Article
Biochemistry & Molecular Biology
William Franz Lamberti, Chongzhi Zang
Summary: Higher-order chromatin structures play a role in gene regulation and cell identity determination. This study introduces EPICS, a machine-learning based computational method for processing high-resolution chromatin 3D image data. EPICS allows for the extraction of physical characteristics from the images, such as identifying major chromatin domains and determining their open or closed status. The method demonstrates explainability and interpretability of the features extracted, providing insights into the functional characteristics of chromatin structures.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Multidisciplinary Sciences
Susanne Wegmann, Sarah L. DeVos, Bryan Zeitler, Kimberly Marlen, Rachel E. Bennett, Marta Perez-Rando, Danny MacKenzie, Qi Yu, Caitlin Commins, Riley N. Bannon, Bianca T. Corjuc, Alison Chase, Lisa Diez, Hoang-Oanh B. Nguyen, Sarah Hinkley, Lei Zhang, Alicia Goodwin, Annemarie Ledeboer, Stephen Lam, Irina Ankoudinova, Hung Tran, Nicholas Scarlott, Rainier Amora, Richard Surosky, Jeffrey C. Miller, Ashley B. Robbins, Edward J. Rebar, Fyodor D. Urnov, Michael C. Holmes, Amy M. Pooler, Brigit Riley, H. Steve Zhang, Bradley T. Hyman
Summary: The study demonstrates that reducing tau protein expression using gene-silencing technology can effectively rescue neuronal damage in an Alzheimer's disease model, with sustained effects and no detectable side effects. This approach shows promise for the treatment of tau-related human brain diseases.
Article
Biochemical Research Methods
Sofia A. Quinodoz, Prashant Bhat, Peter Chovanec, Joanna W. Jachowicz, Noah Ollikainen, Elizabeth Detmar, Elizabeth Soehalim, Mitchell Guttman
Summary: A fundamental question in gene regulation is how cell-type-specific gene expression is influenced by the packaging of DNA within the nucleus. SPRITE is a recently developed method that accurately maps higher-order DNA interactions within the nucleus by cross-linking interacting molecules and using a barcoding method for sequencing. We provide a detailed experimental protocol and an automated computational pipeline for SPRITE.
Article
Multidisciplinary Sciences
Yuhan Liu, Zhen Xu, Jiajia Shi, Yu Zhang, Shuting Yang, Qian Chen, Chenglin Song, Shuhui Geng, Qing Li, Jinsong Li, Guo-Lian Xu, We Xie, Haodong Lin, Xiajun Li
Summary: ZFP57 and ZFP445 are responsible for maintaining genomic imprinting in mouse embryos. DNA methylation was found to be lost in most imprinting control regions (ICRs) in Zfp57 mutant ES cells, and this loss was not prevented by the elimination of three TET proteins. In the absence of three major DNA methyltransferases (DNMTs), DNMT3A and DNMT3B were essential for DNA methylation at specific ICRs in mouse ES cells, while DNMT1 maintained methylation at most known ICRs. Germline-derived DNA methylation was also lost at ICRs lacking DNMTs. Hence, the three DNA methyltransferases play complementary roles in maintaining DNA methylation in mouse ES cells, including methylation at ICRs primarily mediated through the ZFP57-dependent pathway.
Review
Biochemistry & Molecular Biology
Ruize Sun, Jue Wang, Juan Feng, Bin Cao
Summary: Zinc is an essential micronutrient for both plant and animal growth, playing a critical role in the development of the central nervous system. Zinc deficiency can lead to various diseases and pathological conditions, including cognitive impairment and premature aging. This study reviews the important effects of zinc in cognitive impairment and aging, explores its molecular mechanism, and highlights potential interventions for zinc-related aging and cognitive impairments.
Editorial Material
Plant Sciences
Li Song, Weitao Li, Xuewei Chen
Summary: A recent study demonstrates the role of the rice TF APIP5 in immune regulation, expanding our understanding of plant TFs beyond their transcription factor functions.
TRENDS IN PLANT SCIENCE
(2022)
Review
Immunology
Sohei Makita, Hiroaki Takatori, Hiroshi Nakajima
Summary: Post-transcriptional regulation of inflammatory genes is mediated by ZFP36 family proteins, which bind to mRNA and lead to target mRNA decay. Despite structural similarities, ZFP36 family members have distinct functions and regulate different target mRNAs, likely due to cell-type-specific expression patterns.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Vianney Poignavent, Francois Hoh, Guillaume Terral, Yinshan Yang, Francois-Xavier Gillet, Jeong-Hyeon Kim, Frederic Allemand, Eric Lacombe, Christophe Brugidou, Sarah Cianferani, Helene Demene, Florence Vignols
Summary: Viruses of the sobemovirus genus, including the rice yellow mottle virus (RYMV), cause significant losses in agriculture. In this study, the complete 3D structure and dynamics of the P1 protein, responsible for RYMV infectivity, were determined. The P1 protein consists of two independent domains with distinct zinc fingers and different sensitivities to oxidoreduction conditions. The capacity of P1 to oligomerize and key residues essential for infectivity in rice tissues were also identified. These findings provide insights into RYMV functions and its interaction with the host plant.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Osama Garwain, Xiaoming Sun, Divya Ramalingam Iyer, Rui Li, Lihua Julie Zhu, Paul D. Kaufman
Summary: The depletion of Ki-67 in vertebrate mammals can cause DNA damage, particularly in mitotic cells. The C-terminal chromatin-binding domain of Ki-67 plays a crucial role in protecting cells from this damage. Simultaneous depletion of Ki-67 and p53 results in increased chromosome bridges and micronuclei, highlighting the importance of Ki-67 in maintaining genome stability.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Computer Science, Artificial Intelligence
Chakkarai Sathyaseelan, L. Ponoop Prasad Patro, Thenmalarchelvi Rathinavelan
Summary: Zinc finger (ZnF) is an important class of nucleic acid and protein recognition domain with diverse structures and biological functions. In order to accurately predict ZnF motifs, researchers collected 74 ZnF sequence patterns and used Pfam HMM profiles for prediction. They developed a web server called ZnF-Prot that can predict 31 ZnF domains in protein sequences of any organism.
PATTERN RECOGNITION
(2023)
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.
Article
Genetics & Heredity
Havva Ortabozkoyun, Pin-Yao Huang, Hyunwoo Cho, Varun Narendra, Gary LeRoy, Edgar Gonzalez-Buendia, Jane A. Skok, Aristotelis Tsirigos, Esteban O. Mazzoni, Danny Reinberg
Summary: The study identifies MAZ as a cofactor involved in CTCF-mediated insulation, regulating gene expression and genomic architecture. Its deletion leads to derepression of genes and homeotic transformations in mice.
Review
Biochemistry & Molecular Biology
Namyoung Jung, Tae-Kyung Kim
Summary: The genome in eukaryotes is packed hierarchically inside the nucleus, allowing for contact between cis-regulatory elements and playing a critical role in gene expression regulation. Technologies like Hi-C and FISH have revealed key genome folding principles, while new tools focus on improving resolution, throughput, and singe-cell analysis, challenging conventional knowledge. This review discusses recent advances in understanding higher-order chromosome conformation principles and technologies for investigating 4D chromatin interactions.
Article
Multidisciplinary Sciences
Ranjeet Maurya, Aparna Swaminathan, Uzma Shamim, Smriti Arora, Pallavi Mishra, Aakarshan Raina, Varsha Ravi, Bansidhar Tarai, Sandeep Budhiraja, Rajesh Pandey
Summary: The emergence of multiple SAR-CoV-2 variants during the COVID-19 pandemic has led to an increased understanding of the host-immune kinetics associated with these variants. A longitudinal investigation revealed a robust antiviral response in Omicron infection, which was largely absent in the Pre-VOC and Delta waves. The study also highlighted differential protein-protein interactions and gene expression patterns, particularly in relation to zinc finger proteins, that contribute to the immune response.
Article
Biochemistry & Molecular Biology
Sebastian Zahn, Nina Kubatova, Dennis J. Pyper, Liam Cassidy, Krishna Saxena, Andreas Tholey, Harald Schwalbe, Joerg Soppa
Summary: The genome of the halophilic archaeon Haloferax volcanii encodes more than 40 one-domain zinc finger mu-proteins. Among them, HVO_2753 stands out for containing four C(P)XCG motifs, indicating the presence of two zinc binding pockets (ZBPs). Surprisingly, despite having two ZBPs, HVO_2753 only binds to one zinc ion, with all four C(P)XCG motifs being essential for folding and function. This study represents the first in-depth analysis of a zinc finger mu-protein in all three domains of life.
Article
Multidisciplinary Sciences
Kotaro Mori, Kensaku Murano, Ryosuke L. Ohniwa, Atsushi Kawaguchi, Kyosuke Nagata
SCIENTIFIC REPORTS
(2015)
Article
Biochemistry & Molecular Biology
Yuka W. Iwasaki, Kensaku Murano, Hirotsugu Ishizu, Aoi Shibuya, Yumiko Iyoda, Mikiko C. Siomi, Haruhiko Siomi, Kuniaki Saito
Article
Cell & Tissue Engineering
Taketaro Sadahiro, Mari Isomi, Naoto Muraoka, Hidenori Kojima, Sho Haginiwa, Shota Kurotsu, Fumiya Tamura, Hidenori Tani, Shugo Tohyama, Jun Fujita, Hiroyuki Miyoshi, Yoshifumi Kawamura, Naoki Goshima, Yuka W. Iwasaki, Kensaku Murano, Kuniaki Saito, Mayumi Oda, Peter Andersen, Chulan Kwon, Hideki Uosaki, Hirofumi Nishizono, Keiichi Fukuda, Masaki Ieda
Article
Cell Biology
Kensaku Murano, Mitsuru Okuwaki, Fumitaka Momose, Michiko Kumakura, Shuhei Ueshima, Robert F. Newbold, Kyosuke Nagata
JOURNAL OF CELL SCIENCE
(2014)
Article
Biochemistry & Molecular Biology
Miharu Hisaoka, Shuhei Ueshima, Kensaku Murano, Kyosuke Nagata, Mitsuru Okuwaki
MOLECULAR AND CELLULAR BIOLOGY
(2010)
Article
Biochemistry & Molecular Biology
Kensaku Murano, Yuka W. Iwasaki, Hirotsugu Ishizu, Akane Mashiko, Aoi Shibuya, Shu Kondo, Shungo Adachi, Saori Suzuki, Kuniaki Saito, Tohru Natsume, Mikiko C. Siomi, Haruhiko Siomi
Article
Biochemistry & Molecular Biology
Ken Osumi, Kaoru Sato, Kensaku Murano, Haruhiko Siomi, Mikiko C. Siomi
Article
Cell Biology
Phuong Linh Bui, Ken Nishimura, Gonzalo Seminario Mondejar, Arun Kumar, Shiho Aizawa, Kensaku Murano, Kyosuke Nagata, Yohei Hayashi, Aya Fukuda, Yasuko Onuma, Yuzuru Ito, Mahito Nakanishi, Koji Hisatake
Article
Multidisciplinary Sciences
Ryo Onishi, Kaoru Sato, Kensaku Murano, Lumi Negishi, Haruhiko Siomi, Mikiko C. Siomi
Review
Biochemistry & Molecular Biology
Kensaku Murano, Youjia Guo, Haruhiko Siomi
Summary: The COVID-19 pandemic caused by the novel coronavirus has infected over 200 million people and resulted in 4.3 million deaths as of August 2021. Human-origin monoclonal antibodies have been isolated from convalescent patients for therapeutic and prophylactic purposes, while vaccines have been rapidly administered to restrict the spread of the virus. However, the emergence of new variants presents challenges to neutralizing antibodies and threatens the efficacy of current vaccines.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2021)
Article
Immunology
Setsuko Mise-Omata, Mari Ikeda, Masaru Takeshita, Yoshifum Uwamino, Masatoshi Wakui, Tomoko Arai, Ayumi Yoshifuji, Kensaku Murano, Haruhiko Siomi, Kensuke Nakagawara, Masaki Ohyagi, Makoto Ando, Naoki Hasegawa, Hideyuki Saya, Mitsuru Murata, Koichi Fukunaga, Ho Namkoong, Xiuyuan Lu, Sho Yamasaki, Akihiko Yoshimura
Summary: This study evaluated the memory B and T cell responses to the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a Japanese cohort, and found that after the third booster vaccination, the antibody levels and memory B cell numbers increased significantly, while memory T cell numbers recovered to pre-vaccination levels. Furthermore, the presence of memory B and T cells could rapidly upregulate antibody production and T cell responses, preventing severe illness and death caused by coronavirus disease 2019.
JOURNAL OF IMMUNOLOGY
(2022)
Article
Multidisciplinary Sciences
Ten D. Li, Kensaku Murano, Tomohiro Kitano, Youjia Guo, Lumi Negishi, Haruhiko Siomi
Summary: This study reveals the inhibitory effect of TDP-43 on L1 retrotransposition and identifies TDP-43 as a guardian of the embryonic genome. Loss of TDP-43 leads to genomic mutations and impaired cell growth.
Article
Genetics & Heredity
Akihiko Sakashita, Tomohiro Kitano, Hirotsugu Ishizu, Youjia Guo, Harumi Masuda, Masaru Ariura, Kensaku Murano, Haruhiko Siomi
Summary: The study reveals that MERVL transcripts are crucial for mouse preimplantation development. Depletion of MERVL RNA disrupts lineage specification and enhances chromatin accessibility and transcription of two-cell-specific genes. These findings highlight the key role of an endogenous retrovirus in regulating host cell fate potential during mouse embryogenesis.
Article
Biochemistry & Molecular Biology
Youjia Guo, Atsushi Kawaguchi, Masaru Takeshita, Takeshi Sekiya, Mikako Hirohama, Akio Yamashita, Haruhiko Siomi, Kensaku Murano
Summary: In response to the global pandemic of COVID-19, researchers have isolated various human recombinant monoclonal antibodies that can neutralize SARS-CoV-2 infection. However, there is still a need for suitable monoclonal antibodies for molecular pathology research. By producing mouse anti-SARS-CoV-2 spike monoclonal antibodies, researchers have created a useful tool for future research and potential application in clinical settings.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
