Article
Multidisciplinary Sciences
Leah F. Rosin, Dahong Chen, Yang Chen, Elissa P. Lei
Summary: Research on the chromatin structure in the silkmoth, Bombyx mori, reveals that the two male sex chromosomes are equally downregulated after dosage compensation (DC) is established. In females, the Z chromosome chromatin becomes more accessible and repositions towards the nuclear center during the early stages of DC. This study also uncovers intriguing similarities between DC mechanisms in B. mori and C. elegans, despite having evolutionarily distinct sex chromosomes, suggesting a possible role for holocentricity in DC mechanisms.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Ikuhiro Okamoto, Tomonori Nakamura, Kotaro Sasaki, Yukihiro Yabuta, Chizuru Iwatani, Hideaki Tsuchiya, Shin-Ichiro Nakamura, Masatsugu Ema, Takuya Yamamoto, Mitinori Saitou
Summary: The mechanism of X chromosome inactivation in cynomolgus monkeys is unique, with females achieving X chromosome inactivation and up-regulation coincidentally by one week after implantation, while males show progressive X chromosome up-regulation. This finding provides a foundation for understanding dosage compensation mechanisms in primates, including humans.
Article
Multidisciplinary Sciences
Serena F. Generoso, Maria Victoria Neguembor, Elliot A. Hershberg, Ruslan I. Sadreyev, Kazuki Kurimoto, Yukihiro Yabuta, Raffaele Ricci, Pauline Audergon, Moritz Bauer, Mitinori Saitou, Konrad Hochedlinger, Brian J. Beliveau, Maria Pia Cosma, Jeannie T. Lee, Bernhard Payer
Summary: Reactivation of the inactive X chromosome is a key event during reprogramming, and the cohesin complex member SMC1a plays a crucial role in this process. Depletion of SMC1a affects X chromosome reactivation without interfering with iPSC-reprogramming, and it is necessary for the decompacted state of the active X chromosome. Our findings highlight the importance of cohesin in the remodeling of the X chromosome and its critical role in iPSC-reprogramming.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Ryoma Ota, Makoto Hayashi, Shumpei Morita, Hiroki Miura, Satoru Kobayashi
Summary: Dosage compensation equalizes sex chromosome gene expression between the sexes in Drosophila, achieved by the male-specific lethal (MSL) complex in somatic cells. However, it remains unclear whether dosage compensation occurs in germline cells. Transcriptome analysis showed higher expression of X-linked genes in female primordial germ cells (PGCs) compared to males, with absence of H4K16ac due to failure of MSL complex formation in male PGCs.
SCIENTIFIC REPORTS
(2021)
Article
Biology
Yoshikazu Haramoto, Mino Sakata, Shin Kobayashi
Summary: X chromosome reactivation (XCR) progresses along with the proliferation and clustering of primordial germ cells (PGCs) within the genital ridge, with epigenetic memory erasure timing varying according to the locus of X-linked genes.
Article
Biochemistry & Molecular Biology
Vladimir Baran, Jozef Pisko
Summary: The preimplantation period of embryogenesis plays a crucial role in mammalian development, and cellular abnormalities during this period are the main cause of fetal developmental disorders. Research has found that DNA damage induced before DNA synthesis can significantly affect the preimplantation development of the embryo, and the extent of DNA damage is related to this developmental ability. Although one-cell embryos can correct the first cleavage cycle, a segregation disorder of condensed chromatin after the first cleavage can result in the formation of micronuclei.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Hsiang-Hsuan Fan, Kuo-Hong Lee, You-Tzung Chen, Li-Jyuan Lin, Tsung-Lin Yang, Shu-Wha Lin, I-Shing Yu
Summary: The study indicates that Wdhd1 plays a critical role in mouse embryonic development, with Wdhd1 homozygous null mutation resulting in reduced cell proliferation, affecting embryonic growth and viability.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH
(2021)
Review
Biochemistry & Molecular Biology
Alessandra Spaziano, Irene Cantone
Summary: Mammalian females silence transcription on one of the X chromosomes to compensate the expression dosage with males. X-chromosome inactivation involves various epigenetic modifications to maintain silencing and make it heritable. Despite genes on the inactive X chromosome being refractory to reactivation, reactivation can occur alongside epigenome reprogramming or by perturbing silencing pathways.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2021)
Article
Biochemistry & Molecular Biology
Jacqueline Severino, Moritz Bauer, Tom Mattimoe, Niccolo Arecco, Luca Cozzuto, Patricia Lorden, Norio Hamada, Yoshiaki Nosaka, So Nagaoka, Pauline Audergon, Antonio Tarruell, Holger Heyn, Katsuhiko Hayashi, Mitinori Saitou, Bernhard Payer
Summary: This study investigated the dynamics and biological function of X-chromosome inactivation and reactivation using a tailor-made in vitro system of primordial germ cell-like cell differentiation from mouse embryonic stem cells. The research revealed that fine-tuned X-chromosome remodeling is a critical feature of female germ cell development towards meiosis and oogenesis.
Article
Cell Biology
Nami Motosugi, Chisa Okada, Akiko Sugiyama, Tomoyuki Kawasaki, Minoru Kimura, Takashi Shiina, Akihiro Umezawa, Hidenori Akutsu, Atsushi Fukuda
Summary: The erosion of X chromosome inactivation in female human pluripotent stem cells is initiated by the loss of XIST, rather than the accumulation of XACT. While XACT is dispensable for maintaining X-lined gene repression on inactive X chromosomes, it plays a role in neural differentiation in hPSCs.
Article
Engineering, Environmental
Min Li, Jiahuan Li, Yunlong Yang, Wenhui Liu, Zhihui Liang, Guanyu Ding, Xiaohe Chen, Qi Song, Changying Xue, Bingbing Sun
Summary: The study demonstrates that 254 nm ultraviolet-C (UVC) is an effective method to inactivate coronavirus, with an inactivation rate of up to 99.99%. Mechanistic study shows that UVC induces damage to spike proteins and genome, which affects virus attachment and replication processes.
JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING
(2022)
Article
Engineering, Chemical
Junshu Wang, Lingjun Bu, Yangtao Wu, Julong Sun, Guangchao Li, Shiqing Zhou
Summary: The performance of the UV365/chlorine process on bacterial inactivation was comprehensively investigated in this study, showing better performance than UV365 alone and chlorine alone processes. This better performance can be attributed to the reactive species generated in the UV365/chlorine process. Inactivation of E. coli, S. aureus, and B. subtilis was confirmed through various evaluations, and the order of bacterial inactivation was found. Additionally, the combined UV365/chlorine process showed the lowest reactivation potential and fewer disinfection byproducts compared to direct chlorination.
SEPARATION AND PURIFICATION TECHNOLOGY
(2022)
Article
Biology
Kenta Tomihara, Munetaka Kawamoto, Yutaka Suzuki, Susumu Katsuma, Takashi Kiuchi
Summary: The evolution of dosage compensation leads to the transcriptional downregulation of both Z chromosomes in male silkworms.
Review
Genetics & Heredity
Niklas-Benedikt Grimm, Jeannie T. Lee
Summary: This article discusses the treatment of Rett syndrome and other X-linked disorders. By activating the inactive X-chromosome, the root cause of X-linked disorders can be addressed.
TRENDS IN GENETICS
(2022)
Article
Biotechnology & Applied Microbiology
Irene Talon, Adrian Janiszewski, Bart Theeuwes, Thomas Lefevre, Juan Song, Greet Bervoets, Lotte Vanheer, Natalie De Geest, Suresh Poovathingal, Ryan Allsop, Jean-Christophe Marine, Florian Rambow, Thierry Voet, Vincent Pasque
Summary: Our study reveals that intrinsic compensatory mechanisms exist in mammalian cells, involving modulation of chromatin accessibility to counteract imbalances in gene dosage between the X chromosome and autosomes caused by evolutionary changes or X chromosome inactivation in vitro. Through genome-wide approaches, allele-specific ATAC-seq, and single-cell RNA-seq, we demonstrate increased chromatin accessibility on the upregulated active X chromosome compared to autosomes in female embryonic fibroblasts and during reprogramming to pluripotency. Additionally, our data show that ZFP42/REX1, a gene associated with pluripotency that evolved specifically in placental mammals, targets multiple X-linked genes, suggesting an evolutionary link between ZFP42/REX1, X chromosome reactivation, and pluripotency.
Article
Multidisciplinary Sciences
Long Wang, Tao Yang, Bingqian Wang, Qinlu Lin, Sirui Zhu, Chiyu Li, Youchu Ma, Jing Tang, Junjie Xing, Xiushan Li, Hongdong Liao, Dorothee Staiger, Zhiqiang Hu, Feng Yu
Article
Cell Biology
Binbin Ma, Tung-Jui Trieu, Ji Cheng, Shuang Zhou, Qingsong Tang, Jing Xie, Ji-Long Liu, Keji Zhao, Shukry J. Habib, Xin Chen
Article
Biochemical Research Methods
Van-Kien Bui, Chaochun Wei
BMC BIOINFORMATICS
(2020)
Article
Biochemistry & Molecular Biology
Fan Zhang, Chunchao Wang, Min Li, Yanru Cui, Yingyao Shi, Zhichao Wu, Zhiqiang Hu, Wensheng Wang, Jianlong Xu, Zhikang Li
Summary: This study characterized the gene-coding sequence-haplotype (gcHap) diversity of 45,963 rice genes in 3010 rice accessions, revealing three main categories of rice genes and a large number of potentially functional important gcHaps. The inferred proto-ancestors of local landrace populations correlated with wild rice accessions, supporting a multiorigin model of Oryza sativa. Breeding efforts have increased gcHap diversity in modern varieties and caused frequency shifts in predominant gcHaps, highlighting the potential for rice improvement through favorable gcHaps mining.
Article
Biochemistry & Molecular Biology
Peng Xu, Lan Zhang, Yao Xiao, Wei Li, Zhiqiang Hu, Rukui Zhang, Jin Li, Feizhen Wu, Yanping Xi, Qingping Zou, Zhentian Wang, Rui Guo, Honghui Ma, Shihua Dong, Min Xiao, Zhicong Yang, Xiaoguang Ren, Chaochun Wei, Wenqiang Yu
Summary: The well-established functions of UHRF1 in DNA biological processes have been expanded to show that UHRF1 also plays a role in RNA metabolism by regulating alternative RNA splicing. The interaction of UHRF1 with various splicing factors and its involvement in U snRNAs suggest a complex mechanism at play, providing insights into UHRF1-mediated alternative RNA splicing and its implications in disease development.
HUMAN MOLECULAR GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Xiaorui Dong, Hongzhang Xue, Chaochun Wei
Summary: ivTerm is an R-shiny package that allows users to visualize functional analysis results, compare results across multiple experiments, create customized charts, and download these charts. It provides users with various basic and innovative chart types to display functional terms and involved genes.
JOURNAL OF CELLULAR BIOCHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Fan Zhang, Zhiqiang Hu, Zhichao Wu, Jialing Lu, Yingyao Shi, Jianlong Xu, Xiyin Wang, Jinpeng Wang, Mingming Wang, Xiaorong Shi, Yanru Cui, Casiana Vera Cruz, Dalong Zhuo, Dandan Hu, Min Li, Wensheng Wang, Xiuqin Zhao, Tianqing Zheng, Binying Fu, Jauhar Ali, Yongli Zhou, Zhikang Li
Summary: Through a genome-wide association study approach, this research identified a complex genetic interaction system between rice and the bacterial pathogen Xanthomonas oryzae pv. oryzae, characterized by genome-wide interactions between rice quantitative resistance genes and Xoo virulence genes. This genetic system may lead to dynamic coevolutionary consequences during the reciprocal adaptation of rice and Xoo.
Article
Cell Biology
Duygu Kuzuoglu-Ozturk, Zhiqiang Hu, Martina Rama, Emily Devericks, Jacob Weiss, Gary G. Chiang, Stephen T. Worland, Steven E. Brenner, Hani Goodarzi, Luke A. Gilbert, Davide Ruggero
Summary: eIF4E controls the translation of Tfeb, a key executor of the autophagy response; eIF4E has a functional interaction with Bcl-xL in tumor growth; eIF4E interacts with the exon-junction complex (EJC) to control the migratory properties of cancer cells.
Article
Genetics & Heredity
Andrew G. Sharo, Zhiqiang Hu, Shamil R. Sunyaev, Steven E. Brenner
Summary: This article introduces a method called StrVCTVRE to distinguish between pathogenic and benign structural variants (SVs). By integrating multiple features and using a rare training set for classification, this method reduces about half of the SVs while maintaining a high sensitivity. It provides support for further investigation into unresolved cases and understanding new mechanisms of disease.
AMERICAN JOURNAL OF HUMAN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Fan Zhang, Hongzhang Xue, Xiaorui Dong, Min Li, Xiaoming Zheng, Zhikang Li, Jianlong Xu, Wensheng Wang, Chaochun Wei
Summary: This study introduced new steps for handling long-read data and constructed a high-quality rice pan-genome that is more comprehensive than the one based on short-read sequencing. The main components of novel sequences are repetitive sequences, and the pan-genome constructed from long-read data is more representative than the one constructed from short-read data.
Article
Oncology
Xiaopeng Zhao, Binbin Ma, Hongli Zhu, Jun Bai, Lixiu Liu, Xiaoning Li, Jing Cai, Beibei Wang, Lijun Wang, Yuan Pang, Hui Zhang, Y. Yang, Nan Li, Mei Chen
Summary: TNF-alpha affects the activities of NF-kappa B, PI3K/Akt, and Wnt/beta-catenin signaling pathways in human Lgr5(+) ISCs. Lgr5(+) ISCs exhibit higher proliferation capacity, invasive ability, and drug resistance compared to Lgr5(-) cells, as well as higher expression levels of anti-apoptotic proteins and lower expression levels of pro-apoptotic proteins.
ANTICANCER RESEARCH
(2022)
Article
Multidisciplinary Sciences
Yan Wang, Binbin Ma, Xiaoxu Liu, Ge Gao, Zhuanzhuan Che, Menghan Fan, Siyan Meng, Xiru Zhao, Rio Sugimura, Hua Cao, Zhongjun Zhou, Jing Xie, Chengqi Lin, Zhuojuan Luo
Summary: ZFP281 cooperates with BRCA2 to prevent R-loop accumulation and facilitate DNA replication in embryonic stem cells. ZFP281 interacts with BRCA2 and recruits it to the bivalent chromatin regions at the genome-wide scale.
NATURE COMMUNICATIONS
(2022)
Article
Cell Biology
Yingying Gao, Bin Ma, Yifan Li, Xiangyu Wu, Shifeng Zhao, Huiping Guo, Yiwei Wang, Lihua Sun, Jing Xie
Summary: The study shows that Haspin is essential for maintaining a balanced ratio of asymmetric cell division (ACD) in mouse embryonic stem cells (mESCs). Knockout of Haspin leads to an increased ratio of ACD. This imbalance is rescued by overexpression of Wnt5a, suggesting that Haspin regulates ACD through the Wnt5a pathway.
CELL DEATH DISCOVERY
(2023)
Article
Biochemical Research Methods
Binbin Ma, Tung-Jui Trieu, Shukry J. Habib, Xin Chen
Article
Biotechnology & Applied Microbiology
Zhongqu Duan, Yuyang Qiao, Jinyuan Lu, Huimin Lu, Wenmin Zhang, Fazhe Yan, Chen Sun, Zhiqiang Hu, Zhen Zhang, Guichao Li, Hongzhuan Chen, Zhen Xiang, Zhenggang Zhu, Hongyu Zhao, Yingyan Yu, Chaochun Wei