Article
Multidisciplinary Sciences
Cheng Zeng, Jiwei Chen, Emmalee W. Cooke, Arijita Subuddhi, Eliana T. Roodman, Fei Xavier Chen, Kaixiang Cao
Summary: This study reveals the catalytic-independent role of LSD1 in regulating gene expression and cellular differentiation, demonstrating that the loss of LSD1 protein globally de-represses enhancers and impairs cell fate transition. The researchers found that the increase of H3K27ac catalyzed by P300/CBP, rather than the loss of CoREST complex components from chromatin, contributes to the transcription de-repression of LSD1 targets and differentiation defects caused by LSD1 loss.
NATURE COMMUNICATIONS
(2023)
Article
Agronomy
Feng Luo, Guo-Bao Niu, Qian Zhou, Li-Jie Wang, Li-Juan Bai, Wen-Zheng Gao
Summary: This study identified six anthocyanin-related metabolites in postharvest Pr mutants of purple cauliflower using metabolomic analyses. The main component responsible for the pungent flavor of the Pr mutant was found to be 6-gingerol, which is involved in several biosynthesis pathways. The expression level of caffeoyl coenzyme A O-methyltransferase (CCoAOMT) was correlated with the pungent flavor, and the transcription factor (TF) BoMYB2 was found to negatively regulate BoCCoAOMT transcription and promote 6-gingerol accumulation.
POSTHARVEST BIOLOGY AND TECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Se-Young Jo, Namki Hong, Seunghyun Lee, Jong Ju Jeong, Jeongsoo Won, Jiho Park, Gi Jeong Kim, Sang Kyum Kim, Sangwoo Kim, Yumie Rhee
Summary: Genomic and transcriptomic profiling of parathyroid tissues revealed multiple two-hit mutation patterns in the CDC73 gene, suggesting potential therapeutic targets. Transcriptomic analysis identified upregulated expression of E2F targets, KRAS and TNF-alpha signaling, and epithelial-mesenchymal transition pathways in parathyroid carcinomas. A molecular classification model based on carcinoma-specific genes could effectively distinguish between carcinomas, adenomas, and normal tissues, with potential clinical utility.
EXPERIMENTAL AND MOLECULAR MEDICINE
(2023)
Article
Plant Sciences
Ningning Tong, Qingyan Shu, Baichen Wang, Liping Peng, Zheng'an Liu
Summary: This study investigated the developmental dynamics of tree peony annual shoots using anatomy, physiology, transcriptome, and metabolome analysis. The results showed that the developmental dynamics of the two cultivars were similar. The withering degree of P. suffruticosa 'Luoyanghong' was higher than that of P. ostii 'Fengdan'. Additionally, the study identified key genes and metabolic pathways related to the withering process of the annual shoots.
HORTICULTURE RESEARCH
(2023)
Article
Immunology
Yan Wang, Hongxia Jia, Wei Li, Hongping Liu, Meng Tu, Jing Li, Jiuling Cheng, Guojun Zhang
Summary: This study investigated the correlation between anti-MDA5 antibody titers and type I IFN signature in patients with MDA5+ DM. Transcriptome profiling of PBMCs in MDA5+ DM patients revealed enrichment of differentially expressed genes related to viral and cytokine pathways. Significant correlations were found between anti-MDA5 titers and type I IFN scores, and higher titers were observed in patients with ultra-high type I IFN scores. Furthermore, the asynchrony between type I IFN scores and anti-MDA5 titers was observed during the course of treatment.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Biology
Yuka Takemon, Joel M. Chick, Isabela Gerdes Gyuricza, Daniel A. Skelly, Olivier Devuyst, Steven P. Gygi, Gary A. Churchill, Ron Korstanje
Summary: By measuring mRNA and protein levels in genetically diverse mice at different ages, we found distinctive changes in mRNA and protein levels as age increases. These changes are associated with increased immune infiltration and decreased mitochondrial function. Proteins show a greater extent of change and reveal a wide array of biological processes affected, including unique features of aging in kidney. Most importantly, functionally important age-related protein changes were observed in the absence of corresponding mRNA changes, suggesting that mRNA profiling alone does not provide a complete picture of molecular aging in the kidney.
Article
Cell Biology
Qiting He, Jie Shi, Wei Liu, Wei Zhao, Zihao Wang, Kaiwen Liu, Dawang Zhao, Shaoyi Wang, Yongyuan Guo, Lei Cheng, Yuan Gao
Summary: This study found that epigenetic mechanisms play an important role in the migration of mesenchymal stem cells and that H3K27me3 is at least partially involved in the migration of mesenchymal stem cells induced by TGF-beta 1.
CELL DEATH DISCOVERY
(2022)
Article
Biochemistry & Molecular Biology
Jiahui Liang, Jing Zheng, Ze Wu, Hongqing Wang
Summary: This study investigated the gene activity and regulatory mechanisms during the key period of floral induction in strawberries through transcriptome analysis. Several important genes involved in floral induction were identified, and a preliminary regulatory network was constructed. This provides potential candidate genes for future studies of flowering in strawberries.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Matthew W. W. Kenaston, Oanh H. H. Pham, Marine J. J. Petit, Priya S. S. Shah
Summary: This study investigates the role of polymerase associated factor 1 complex (PAF1C) in innate immunity by analyzing gene expression patterns in PAF1 knockout cells exposed to various immune stimuli. The results confirm PAF1 as an activator of immune response pathways and provide insights into its potential regulatory functions. The findings highlight the importance of PAF1C in innate immunity and pave the way for further studies on its role as a regulator.
Article
Biochemistry & Molecular Biology
Ziyang Liu, Anqiang Wang, Yingying Pu, Zhongwu Li, Ruidong Xue, Chong Zhang, Xiao Xiang, E. Jian-Yu, Zhaode Bu, Fan Bai, Jiafu Ji
Summary: Hepatoid adenocarcinoma of the stomach (HAS) is a rare subtype of gastric cancer with high mortality rate. Research suggests that HAS may originate from pluripotent precursor cells and has high stemness and methionine cycle activity. Genes involved in the methionine cycle, such as MAT2A and AHCY, are potential targets for HAS treatment.
Article
Cell Biology
Yu Li, Bingbing Wu, Chengrui An, Deming Jiang, Lin Gong, Yanshan Liu, Yixiao Liu, Jun Li, Hongwei Ouyang, XiaoHui Zou
Summary: This study developed a novel method to determine the functions of LOXL1 and found its important biological roles in multiple organs, especially involving cell proliferation and systemic immunity.
CELL PROLIFERATION
(2021)
Article
Multidisciplinary Sciences
Leroy C. Joseph, Jianting Shi, Quynh N. Nguyen, Victoria Pensiero, Chris Goulbourne, Robert C. Bauer, Hanrui Zhang, John P. Morrow
Summary: This study examines the response of the heart to a high-fat diet at the metabolomic and transcriptomic levels, revealing significant sex differences in cardiac metabolites and gene expression.
Article
Biochemistry & Molecular Biology
Nobutoshi Yamaguchi, Toshiro Ito
Summary: This study computationally characterized the expression patterns of JMJ H3K27me3 demethylase genes using public transcriptome datasets, revealing JMJ30 to be highly expressed in the L1 layer of Arabidopsis shoot apical meristem and most affected by abiotic and biotic stress. The expression of JMJ30 varied among Arabidopsis thaliana accessions, suggesting that transcriptional changes of H3K27me3 demethylase genes may play key roles in development and environmental responses. Additionally, the expression of a JMJ30 orthologue from Arabidopsis halleri fluctuated under field conditions, further supporting the importance of these genes in plant adaptation.
PLANT SIGNALING & BEHAVIOR
(2021)
Article
Plant Sciences
Congping Xu, Hafiz Muhammad Khalid Abbas, Chuansong Zhan, Yuxiao Huang, Sishu Huang, Haizhen Yang, Yulin Wang, Hongjun Yuan, Jie Luo, Xingquan Zeng
Summary: This study investigates the metabolic and transcriptomic changes associated with grain coloration in Tibetan hulless barley. It reveals the genes and metabolites involved in anthocyanin accumulation and identifies HvMYC2 as a critical regulator of anthocyanin biosynthesis. The study also unravels the major anthocyanin modification pathway in colored qingke.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Yingyu Xue, Zhiyan Shen, Fei Tao, Jingjiang Zhou, Bingliang Xu
Summary: In this study, the sequencing analysis of seed coats from hulled and hull-less Cucurbita pepo revealed lower lignin accumulation in the seed coat of the hull-less variety. The differentially expressed genes were enriched in different pathways between the two varieties. Several key proteins and transcription factors related to seed coat development were identified. Quantitative real-time PCR analysis confirmed the reliability of the RNA-Seq results.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Medicine, Research & Experimental
Benjamin N. Ediger, Hee-Woong Lim, Christine Juliana, David N. Groff, LaQueena T. Williams, Giselle Dominguez, Jin-Hua Liu, Brandon L. Taylor, Erik R. Walp, Vasumathi Kameswaran, Juxiang Yang, Chengyang Liu, Chad S. Hunter, Klaus H. Kaestner, Ali Naji, Changhong Li, Maike Sander, Roland Stein, Lori Sussel, Kyoung-Jae Won, Catherine Lee May, Doris A. Stoffers
JOURNAL OF CLINICAL INVESTIGATION
(2017)
Article
Cell Biology
Suzanne N. Shapira, Hee-Woong Lim, Sona Rajakumari, Alexander P. Sakers, Jeff Ishibashi, Matthew J. Harms, Kyoung-Jae Won, Patrick Seale
GENES & DEVELOPMENT
(2017)
Article
Medicine, Research & Experimental
Raymond E. Soccio, Zhenghui Li, Eric R. Chen, Yee Hoon Foong, Kiara K. Benson, Joanna R. Dispirito, Shannon E. Mullican, Matthew J. Emmett, Erika R. Briggs, Lindsey C. Peed, Richard K. Dzeng, Carlos J. Medina, Jennifer F. Jolivert, Megan Kissig, Satyajit R. Rajapurkar, Manashree Damle, Hee-Woong Lim, Kyoung-Jae Won, Patrick Seale, David J. Steger, Mitchell A. Lazar
JOURNAL OF CLINICAL INVESTIGATION
(2017)
Article
Biochemistry & Molecular Biology
Pau Pascual-Garcia, Brian Debo, Jennifer R. Aleman, Jessica A. Talamas, Yemin Lan, Nha H. Nguyen, Kyoung J. Won, Maya Capelson
Article
Biochemical Research Methods
David E. Condon, Phu V. Tran, Yu-Chin Lien, Jonathan Schug, Michael K. Georgieff, Rebecca A. Simmons, Kyoung-Jae Won
BMC BIOINFORMATICS
(2018)
Article
Biochemistry & Molecular Biology
Dongha Kim, Hye Jin Nam, Wonhwa Lee, Hwa Young Yim, Jun-Yeong Ahn, Se Won Park, Hi-Jai R. Shin, Reynold Yu, Kyoung-Jae Won, Jong-Sup Bae, Keun Il Kim, Sung Hee Baek
Article
Biochemistry & Molecular Biology
Daniel M. Cohen, Hee-Woong Lim, Kyoung-Jae Won, David J. Steger
NUCLEIC ACIDS RESEARCH
(2018)
Article
Multidisciplinary Sciences
David A. Hill, Hee-Woong Lim, Yong Hoon Kim, Wesley Y. Ho, Yee Hoon Foong, Victoria L. Nelson, Hoang C. B. Nguyen, Kavya Chegireddy, Jihoon Kim, Andreas Habertheuer, Prashanth Vallabhajosyula, Taku Kambayashi, Kyoung-Jae Won, Mitchell A. Lazar
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2018)
Article
Multidisciplinary Sciences
Yong Hoon Kim, Sajid A. Marhon, Yuxiang Zhang, David J. Steger, Kyoung-Jae Won, Mitchell A. Lazar
Article
Biochemistry & Molecular Biology
Junil Kim, Diana E. Stanescu, Kyoung Jae Won
NUCLEIC ACIDS RESEARCH
(2018)
Article
Developmental Biology
Victor Muthu, Alex M. Rohacek, Yao Yao, Staci M. Rakowiecki, Alexander S. Brown, Ying-Tao Zhao, James Meyers, Kyoung-Jae Won, Shweta Ramdas, Christopher D. Brown, Kevin A. Peterson, Douglas J. Epstein
Article
Biochemistry & Molecular Biology
Shibiao Wan, Junil Kim, Kyoung Jae Won
Article
Endocrinology & Metabolism
Cetewayo S. Rashid, Yu-Chin Lien, Amita Bansal, Lane J. Jaeckle-Santos, Changhong Li, Kyoung-Jae Won, Rebecca A. Simmons
Review
Chemistry, Medicinal
Su Jin Choi, Yu Su Shin, Byung Woog Kang, Jong Gwang Kim, Kyoung-Jae Won, Paul M. Lieberman, Hyosun Cho, Hyojeung Kang
ARCHIVES OF PHARMACAL RESEARCH
(2017)
Article
Biochemistry & Molecular Biology
Megan Kissig, Jeff Ishibashi, Matthew J. Harms, Hee-Woong Lim, Rachel R. Stine, Kyoung-Jae Won, Patrick Seale
