Article
Multidisciplinary Sciences
Lennart Hilbert, Yuko Sato, Ksenia Kuznetsova, Tommaso Bianucci, Hiroshi Kimura, Frank Julicher, Alf Honigmann, Vasily Zaburdaev, Nadine L. Vastenhouw
Summary: This study observed the dynamics of euchromatin organization in pluripotent zebrafish cells during transcription initiation, revealing that accumulation of RNA induces the formation of transcriptionally active regions that tend to separate from transcriptionally inactive euchromatin, forming smaller scale microphases.
NATURE COMMUNICATIONS
(2021)
Article
Cell Biology
Stephen P. Methot, Jan Padeken, Giovanna Brancati, Peter Zeller, Colin E. Delaney, Dimos Gaidatzis, Hubertus Kohler, Alexander van Oudenaarden, Helge Grosshans, Susan M. Gasser
Summary: The deposition of H3K9me2 and H3K9me3 can repress lineage-specific and germline genes in terminally differentiated Caenorhabditis elegans tissues by restricting the activity of specific transcription factors. Changes in H3K9me during development affect gene regulation and the maintenance of cellular functions.
NATURE CELL BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Shinya Takahata, Yota Murakami
Summary: DNA is stored in a folded state in the nucleus, and only necessary genetic information is extracted. The key to extracting genetic information lies in chromatin ambivalence, which is characterized into low-density euchromatin and high-density heterochromatin. The yeast FACT complex plays a role in both euchromatin and heterochromatin, regulating gene expression and chromatin structures. It interacts with different partners to activate promoter chromatin or induce transcriptional repression, making it an interesting phenomenon.
Article
Multidisciplinary Sciences
Louis-Valentin Meteignier, Cecile Lecampion, Florent Velay, Cecile Vriet, Laura Dimnet, Martin Rougee, Christian Breuer, Ludivine Soubigou-Taconnat, Keiko Sugimoto, Fredy Barneche, Christophe Laloi
Summary: This study reveals the important role of DNA Topoisomerase VI in maintaining a chromatin boundary function that safeguards gene expression within euchromatic islands in silenced heterochromatic regions.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Cell Biology
Zulong Chen, Jessica K. Tyler
Summary: This review presents our current understanding of how DNA double-strand break repair pathways are employed in various chromatin landscapes, with a focus on the impact of histone post-translational modifications and damage-induced chromatin modifications on repair pathway choice. The potential roles of RNA transcripts from DSBs in actively transcribed regions in regulating repair pathway choice are also discussed.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Olivia Morrison, Jitendra Thakur
Summary: Chromatin is composed of DNA and histone proteins and is important for packaging DNA and regulating DNA metabolic pathways. It is categorized into euchromatin (active transcription), heterochromatin (silencing), and centromeric chromatin (chromosome segregation).
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Antonio Sermek, Isidoro Feliciello, Durdica Ugarkovic
Summary: In the flour beetle, the major satellite DNA TCAST1 and minor satellite TCAST2 exhibit different transcription patterns during development and heat stress, possibly related to the chromatin state in different genomic regions. The processing of TCAST1 transcripts into piRNAs and siRNAs, as well as the enrichment of histone mark H3K9me3, suggest distinct regulatory mechanisms for major and minor satellite RNAs in response to development and stress.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Jeremy Berthelier, Leonardo Furci, Shuta Asai, Munissa Sadykova, Tomoe Shimazaki, Ken Shirasu, Hidetoshi Saze
Summary: TE-gene transcripts are generated in thousands of gene loci in Arabidopsis thaliana, with TE sequences often associated with transcription start or termination sites. The epigenetic state of intragenic TEs affects the production of TE-gene transcripts, as well as RNA stability and environmental responses.
NATURE COMMUNICATIONS
(2023)
Article
Cell Biology
Amir N. Zakirov, Sophie Sosnovskaya, Ekaterina D. Ryumina, Ekaterina Kharybina, Olga S. Strelkova, Oxana A. Zhironkina, Sergei A. Golyshev, Andrey Moiseenko, Igor I. Kireev
Summary: A detailed understanding of the principles of the structural organization of genetic material is crucial for explaining the mechanisms of gene regulation during development. Modern ideas about the spatial organization of the genome are based on microscopic analysis of chromatin structure and molecular data on DNA-DNA interaction. Chromatin structure heterogeneity, depending on functional states and cell cycle progression, adds complexity to the interpretation of structural data and requires selective labeling of different transcriptional states.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Chengcheng Zhang, Yuan Tian, Shuang Song, Lu Zhang, Yunkun Dang, Qun He
Summary: The deposition of H2A.Z and deacetylation of histone H3 lysine 56 play crucial roles in restricting heterochromatin spreading.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biology
Sujeet Kumar Mishra, Kunhe Li, Simon Brauburger, Arnab Bhattacherjee, Nestor Norio Oiwa, Dieter W. Heermann
Summary: Nucleosome positioning plays a crucial role in important biological processes and can be used to predict genome function and chromatin organization. This study developed a theoretical model to analyze nucleosome positioning data and obtained genome-wide clustering in Candida albicans. The clustering revealed different nucleosome distributions and gene densities that govern differential gene expression patterns. Furthermore, these distribution patterns were conserved throughout the genome and within species.
Article
Biochemistry & Molecular Biology
Pragya Sidhwani, Aaron F. Straight
Summary: Centromeres are crucial for chromosome segregation during cell division. Understanding their epigenetic regulation and boundary establishment is important for genome stability. While boundaries between centromeres and heterochromatin have been identified in yeast, the mechanisms in humans remain unclear.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2023)
Article
Biology
Ranjith K. Papareddy, Katalin Paldi, Anna D. Smolka, Patrick Huther, Claude Becker, Michael D. Nodine
Summary: MicroRNA-mediated repression of CHROMOMETHYLASE 3 (CMT3) and the chromatin features preferred by CMT3 help prevent ectopic methylation of thousands of genes during embryogenesis, potentially avoiding harmful effects for weeks afterwards.
Review
Biochemistry & Molecular Biology
Niamat Khan, Sidra Shahid, Abdul R. Asif
Summary: Chromatin is a dynamic structure consisting of DNA and proteins, playing key roles in DNA packaging, gene expression regulation, and DNA protection. Studying chromatin-associated proteins can enhance our understanding of disease pathophysiology and aid in designing new drugs.
Article
Biochemistry & Molecular Biology
Ji-Yun Shang, Yu-Jia Lu, Xue-Wei Cai, Yin-Na Su, Chao Feng, Lin Li, She Chen, Xin-Jian He
Summary: The accessory subunits of the INO80 chromatin remodeling complex interact with different domains of the INO80 protein, playing roles in chromatin remodeling and transcriptional activation. These interactions are essential for maintaining the balance between vegetative growth and flowering in plants under various environmental conditions.
