Article
Biochemistry & Molecular Biology
Daigo Okada, Yosuke Okamoto, Toshiro Io, Miho Oka, Daiki Kobayashi, Suzuka Ito, Ryo Yamada, Kuniaki Ishii, Kyoichi Ono
Summary: The study analyzed transcriptome data from different species to compare the species differences in gene expression in different regions of the heart. The findings showed that the species differences were the greatest in the sinoatrial nodes (SA) region. By calculating specificity measure values, the study identified SHOX2 as an important gene that determines the characteristics of the SA region. Additionally, the study identified tissue-specific markers and species-dependent gene expression patterns.
Article
Neurosciences
Pin Xu, Stefano Berto, Ashwinikumar Kulkarni, Byeongha Jeong, Chryshanthi Joseph, Kimberly H. Cox, Michael E. Greenberg, Tae-Kyung Kim, Genevieve Konopka, Joseph S. Takahashi
Summary: The suprachiasmatic nucleus (SCN) in mammals is regulated by environmental light and shows responses to light through different peptidergic cell types. The study found that NPAS4 plays a critical role in normal transcriptional responses to light in the SCN, affecting circadian behavior and light-induced gene expression.
Article
Biology
Katherine Rhodes, Kenneth A. Barr, Joshua M. Popp, Benjamin J. Strober, Alexis Battle, Yoav Gilad
Summary: Most studies on gene expression in humans have focused on a small number of adult tissues, limiting our understanding of dynamic gene regulation. To better understand the connection between gene regulation and complex traits, including disease, it is essential to study gene expression in a wider range of relevant cell types, tissues, and developmental stages. Embryoid bodies (EBs) have been proposed as a model system to study dynamic regulatory processes in various cell types. The use of EBs allows for the exploration of inter-individual regulatory differences and provides insights into gene regulation at high resolution.
Article
Multidisciplinary Sciences
Zaniar Ghazizadeh, Jiajun Zhu, Faranak Fattahi, Alice Tang, Xiaolu Sun, Sadaf Amin, Su-Yi Tsai, Mona Khalaj, Ting Zhou, Ryan M. Samuel, Tuo Zhang, Francis A. Ortega, Miriam Gordillo, Dorota Moroziewicz, Daniel Paull, Scott A. Noggle, Jenny Zhaoying Xiang, Lorenz Studer, David J. Christini, Geoffrey S. Pitt, Todd Evans, Shuibing Chen
Summary: Researchers developed a dual reporter system that enables efficient derivation of SAN-like cells and exploration of their single-cell transcriptional profile. This has potential applications in disease modeling and drug discovery.
Article
Biochemistry & Molecular Biology
Praphawi Nattasit, Kunimichi Niibe, Masahiro Yamada, Yumi Ohori-Morita, Phoonsuk Limraksasin, Watcharaphol Tiskratok, Masaya Yamamoto, Hiroshi Egusa
Summary: The stiffness of the substrate can regulate the behavior and differentiation of induced pluripotent stem cell (iPSC)-derived embryoid bodies (EB). A 3D hydrogel-sandwich culture (HGSC) system was developed to investigate the effects of mechanical cues on iPSC-EB differentiation. The moderate-stiffness HGSC promotes ectoderm and mesoderm lineage differentiation, as well as cardiomyocyte differentiation and myofibril structural maturation.
MACROMOLECULAR BIOSCIENCE
(2023)
Article
Biology
Xianguo Zhao, Xingzhuo Yang, Pengfei Lv, Yuetong Xu, Xiangfeng Wang, Zhangwu Zhao, Juan Du
Summary: This study shows the crucial role of the epigenetic regulator Polycomb (Pc) in regulating the circadian rhythm in Drosophila clock neurons. By using targeted DamID technology, the study identifies Pc targets in different neuron clusters, providing important insights into the regulatory mechanisms of circadian rhythms.
LIFE SCIENCE ALLIANCE
(2023)
Article
Cell Biology
Hironori Hojo, Taku Saito, Xinjun He, Qiuyu Guo, Shoko Onodera, Toshifumi Azuma, Michinori Koebis, Kazuki Nakao, Atsu Aiba, Masahide Seki, Yutaka Suzuki, Hiroyuki Okada, Sakae Tanaka, Ung-il Chung, Andrew P. McMahon, Shinsuke Ohba
Summary: This study investigated Runx2-DNA binding and chromatin accessibility in neonatal osteoblasts and chondrocytes, revealing that Runx2 interacts with cell-type-specific chromatin-accessible regions and enhances chromatin accessibility. It was found that Runx2 is essential for establishing chromatin accessibility in osteoblasts and specific enhancers driven by Runx2 contribute to normal osteoblast differentiation.
Article
Biology
Yunkai Dai, Fatemeh Nasehi, Charles D. Winchester, Ann C. Foley
Summary: Genetic studies have identified Tbx5 as a key player in the differentiation of sinoatrial node (SAN) cells. Overexpression of Tbx5, Islet1, and TAK1 has been shown to promote faster beating of cardiac cells and increase the expression of SAN genes. Blocking the phosphorylation of TAK1 can also activate the SAN transcriptional network and induce cardiac differentiation into SAN cells.
Article
Biochemistry & Molecular Biology
Atsushi Morii, Tetsuya Inazu
Summary: HDAC8 is involved in embryoid body formation and neuronal differentiation in P19EC cells by regulating the canonical Hedgehog (Hh) signaling pathway.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Hisashi Yano, Takashi Inoue, Satoshi Murakami, Hiroyuki Kaneko
Summary: The aim of this study was to investigate the impact of oxygen tension on mouse induced pluripotent stem (iPS) cells in terms of differentiation and expression levels of collagen type 1 and Runx2. Under hypoxia, normoxia, and hyperoxia conditions, embryoid bodies (EBs) and outgrowth cells (OGCs) were cultured. In comparison to the hypoxia group, significantly larger EBs were observed in the hyperoxia and normoxia groups on Days 8 and 10. Furthermore, the hyperoxia group exhibited significantly higher expression levels of collagen type 1 and Runx2 mRNA and protein on Days 10 and 26, indicating accelerated differentiation of iPS cells.
APPLIED SCIENCES-BASEL
(2023)
Article
Plant Sciences
Tatsunosuke Tomita, Renu Wadhwa, Sunil C. Kaul, Ryoji Kurita, Naoshi Kojima, Yoshiaki Onishi
Summary: Withanolide derivatives, particularly 3 beta mWi-A, have been shown to lengthen the circadian clock, upregulate the expression of key genes involved in circadian rhythms, and act as an inverse agonist for RORa. These findings suggest that 3 beta mWi-A may serve as a novel modulator of circadian rhythms.
JOURNAL OF NATURAL PRODUCTS
(2021)
Article
Microbiology
Yuhui Qi, Chenyang Huang, Mengran Zhao, Xiangli Wu, Guangyu Li, Yingjie Zhang, Lijiao Zhang
Summary: This study investigates the role of milRNAs in the development of fruit bodies of Pleurotus cornucopiae. Comparative analysis of mRNAs and milRNAs at different stages of development reveals important genes involved in the expression and function of milRNAs. The study shows that miRNAs and its target genes are involved in several metabolic pathways and play significant roles in the development of fruit bodies in P. cornucopiae.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Liu Teng, Yu Chen Feng, Su Tang Guo, Pei Lin Wang, Teng Fei Qi, Yi Meng Yue, Shi Xing Wang, Sheng Nan Zhang, Cai Xia Tang, Ting La, Yuan Yuan Zhang, Xiao Hong Zhao, Jin Nan Gao, Li Yuan Wei, Didi Zhang, Jenny Y. Wang, Yujie Shi, Xiao Ying Liu, Jin Ming Li, Huixia Cao, Tao Liu, Rick F. Thorne, Lei Jin, Feng-Min Shao, Xu Dong Zhang
Summary: The study identified the lncRNA PLANE as a non-protein product of chromosome 3q amplification that promotes tumorigenesis by disrupting the splicing of transcriptional corepressor NCOR2 pre-mRNA.
NATURE COMMUNICATIONS
(2021)
Article
Reproductive Biology
Muhammad Nihad, Utsav Sen, Debajit Chaudhury, Undurti N. Das, P. Sudheer Shenoy, Bipasha Bose
Summary: This study investigated the protective effects of arachidonic acid (AA) against the embryotoxic drug valproic acid (VA). The results showed that AA played an important regulatory role in the proliferation and differentiation of induced pluripotent stem cells (iPSCs) and pluripotent NTERA-2 embryonal carcinoma (EC) cells, and protected the embryoid bodies (EBs) from cytotoxic damage, ensuring normal embryogenesis.
REPRODUCTIVE TOXICOLOGY
(2023)
Article
Cell Biology
Tsung-Yen Huang, Masato Hirota, Daiki Sasaki, Rajkumar Singh Kalra, Hsiao-Chiao Chien, Miho Tamai, Shukla Sarkar, Yang Mi, Mio Miyagi, Yu Seto, Hiroki Ishikawa
Summary: Aerobic glycolysis, essential for effector T cell survival and proliferation, regulates Th17 differentiation through the negative regulation of phosphoenolpyruvate (PEP). PEP supplementation or inhibition of downstream glycolytic enzymes increases PEP levels and inhibits IL-17A expression. Mechanistically, PEP binds to JunB and inhibits DNA binding of the JunB/BATF/IRF4 complex, thereby modulating the Th17 transcriptional program. PEP administration inhibits Th17 generation and improves Th17-dependent autoimmune encephalomyelitis.