Article
Biochemistry & Molecular Biology
Wing-Keung Chu, Li-Man Hung, Chun-Wei Hou, Jan-Kan Chen
Summary: This study found that MIR630 represses the expression of NANOG through transcriptional and post-transcriptional regulation, leading to the differentiation of NT2/D1 cells. MIR630 may have multiple binding sites in the 3'UTR of NANOG and may act together with other miRNAs to maximally suppress NANOG expression.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Tianjiao Zhang, Liangyu Li, Hailong Sun, Dali Xu, Guohua Wang
Summary: This article introduces a deep learning framework called DeepICSH for identifying silencers in specific cells. DeepICSH leverages multiple biological data sources and a convolutional neural network to capture biologically relevant signal combinations associated with silencers. Through extensive experiments, DeepICSH has shown superior performance in silencer identification.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Cell Biology
Junjun Li, Yongchang Zhang, Li Wang, Min Li, Jianbo Yang, Pan Chen, Jie Zhu, Xiayu Li, Zhaoyang Zeng, Guiyuan Li, Wei Xiong, James B. McCarthy, Bo Xiang, Mei Yi
Summary: This study uncovered a previously unrecognized role of FOXA1 in mediating loss of imprinting of IGF2, which confers enhanced survival ability to LUAD cells against nutrient deprivation by suppressing autophagic cell death. FOXA1 can regulate the LOI of IGF2 and enhance its inhibitory effect on cell death-related genes. Additionally, FOXA1 also enhances cell survival by suppressing GBA1 expression.
CELL DEATH & DISEASE
(2022)
Article
Biochemistry & Molecular Biology
Li Liu, Haojie Li, Mengjie Wang, Xiangzheng Zhang, Jie Ren, Yan Yuan, Jiahao Sha, Xuejiang Guo
Summary: Epigenetic regulation, specifically histone post-translational modifications (PTMs), is involved in the differentiation of spermatogonial stem cells (SSCs). However, due to the low number of SSCs in vivo, there is a lack of systematic studies on the regulation of histone PTMs during SSCs differentiation. In this study, we used targeted quantitative proteomics with mass spectrometry and RNA-seq data to quantify the dynamic changes of 46 different PTMs on histone H3.1 during SSCs differentiation in vitro. We identified seven differentially regulated histone H3.1 modifications and further identified specific binding proteins for H3K9me2 and H3S10ph, including transcription factors GTF2E2 and SUPT5H, which appear to play a crucial role in the epigenetic regulation of SSC differentiation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Oncology
Ke Xia, Wenqiang Huang, Xiaoyun Zhao, Xiaoqin Huang, Yan Chen, Li Yu, Yongjun Tan
Summary: FOXA1 plays a crucial role in breast cancer progression, and its high levels improve the survival of patients by inducing apoptosis and inhibiting cell proliferation in basal breast cancer cells. Low levels of Estrogen Receptor-1 (ESR1) are critical for FOXA1's repressive roles.
AMERICAN JOURNAL OF CANCER RESEARCH
(2022)
Review
Biochemistry & Molecular Biology
Xuejing Wang, Nicholas Wui Kiat Tan, Fong Yi Chung, Nobutoshi Yamaguchi, Eng-Seng Gan, Toshiro Ito
Summary: Heat stress is a growing threat to food security due to global warming. Plants, as sessile species, have developed different mechanisms to cope with the disruption of cellular homeostasis caused by heat stress. This article summarizes the transcriptional regulation mechanisms mediated by transcription factors, epigenetic regulators, and regulatory RNAs in response to heat stress. Additionally, cellular activities such as protein homeostasis maintenance and regulation of ROS homeostasis are discussed. The harmonious regulation of plant cells allows them to adapt to unfavorable environments. Future studies on improving crop resilience to heat stress for urban agriculture are also suggested.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Kevin G. Mark, Michael Rape
Summary: Research has shown that ubiquitylation plays a crucial role in transcription, ensuring the correct expression of genes during development. Disruption of these regulatory circuits can lead to a wide array of human diseases.
Article
Biotechnology & Applied Microbiology
Ying Wang, Hui-Liang Li, Yong-Kai Zhou, Dong Guo, Jia-Hong Zhu, Shi-Qing Peng
Summary: The study analyzed the transcriptomes of rubber tree late SE and identified differentially expressed genes involved in hormone signaling pathways, phenylpropanoid biosynthesis, and starch metabolism. Molecular markers for rubber tree late SE include genes related to hormone signaling and transcription factors, as well as genes related to histone modification.
Review
Biochemistry & Molecular Biology
Chia-Chun Tseng, Man-Chun Wong, Wei-Ting Liao, Chung-Jen Chen, Su-Chen Lee, Jeng-Hsien Yen, Shun-Jen Chang
Summary: Variants of TFBS play a crucial role in regulating gene expression in the human genome, impacting human phenotypes through various mechanisms. However, challenges persist in studying such polymorphisms.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Chi-Nga Chow, Chien-Wen Yang, Wen-Chi Chang
Summary: This article summarizes the mechanisms by which DNA polymerases catalyze a variety of RNA products in spatial and temporal patterns in eukaryotes through dynamic regulation. Dynamic gene expression is regulated by transcription factors and epigenetics. Integration of genome-wide maps and functional genomic annotation has led to the development of databases for retrieving metadata related to these regulations.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Pharmacology & Pharmacy
Fei Ren, Hongmei Ning, Yaming Ge, Zhihong Yin, Lingli Chen, Dongfang Hu, Shanshan Shen, Xinrui Wang, Siting Wang, Rongbo Li, Junping He
Summary: This study investigated the effects of Bisphenol A (BPA) on embryonic development and the involved signaling pathways and protein-protein interactions. Results showed that BPA affected multiple embryonic development pathways, and the c-Abl/YAP(Y357)/p73 pathway played a key role in apoptosis induction in response to DNA damage.
Article
Oncology
Kai Xie, Jian Feng, Shi Wang, Jing Luo, Zhijian Ren, Chao Zheng, Yifei Diao, Ramon Andrade De Mello, Simona Tavolari, Giovanni Brandi, Anja C. Roden, Binhui Ren, Yi Shen, Lin Xu, Dingwei Fan
Summary: BARX2 is up-regulated in LUAD tissues and associated with advanced stage and poor prognosis. It promotes glucose metabolism reprogramming and LUAD progression through the BARX2/FOXA1/HK2 axis.
TRANSLATIONAL LUNG CANCER RESEARCH
(2022)
Article
Cell Biology
Jonathan Lerner, Andrew Katznelson, Jingchao Zhang, Kenneth S. Zaret
Summary: Pioneer transcription factors interact with nucleosomes to scan silent, compact chromatin, enabling cooperative events that modulate gene activity. While at a subset of sites pioneer factors access chromatin by assisted loading with other transcription factors, the nucleosome-binding properties of pioneer factors enable them to initiate zygotic genome activation, embryonic development, and cellular reprogramming. Thus, pioneer factors target compact chromatin through distinct processes.
Review
Plant Sciences
Yu Chen, Fu-Yu Hung, Keiko Sugimoto
Summary: Plants have remarkable regeneration abilities, which are influenced by environmental conditions. Previous research has shown the positive effects of wound signaling and warm temperature on plant regeneration, and recent studies suggest that light and nutrient signals also play a role. Epigenetic factors, such as histone acetyl-transferases H2A variants, are important in regulating the expression of genes involved in plant regeneration. However, the specific mechanisms of how these epigenetic factors recognize genomic regions to regulate regeneration genes are still unclear. This article discusses the latest research on epigenetic regulation and the coordination between transcription factors and epigenetic modifiers in plant regeneration.
CURRENT OPINION IN PLANT BIOLOGY
(2023)
Article
Cell Biology
Grace Orstad, Gabriela Fort, Timothy J. Parnell, Alex Jones, Chris Stubben, Brian Lohman, Katherine L. Gillis, Walter Orellana, Rushmeen Tariq, Olaf Klingbeil, Klaus Kaestner, Christopher R. Vakoc, Benjamin T. Spike, Eric L. Snyder
Summary: Changes in cellular identity can drive malignant progression and resistance to therapy in lung adenocarcinoma. Loss of FoxA1/2 impairs tumorigenesis in NKX2-1-positive LUAD and leads to collapse of a dual-identity state, driving alternative cellular identity programs associated with non-proliferative states.
DEVELOPMENTAL CELL
(2022)
Article
Multidisciplinary Sciences
Juli Bai, Christopher Cervantes, Juan Liu, Sijia He, Haiyan Zhou, Bilin Zhang, Huan Cai, Dongqing Yin, Derong Hu, Zhi Li, Hongzhi Chen, Xiaoli Gao, Fang Wang, Jason C. O'Connor, Yong Xu, Meilian Liu, Lily Q. Dong, Feng Liu
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2017)
Article
Cell Biology
Meilian Liu, Juli Bai, Sijia He, Ricardo Villarreal, Derong Hu, Chuntao Zhang, Xin Yang, Huiyun Liang, Thomas J. Slaga, Yonghao Yu, Zhiguang Zhou, John Blenis, Philipp E. Scherer, Lily Q. Dong, Feng Liu
Article
Biology
Juli Bai, Christopher Ceryantes, Sijia He, Jieyu He, George R. Plasko, Jie Wen, Zhi Li, Dongqing Yin, Chuntao Zhang, Meilian Liu, Lily Q. Dong, Feng Liu
COMMUNICATIONS BIOLOGY
(2020)
Article
Neurosciences
Shulan Qiu, Juan Pablo Palavicini, Jianing Wang, Nancy S. Gonzalez, Sijia He, Elizabeth Dustin, Cheng Zou, Lin Ding, Anindita Bhattacharjee, Candice E. Van Skike, Veronica Galvan, Jeffrey L. Dupree, Xianlin Han
Summary: This study investigated the impact of CNS sulfatide deficiency on AD pathology using different mouse models. The results showed that mild sulfatide losses within myelinating cells can activate disease-associated microglia and astrocytes, leading to chronic AD-like neuroinflammation and mild cognitive impairment, with gender differences. Additionally, sulfatide deficiency was found to be an important contributor to neuroinflammation and cognitive impairment in AD.
MOLECULAR NEURODEGENERATION
(2021)
Article
Biochemistry & Molecular Biology
Shulan Qiu, Sijia He, Jianing Wang, Hu Wang, Anindita Bhattacharjee, Xin Li, Moawiz Saeed, Jeffrey L. Dupree, Xianlin Han
Summary: The interaction between obesity and central nervous system (CNS) neurological dysfunction is well recognized. Evidence shows that obesity is a risk factor for CNS neuroinflammation and cognitive impairment. This study investigates how CNS sulfatide deficiency affects peripheral metabolism, considering sex- and age-specific effects. Results show that female sulfatide-deficient mice gained more body weight, had higher basal glucose levels, and were glucose intolerant compared to controls, while male sulfatide-deficient mice only showed glucose intolerance at a later age compared to females. Increased body weight was associated with increased food intake and elevated neuroinflammation in a sex-specific manner, suggesting that CNS sulfatide deficiency leads to sex-specific alterations in energy homeostasis via dysregulated hypothalamic control of food intake.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Oncology
Sijia He, Shulan Qiu, Meixia Pan, Juan P. P. Palavicini, Hu Wang, Xin Li, Anindita Bhattacharjee, Savannah Barannikov, Kevin F. F. Bieniek, Jeffrey L. L. Dupree, Xianlin Han
Summary: Despite being a brain disorder, Alzheimer's disease (AD) often leads to peripheral organ dysregulations, which depend on spinal cord coordination. The study found that the lipid composition of the central nervous system (CNS) is associated with AD. The changes in spinal cord lipidome may be the underlying cause of peripheral organ dysregulation.
CLINICAL AND TRANSLATIONAL MEDICINE
(2023)
Article
Medicine, Research & Experimental
Sijia He, Jiyoon Ryu, Juanhong Liu, Hairong Luo, Ying Lv, Paul R. Langlais, Jie Wen, Feng Dong, Zhe Sun, Wenjuan Xia, Jane L. Lynch, Ravindranath Duggirala, Bruce J. Nicholson, Mengwei Zang, Yuguang Shi, Fang Zhang, Feng Liu, Juli Bai, Lily Q. Dong
Summary: The study identified LRG1 as an obesity-associated adipokine that exacerbates hepatic steatosis and insulin resistance induced by high-fat diet. LRG1 may promote hepatic steatosis by increasing de novo lipogenesis and suppressing fatty acid beta-oxidation, as well as inhibiting insulin signaling in the liver.
JOURNAL OF CLINICAL INVESTIGATION
(2021)
Article
Endocrinology & Metabolism
Wen Meng, Xiuci Liang, Hongzhi Chen, Hairong Luo, Juli Bai, Guangdi Li, Qinghai Zhang, Ting Xiao, Sijia He, Yacheng Zhang, Zhipeng Xu, Bo Xiao, Meilian Liu, Fang Hu, Feng Liu
