Article
Biochemistry & Molecular Biology
Anthony Leon, Lucie Subirana, Kevin Magre, Ildefonso Cases, Juan J. Tena, Manuel Irimia, Jose Luis Gomez-Skarmeta, Hector Escriva, Stephanie Bertrand
Summary: Neurons are specialized cells found only in metazoans. How pluripotent ectodermal cells are directed towards neural or epidermal fates is an open question. This study used micromere explants to investigate the gene regulatory networks underlying the formation of the central nervous system and epidermis in the cephalochordate amphioxus.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Miki Tokuoka, Kazuki Maeda, Kenji Kobayashi, Atsushi Mochizuki, Yutaka Satou
Summary: The study revealed how gene regulatory networks control gene expression dynamics in ascidian embryos, including the regulatory logic and core mechanism at the 32-cell stage, offering important insights into the operating principles of gene regulatory networks.
Article
Multidisciplinary Sciences
Michal Levo, Joao Raimundo, Xin Yang Bing, Zachary Sisco, Philippe J. Batut, Sergey Ryabichko, Thomas Gregor, Michael S. Levine
Summary: The prevailing view of metazoan gene regulation is challenged by recent findings that reveal physical and functional connections between genes separated by large genomic distances, providing new insights into gene regulation mechanisms.
Article
Cell Biology
Yuting Liu, Xin Wan, Hu Li, Yingxi Chen, Xiaodi Hu, Hebing Chen, Dahai Zhu, Cheng Li, Yong Zhang
Summary: CTCF cooperates with lineage-specific pioneer transcription factors to control cell identity genes, facilitating CTFC occupancy and forming regulatory hubs at both 1D and 3D levels.
Article
Genetics & Heredity
Jianfei Wu, Fan Gao, Tongtong Li, Haixia Guo, Li Zhang, Yijie Fan, Aiyun Chen, Jianjun Wang, Fengjuan Shi, Guangyao Shan, Huihui Guo, Fanchang Zeng
Summary: Auxin, a hormone, plays a crucial role in various aspects of plant development. This study proposes a method to identify genes responsive to auxin in the model plant Arabidopsis thaliana. By analyzing specific regulatory elements in gene promoters, the researchers were able to predict candidate genes with an accuracy rate of 65.2%. The results provide valuable insights into the understanding of auxin-responsive genes and improve gene annotation.
Article
Agriculture, Dairy & Animal Science
Bing Pan, Haoyuan Long, Ying Yuan, Haoyuan Zhang, Yangyang Peng, Dongke Zhou, Chengli Liu, Baiju Xiang, Yongfu Huang, Yongju Zhao, Zhongquan Zhao, Guangxin E
Summary: This study used genome-wide selection analysis to identify candidate regions and genes related to the body size of pigs. Key genes and molecular pathways associated with body development were discovered, providing a better understanding of the genetic basis of body size determination.
Article
Cell & Tissue Engineering
Y. Jia, X. Qi, M. Ma, S. Cheng, B. Cheng, C. Liang, X. Guo, F. Zhang
Summary: This study aimed to explore novel regulatory genetic variants associated with bone mineral density (BMD). Through an integrative analysis of BMD genome-wide association study and regulatory single nucleotide polymorphism (rSNP) annotation information, we identified 36 common genes associated with BMD, such as FAM3C, CCDC170, and SOX6. Additionally, multiple gene ontology terms related to BMD were detected. These findings support the implication of regulatory genetic variants in the development of osteoporosis.
BONE & JOINT RESEARCH
(2023)
Article
Evolutionary Biology
Nitish Malhotra, Aswin Sai Narain Seshasayee
Summary: Bacterial genome organization is influenced by chromosomal replication and the presence of long identical DNA repeats. The positioning of long DNA repeats in the genome is under selection, as it affects bacterial fitness and growth rate. A study found that the distribution of long DNA repeats differs between fast- and slow-growing bacteria, suggesting that their positioning is a major constraint in maintaining the genome organization and minimizing disruption.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Plant Sciences
Mengyao Li, Xiaoyan Li, Jin Zhou, Yue Sun, Jiageng Du, Zhuo Wang, Ya Luo, Yong Zhang, Qing Chen, Yan Wang, Yuanxiu Lin, Yunting Zhang, Wen He, Xiaorong Wang, Haoru Tang
Summary: This study systematically analyzed the TPS gene family in celery, revealing the functional diversity and biosynthesis pathways of terpenoids. It identified key candidate genes that regulate the biosynthesis of volatile compounds and provided a foundation for the development and utilization of terpenoids in celery.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Immunology
Ashley S. Doane, Chi-Shuen Chu, Dafne Campigli Di Giammartino, Martin A. Rivas, Johannes C. Hellmuth, Yanwen Jiang, Nevin Yusufova, Alicia Alonso, Robert G. Roeder, Effie Apostolou, Ari M. Melnick, Olivier Elemento
Summary: The study reveals that OCT2 plays a key role in regulating the accessibility of GC regulatory elements during the humoral immune response, with pre-positioned key regulators at SEs potentially representing a widely used strategy for facilitating rapid cell fate transitions.
Review
Developmental Biology
Marius Regin, Claudia Spits, Karen Sermon
Summary: About 8 out of 10 human embryos obtained in vitro have chromosomal abnormalities. Chromosomal mosaicism caused by mitotic origin abnormalities has sparked debate and confounds preimplantation genetic testing for aneuploidy (PGT-A). This article focuses on post-zygotic chromosomal abnormalities leading to mosaicism and summarizes the rates of such abnormalities at different developmental stages. Hypotheses on the mechanisms at work in early human development are also discussed.
MOLECULAR HUMAN REPRODUCTION
(2022)
Article
Agricultural Engineering
Shuang Liu, Xuecui Yin, Tinghui Feng, Zepeng Kang, Xuemin Zhang, Juane Dong, Zongsuo Liang
Summary: This study analyzed the TCP genome of S. tora and investigated its evolution and function. The involvement of TCP in jasmonic acid (JA) signal transduction was further analyzed through a protein interaction experiment. The results showed that StTCP4.1 and StTCP11 may regulate the synthesis of anthraquinone compounds in S. tora and be involved in JA response signaling.
INDUSTRIAL CROPS AND PRODUCTS
(2022)
Article
Biology
Max Karlsson, Evelina Sjostedt, Per Oksvold, Asa Sivertsson, Jinrong Huang, Maria Bueno Alvez, Muhammad Arif, Xiangyu Li, Lin Lin, Jiaying Yu, Tao Ma, Fengping Xu, Peng Han, Hui Jiang, Adil Mardinoglu, Cheng Zhang, Kalle von Feilitzen, Xun Xu, Jian Wang, Huanming Yang, Lars Bolund, Wen Zhong, Linn Fagerberg, Cecilia Lindskog, Fredrik Ponten, Jan Mulder, Yonglun Luo, Mathias Uhlen
Summary: This study introduces a new genome-wide annotation strategy based on dimensionality reduction and density-based clustering, and presents a whole-body map of protein-coding genes in the pig. The study provides insights into the expression patterns of these genes across different tissues and organs.
Article
Agronomy
Yurong He, Wei Liu, Zhihao Huang, Jishuai Huang, Yanghong Xu, Qiannan Zhang, Jun Hu
Summary: This study provides a comprehensive analysis of the GA oxidase gene family in rice. The genes were divided into four subgroups and shared some common features with GAox genes in Arabidopsis. Tissue-specific expression patterns were observed for each GAox gene, and some genes may play a major role in regulating the level of bioactive GA.
Review
Genetics & Heredity
Heleen Masset, Olga Tsuiko, Joris R. Vermeesch
Summary: This review provides an overview of genome-wide abnormalities and their clinical consequences, historical proposed mechanisms for ploidy aberrations, and the discovery of a noncanonical zygotic cleavage leading to blastomere ploidy variation in embryos, suggesting a unifying theory for different forms of genome-wide abnormalities.
PRENATAL DIAGNOSIS
(2021)
Article
Biochemistry & Molecular Biology
Jun Inoue, Noriyuki Satoh
MOLECULAR BIOLOGY AND EVOLUTION
(2018)
Article
Biochemistry & Molecular Biology
Ferdinand Marletaz, Katja T. C. A. Peijnenburg, Taichiro Goto, Noriyuki Satoh, Daniel S. Rokhsar
Article
Biochemistry & Molecular Biology
Jun Inoue, Noriyuki Satoh
MOLECULAR BIOLOGY AND EVOLUTION
(2019)
Article
Zoology
Takeshi Noda, Noriyuki Satoh, Takahiro Asami
ZOOLOGICAL LETTERS
(2019)
Article
Ecology
David A. Gold, Takeo Katsuki, Yang Li, Xifeng Yan, Michael Regulski, David Ibberson, Thomas Holstein, Robert E. Steele, David K. Jacobs, Ralph J. Greenspan
NATURE ECOLOGY & EVOLUTION
(2019)
Article
Genetics & Heredity
Asuka Arimoto, Koki Nishitsuji, Yoshimi Higa, Nana Arakaki, Kanako Hisata, Chuya Shinzato, Noriyuki Satoh, Eiichi Shoguchi
Article
Genetics & Heredity
Tatsuya Ueki, Manabu Fujie, Romaidi, Noriyuki Satoh
Article
Multidisciplinary Sciences
Girish Beedessee, Kanako Hisata, Michael C. Roy, Frances M. Van Dolah, Noriyuki Satoh, Eiichi Shoguchi
SCIENTIFIC REPORTS
(2019)
Article
Biochemistry & Molecular Biology
Herve Philippe, Albert J. Poustka, Marta Chiodin, Katharina J. Hoff, Christophe Dessimoz, Bartlomiej Tomiczek, Philipp H. Schiffer, Steven Mueller, Daryl Domman, Matthias Horn, Heiner Kuhl, Bernd Timmermann, Noriyuki Satoh, Tomoe Hikosaka-Katayama, Hiroaki Nakano, Matthew L. Rowe, Maurice R. Elphick, Morgane Thomas-Chollier, Thomas Hankeln, Florian Mertes, Andreas Wallberg, Jonathan P. Rast, Richard R. Copley, Pedro Martinez, Maximilian J. Telford
Article
Genetics & Heredity
Jun Inoue, Keisuke Nakashima, Noriyuki Satoh
Article
Biology
Asuka Arimoto, Tomoe Hikosaka-Katayama, Akira Hikosaka, Kuni Tagawa, Toyoshige Inoue, Tatsuya Ueki, Masa-aki Yoshida, Miyuki Kanda, Eiichi Shoguchi, Kanako Hisata, Noriyuki Satoh
Article
Ecology
Konstantin Khalturin, Chuya Shinzato, Maria Khalturina, Mayuko Hamada, Manabu Fujie, Ryo Koyanagi, Miyuki Kanda, Hiroki Goto, Friederike Anton-Erxleben, Masaya Toyokawa, Sho Toshino, Noriyuki Satoh
NATURE ECOLOGY & EVOLUTION
(2019)
Article
Food Science & Technology
Akiko Isomoto, Eiichi Shoguchi, Kanako Hisata, Jun Inoue, Yinrui Sun, Kenji Inaba, Noriyuki Satoh, Tomohisa Ogawa, Hiroki Shibata
Summary: This study identified genes involved in the modification and functioning of venom proteins in Protobothrops flavoviridis, a venomous snake species. Genes encoding protein disulfide isomerase (PDI) family members, Selenoprotein M (SELENOM), and Calreticulin (CALR) were highly expressed in venom glands, suggesting their potential role in protein folding and modification.
Article
Multidisciplinary Sciences
Yafei Mao, Noriyuki Satoh
Article
Multidisciplinary Sciences
Koki Nishitsuji, Asuka Arimoto, Yoshimi Higa, Munekazu Mekaru, Mayumi Kawamitsu, Noriyuki Satoh, Eiichi Shoguchi
SCIENTIFIC REPORTS
(2019)
Review
Developmental Biology
Cheng Shi, Pengfei Jiao, Zhiyi Chen, Lan Ma, Siyue Yao
Summary: This review discusses the molecular etiology of congenital craniofacial abnormalities, with a focus on the role and mechanism of noncoding RNAs in regulating craniofacial development. Aberrant expression of noncoding RNAs has been implicated in the pathogenesis of craniofacial abnormalities, providing potential therapeutic targets.
DEVELOPMENTAL BIOLOGY
(2024)
Article
Developmental Biology
Hideru Togashi, Steven Ray Davis, Makoto Sato
Summary: Tile patterns, regulated by cell adhesion molecules, are regular arrangements of cells that play important functional roles in multicellular organisms. The physical constraints and cell adhesion regulate both cell shape and tissue morphogenesis.
DEVELOPMENTAL BIOLOGY
(2024)
Article
Developmental Biology
Armen Khanbabei, Lina Segura, Cynthia Petrossian, Aaron Lemus, Ithan Cano, Courtney Frazier, Armen Halajyan, Donnie Ca, Mariano Loza-Coll
Summary: This article investigates the genetic regulatory mechanisms of Drosophila intestinal stem cells. The study found that most target genes co-regulated by Esg and STAT show a consistent gene expression pattern. However, manipulating these validated targets in vivo rarely replicated the effects of manipulating Esg and STAT, suggesting the presence of complex genetic interactions among the downstream targets of these two master regulator genes.
DEVELOPMENTAL BIOLOGY
(2024)
Article
Developmental Biology
Bayley J. Waters, Zoe R. Birman, Matthew R. Wagner, Julia Lemanski, Barak Blum
Summary: Researchers found that conditional deletion of Robo2 in adult mice led to a significant loss of islet architecture without affecting beta cell identity or function, suggesting that Robo2 plays a role in actively maintaining adult islet architecture. Understanding the factors required for islet architecture maintenance is crucial for developing future diabetes therapies.
DEVELOPMENTAL BIOLOGY
(2024)
Article
Developmental Biology
Rhiannon Clements, Tyler Smith, Luke Cowart, Jennifer Zhumi, Alan Sherrod, Aidan Cahill, Ginger L. Hunter
Summary: Cell protrusions play a crucial role in regulating cell activities during development. By studying the regulation mechanism in fruit fly sensory bristle patterning, it was found that Myosin XV is essential for the dynamics of signaling filopodia and promotes long-range Notch signaling.
DEVELOPMENTAL BIOLOGY
(2024)
Article
Developmental Biology
Margaret Keating, Ryan Hagle, Daniel Osorio-Mendez, Anjelica Rodriguez-Parks, Sarah I. Almutawa, Junsu Kang
Summary: Knock-in reporter (KI) animals are essential for studying gene expression in biomedical research. This study developed a new strategy using minicircle technology and a minimal promoter to enhance knock-in events and establish stable KI transgenic reporter lines. The study also highlighted the importance of selecting the proper KI line due to potential inappropriate influence of genome editing on reporter gene expression.
DEVELOPMENTAL BIOLOGY
(2024)
Article
Developmental Biology
Christian Altbuerger, Meta Rath, Daniel Armbruster, Wolfgang Driever
Summary: This study reveals that Neurog1 and Olig2 transcription factors have differential requirements for the development of dopaminergic neurons, and they integrate local patterning signals and Notch neurogenic selection signaling to specify the progenitor population and initiate neurogenesis and differentiation.
DEVELOPMENTAL BIOLOGY
(2024)