemistry & Molecular Biology
Ritu Chaturvedi, Eric C. Long
Summary: This study investigates the alkaline reactivity of CPD lesions in a dinucleotide CPD model system. The results show that water addition occurs at the C4=O groups of saturated rings, and the two C4 carbonyls on adjacent saturated pyrimidine rings undergo water exchange at different rates.
BIOORGANIC & MEDICINAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Jinlei Han, Damar Lopez-Arredondo, Guangrun Yu, Yankun Wang, Baohua Wang, Sarah Brooke Wall, Xin Zhang, Hui Fang, Alfonso Carlos Barragan-Rosillo, Xiaoping Pan, Yanqin Jiang, Jingbo Chen, Hui Zhang, Bao-Liang Zhou, Luis Herrera-Estrella, Baohong Zhang, Kai Wang
Summary: This study examined the genome-wide DNase I-hypersensitive site (DHS) and its variations in domesticated allotetraploid cotton, revealing the interplay among transposable elements, cis-regulatory elements, and histone modifications during polyploidization. These findings advance our understanding of regulatory architecture in plants.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Genetics & Heredity
Preeti Khan, Ronita Nag Chaudhuri
Summary: This study reveals the significance of H3K56 acetylation in the early stages of nucleotide excision repair (NER). H3K56 acetylation is crucial for recruiting the repair factor Rad16 and promoting UV-induced hyperacetylation of H3 tail residues. It also enhances chromatin accessibility, aiding in the recruitment of subsequent repair factors during NER.
Article
Parasitology
Samantha J. Emery-Corbin, Joshua J. Hamey, Balu Balan, Laura Rojas-Lopez, Staffan G. Svard, Aaron R. Jex
Summary: This study provides the first known molecular map of histone post-translational modifications in Giardia, identifying over 50 previously unreported histone modifications. The research suggests conserved histone modifications in Giardia, equivalent to many other eukaryotes, and indicates the presence of similar epigenetic mechanisms in the parasite. The study is a substantial step towards understanding the associations of histone modifications in parasite development and virulence.
INTERNATIONAL JOURNAL FOR PARASITOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Sonia Bedi, Sourabh Sengupta, Anagh Ray, Ronita Nag Chaudhuri
Article
Biochemistry & Molecular Biology
Sourabh Sengupta, Anagh Ray, Drishti Mandal, Ronita Nag Chaudhuri
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2020)
Article
Biochemistry & Molecular Biology
Anagh Ray, Preeti Khan, Ronita Nag Chaudhuri
Summary: The study highlights the importance of lysine acetylation in maintaining chromatin structure and function, specifically focusing on the role of H4K16 acetylation in regulating the expression of constitutive genes. Deacetylation of H4K16 is associated with hypoacetylation of H4K12 and H3K9, along with hyperacetylation of H3K56, creating a chromatin landscape conducive for transcription of constitutive genes.
Review
Genetics & Heredity
Bhushan L. Thakur, Anagh Ray, Christophe E. Redon, Mirit I. Aladjem
Summary: This article reviews the molecular pathways that regulate replication origin dormancy, prevent excessive activation, and detect, encapsulate, and eliminate persistent excess DNA.
TRENDS IN GENETICS
(2022)
Article
Genetics & Heredity
Marit A. E. van Bueren, Aniek Janssen
Summary: Eukaryotic nuclei rely on multiple repair pathways to accurately repair DNA damage, particularly in chromatin domains enriched for repetitive DNA sequences. Tailored repair mechanisms are necessary to maintain genome stability in these domains.