Article
Cell Biology
Koei Okazaki, Megumi Nakano, Jun-ichirou Ohzeki, Koichiro Otake, Kazuto Kugou, Vladimir Larionov, William C. Earnshaw, Hiroshi Masumoto
Summary: Human artificial chromosomes (HACs) are formed by introducing large centromeric sequences into cells, and the balance of chromatin states on the alphoid DNA is crucial for HAC formation. Our study explores the relationship between chromatin architecture and de novo HAC formation efficiency, and found that a combination of mutated and wild-type alphoid repeats enhances HAC formation.
Review
Genetics & Heredity
Evon M. DeBose-Scarlett, Beth A. Sullivan
Summary: Centromeres are crucial for genome inheritance, with abnormal function linked to various diseases. Ectopic centromeres can form at new genomic locations, impacting genome stability and disease development. While certain genome regions influence neocentromere activation, the universal mechanism remains unclear.
ANNUAL REVIEW OF GENETICS, VOL 55
(2021)
Review
Oncology
Rhiannon French, Siim Pauklin
Summary: Cancer stem cells (CSCs) possess stem-like properties and play a crucial role in tumor initiation and progression. Evidence suggests that non-stem tumor cells may undergo dedifferentiation to CSCs, and epigenetic regulation of CSCs provides new opportunities for therapeutic interventions.
INTERNATIONAL JOURNAL OF CANCER
(2021)
Article
Biochemistry & Molecular Biology
Ryan N. Douglas, Hua Yang, Bing Zhang, Chen Chen, Fangpu Han, Jianlin Cheng, James A. Birchler
Summary: Research on maize B chromosomes shows that they undergo nondisjunction during the second pollen mitosis as part of their accumulation mechanism. The study identified 9-Bic-1 as an epigenetically silenced B chromosome centromere that may undergo both centromere reactivation and de novo centromere formation. Breakpoint determination revealed the potential for these processes to occur on fragments derived from the progenitor.
CHROMOSOME RESEARCH
(2021)
Review
Plant Sciences
Antoine Nicolas, Patrick Laufs
Summary: Plant aerial development relies on meristem activity, with shoot apical meristem (SAM) formed in the embryo contributing to the main stem and axillary meristems (AMs) formed post-embryonically contributing to the branched structure. This review discusses recent findings on the de novo establishment of AMs and emphasizes the progressive process of stem cell formation, different from functional meristems.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Cell Biology
Kasuga Takumi, Daiju Kitagawa
Summary: Centrioles can be assembled in the vicinity of pre-existing centrioles or in the absence of pre-existing centrioles, a process known as de novo centriole formation. This process can be triggered by the removal of all pre-existing centrioles in the cell or through the overexpression of certain regulatory proteins. De novo centriole formation can occur naturally in some species. This review summarizes previous findings on de novo centriole formation, particularly under experimental conditions, and discusses its regulatory mechanisms.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Genetics & Heredity
Yin Shen, Ling-Ling Chen, Junxiang Gao
Summary: Chromatin accessibility, a key structural feature for understanding gene transcription regulation, is dynamic during stress and developmental transitions. CharPlant, a bioinformatics tool, is developed for de novo prediction of OCRs in plant genomes, showing promise in prediction power and computational efficiency. This tool fills the gap of identifying potential OCRs in whole genomes.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
Scott R. Burlingham, Nicole F. Wong, Lindsay Peterkin, Lily Lubow, Carolina Dos Santos Passos, Orion Benner, Michael Ghebrial, Thomas P. Cast, Matthew A. Xu-Friedman, Thomas C. Sudhof, Soham Chanda
Summary: The presynaptic release of neurotransmitters can signal the organization of relevant postsynaptic structures and modify the synaptic identity of neurons.
NATURE COMMUNICATIONS
(2022)
Article
Cell Biology
David B. Lyons, Amy Briffa, Shengbo He, Jaemyung Choi, Elizabeth Hollwey, Jack Colicchio, Ian Anderson, Xiaoqi Feng, Martin Howard, Daniel Zilberman
Summary: In Arabidopsis thaliana h1ddm1 mutants, intermediate heterochromatic mCG can be stably inherited across many generations and is quantitatively associated with transposon expression. A mathematical model estimates that mCG can be stably inherited at any level via a dynamic balance of semiconservative maintenance failure and de novo methylation. The core methyltransferase DRM2 catalyzes most of the heterochromatic de novo mCG, with much higher rates than previously thought, while chromomethylases make smaller contributions. These results demonstrate that stable epigenetic inheritance of mCG in plant heterochromatin is enabled by extensive de novo methylation.
Review
Biochemistry & Molecular Biology
Kezia Jack, Graham S. Jackson, Jan Bieschke
Summary: This article reviews a range of experimental approaches for generating PrP amyloid assemblies and discusses the definition of prions, non-protein requirements, and the current state of prion amplification and generation in vitro.
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)
Review
Biochemistry & Molecular Biology
Harsh Nagpal, Beat Fierz
Summary: The centromere is an indispensable chromatin domain in eukaryotes, necessary for chromosome segregation; its unique structure relies on nucleosomes containing CENP-A; CENP-A binding proteins play a crucial role in modulating the structure of centromeric chromatin.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Genetics & Heredity
Xiaodong Lu, Ka-wing Fong, Fang Wang, Galina Gritsina, Sylvan C. Baca, Jacob E. Berchuck, Jenny Ross, Eva Corey, Navdeep Chandel, William J. Catalona, Ximing Yang, Matthew L. Freedman, Jonathan C. Zhao, Jindan Yu, Lourdes T. Brea, Sandor Spisak, CoIm Morrissey
Summary: The study reveals that HOXB13 suppresses lipogenic transcriptional program in prostate cancer through HDAC3 recruitment, which inhibits tumor metastasis. Loss or mutation of HOXB13 leads to lipid accumulation in PCa cells, promoting cell motility and tumor metastasis. This study provides important insights into the roles of HOXB13 in prostate cancer progression and metastasis.
Article
Reproductive Biology
Jingjing Qian, Fan Guo
Summary: Both human and mouse oocytes have unique epigenomic landscapes. New measurement technologies allow us to study genome regulation at different levels, including DNA methylation, transcription, and chromatin accessibility. Recent studies have also explored the relationship between different histone modifications and DNA methylation, revealing the mechanisms behind oocyte DNA methylome formation.
BIOLOGY OF REPRODUCTION
(2022)
Article
Multidisciplinary Sciences
Jonathan Markert, Keda Zhou, Karolin Luger
Summary: The study demonstrates that SMARCAD1 is capable of transferring the entire histone octamer from one DNA segment to another in an ATP-dependent manner, as well as de novo nucleosome assembly from histone octamer due to its ability to simultaneously bind all histones. The low-resolution cryo-electron microscopy structure of SMARCAD1 in complex with a nucleosome reveals a unique engagement of its adenosine triphosphatase domains with the substrate, providing mechanistic insights into nucleosome disassembly and reassembly induced by SMARCAD1.
Article
Biology
Aorarat Suntronpong, Kazuto Kugou, Hiroshi Masumoto, Kornsorn Srikulnath, Kazuhiko Ohshima, Hirohisa Hirai, Akihiko Koga
Article
Plant Sciences
Koichiro Otake, Kazuto Kugou, Jekson Robertlee, Jun-ichirou Ohzeki, Koei Okazaki, Shigeru Hanano, Seiji Takahashi, Daisuke Shibata, Hiroshi Masumoto
Summary: Genetic modifications in plants are essential for research, and transgene expression is influenced by the chromatin structure of the insertion site. This study demonstrates a strategy for manipulating chromatin in plant cells by tethering epigenetic effectors to a synthetic DNA platform. The results highlight the intrinsic interplay between DNA and histone methylation mechanisms in plants and suggest that the induced epigenetic modification states can be maintained even when the effector tethering is inhibited. This system provides a tool to study diverse epigenetic effectors and chromatin assembly mechanisms in plant cells.
