Article
Biochemistry & Molecular Biology
Takashi Fukaya
Summary: Expression of gap and pair-rule genes is crucial for body segmentation in Drosophila embryogenesis, and the length of the transcription period plays a major role in determining spatial patterning of gene expression in early embryos. Enhancer interference can influence transcriptional activation and impact the refinement of gene expression patterns during animal development.
Article
Cell Biology
Jingjing Sun, Chen Zhang, Fan Gao, Angelike Stathopoulos
Summary: This study utilizes single-cell technology and genetic analysis to investigate the dynamic transcriptional changes during Drosophila embryo morphogenesis. The findings reveal stepwise progression in transcriptional patterning, uncovering spatial and temporal regulation of gene expression.
Review
Developmental Biology
Jihyun Irizarry, Angelike Stathopoulos
Summary: Morphogen concentrations in space and time during development are important for specifying cell fate. Bicoid and Dorsal are two morphogens that directly regulate target genes in Drosophila embryos, providing insights into how morphogens interact and change roles over time. In addition to these factors, there are other inputs working together to control spatiotemporal gene expression in embryos.
Article
Developmental Biology
Alejandra C. Lopez-Delgado, Irene Delgado, Vanessa Cadenas, Fatima Sanchez-Cabo, Miguel Torres
Summary: The study explores the role of Meis in axial skeleton formation and its relationship with the retinoic acid pathway in mice. Findings suggest that Meis overexpression can rescue axial skeletal defects in Raldh2 mutants, indicating a positive feedback loop between Meis and Raldh2. This feedback loop is crucial for establishing anterior-posterior identities and patterning of the vertebrate axial skeleton.
Article
Developmental Biology
Min Tang, Isabel Regadas, Sergey Belikov, Olga Shilkova, Lei Xu, Erik Wernersson, Xuewen Liu, Hongmei Wu, Magda Bienko, Mattias Mannervik
Summary: In this study, the crucial functions of HDAC3 in embryo development were investigated in Drosophila. The findings demonstrate that HDAC3 is involved in both gene activation and repression, and that lysine substitution in the N terminus disrupts its catalytic activity and activator function, while a combination of substitutions enhances its repressor activity.
Article
Developmental Biology
Peter H. Whitney, Bikhyat Shrestha, Jiahan Xiong, Tom Zhang, Christine A. Rushlow
Summary: This study investigated the differences between two shadow enhancers controlling the sog gene in terms of transcription kinetics, spatial expression, and transcriptional regulation. The results showed that these enhancers integrate activation and repression signals differently and their loss results in changes in tissue patterning.
Article
Plant Sciences
Xuemei Liu, Xiao Min Bie, Xuelei Lin, Menglu Li, Hongzhe Wang, Xiaoyu Zhang, Yiman Yang, Chunyan Zhang, Xian Sheng Zhang, Jun Xiao
Summary: This study utilized a multi-omic analysis strategy to uncover the transcriptional regulatory network responsible for wheat regeneration, identifying 446 key transcription factors driving the process. It also highlighted two DOF transcription factors that can enhance regeneration efficiency in wheat.
Article
Biochemistry & Molecular Biology
Shicheng Zhu, Hanjing Song, Liangjun Zhong, Suman Huo, Yukun Fang, Wanxin Zhao, Xueqin Yang, Zhong-Min Dai, Rui He, Mengsheng Qiu, Zunyi Zhang, Xiao-Jing Zhu
Summary: The study reveals that MSX1 plays a crucial role in palate development. It regulates the anterior-posterior growth and patterning of the secondary palate, affecting cell proliferation and cell death in the palatal mesenchyme. It also influences palatine bone formation by modulating the expression of osteogenic genes. Furthermore, it is found that MSX1 can directly repress the expression of medial-posterior palate genes, contributing to the regulation of palate development.
JOURNAL OF GENETICS AND GENOMICS
(2022)
Article
Cell Biology
Tao Cheng, Yan-Yi Xing, Cong Liu, Yun-Fei Li, Ying Huang, Xiang Liu, Ying-Jie Zhang, Guo-Qin Zhao, Yang Dong, Xin-Xin Fu, Yi-Meng Tian, Li-Ping Shu, Sean G. Megason, Peng-Fei Xu
Summary: Progress has been made in generating analogs of early embryos in vitro, but there is still a lack of understanding on how to mimic the cell movements of gastrulation and induce head formation. In this study, a regional Nodal gradient was applied to a zebrafish animal pole explant, resulting in the generation of a structure that recapitulates key cell movements of gastrulation. Through analysis of cell fates and patterning, it was found that overexpression of certain genes can induce the formation of a complete or partial head structure in zebrafish embryos.
Article
Developmental Biology
Ludmilla Jurevitz Baltruk, Guilherme Miura Lavezzo, Ariane Machado -Lima, Luciano Antonio Digiampietri, Luiz Paulo Andrioli
Summary: Segments in insects are formed by repeated anatomical units. In the fruit fly Drosophila, the body specification occurs during the blastoderm through a segmentation cascade. Pair-rule genes are expressed in seven transversal stripes along the antero-posterior axis and are regulated by maternal transcription factors and gap proteins. The expression of pair-rule genes is repressed by anterior gap genes, leading to a combinatorial mechanism regulating the expression of these genes in different regions of the embryo.
CELLS & DEVELOPMENT
(2022)
Article
Biochemistry & Molecular Biology
Alireza Fotuhi Siahpirani, Sara Knaack, Deborah Chasman, Morten Seirup, Rupa Sridharan, Ron Stewart, James Thomson, Sushmita Roy
Summary: Dynamic regulatory module networks (DRMNs) are a novel approach to infer cell type-specific cis-regulatory networks and their dynamics by integrating multi-omic data. DRMNs can predict cis-regulators of context-specific expression and capture network dynamics across linearly and hierarchically related contexts.
Article
Multidisciplinary Sciences
Markus Maerker, Maike Getwan, Megan E. Dowdle, Jason C. McSheene, Vanessa Gonzalez, Jose L. Pelliccia, Danielle S. Hamilton, Valeria Yartseva, Charles Vejnar, Melanie Tingler, Katsura Minegishi, Philipp Vick, Antonio J. Giraldez, Hiroshi Hamada, Rebecca D. Burdine, Michael D. Sheets, Martin Blum, Axel Schweickert
Summary: The authors demonstrate that post-transcriptional regulation of the cilia-driven leftward flow gene dand5 is crucial for symmetry breakage in frogs, fish, and mice, with Pkd2 playing a regulatory role. This process is mediated by a 139 nt Bicc1 responsive element in the dand5 3 ' UTR.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Kimiko Takebayashi-Suzuki, Misa Uchida, Atsushi Suzuki
Summary: Xenopus Zbtb21 plays an essential role in AP axis formation during early embryonic development, working in coordination with Zbtb14 to pattern the dorsal-ventral and anterior-posterior axes.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Kimiko Takebayashi-Suzuki, Misa Uchida, Atsushi Suzuki
Summary: Zbtb21 plays a crucial role in AP axis formation and neural development in early Xenopus embryogenesis, working in collaboration with Zbtb14.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Andres F. Lopez-Lopera, Nicolas Durrande, Mauricio A. Alvarez
Summary: The regulatory process of Drosophila is studied using physically-inspired stochastic models, focusing on post-transcriptional events. Two different Gaussian processes models are investigated based on reaction-diffusion equations, with performance assessments on high-resolution datasets.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2021)
Article
Developmental Biology
Junbo Liu, Jun Ma
Article
Multidisciplinary Sciences
Honggang Wu, Manu, Renjie Jiao, Jun Ma
NATURE COMMUNICATIONS
(2015)
Article
Multidisciplinary Sciences
Feng He, Chuanxian Wei, Honggang Wu, David Cheung, Renjie Jiao, Jun Ma
NATURE COMMUNICATIONS
(2015)
Article
Multidisciplinary Sciences
David Cheung, Jun Ma
SCIENTIFIC REPORTS
(2015)
Article
Biochemistry & Molecular Biology
Junbo Liu, Yanyu Xiao, Tongli Zhang, Jun Ma
Review
Developmental Biology
Jun Ma, Feng He, Gengqiang Xie, Wu-Min Deng
WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY
(2016)
Article
Multidisciplinary Sciences
Yue Li, Pengzhen Dong, Yang Yang, Tianyu Guo, Quanyi Zhao, Dan Miao, Huanle Li, Tianfeng Lu, Fanning Xia, Jialan Lyu, Jun Ma, Thomas B. Kornberg, Qiang Zhang, Hai Huang
Summary: This study reveals that the insulin pathway controls the proliferation and migration of tracheal progenitor cells through regulating Yorkie signaling. It also identifies the regulatory mechanism by which metabolic depression drives progenitor cell activation and cell division that underlies tracheal remodeling.
NATURE COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Jiaqi Li, Jingjing Wang, Peijing Zhang, Renying Wang, Yuqing Mei, Zhongyi Sun, Lijiang Fei, Mengmeng Jiang, Lifeng Ma, E. Weigao, Haide Chen, Xinru Wang, Yuting Fu, Hanyu Wu, Daiyuan Liu, Xueyi Wang, Jingyu Li, Qile Guo, Yuan Liao, Chengxuan Yu, Danmei Jia, Jian Wu, Shibo He, Huanju Liu, Jun Ma, Kai Lei, Jiming Chen, Xiaoping Han, Guoji Guo
Summary: This study generated single-cell whole-body expression landscapes of zebrafish, Drosophila, and earthworm using Microwell-seq. By integrating cell landscapes from eight representative species, the researchers developed a deep-learning-based strategy, Nvwa, to predict gene expression and identify regulatory programs. Conserved genetic regulation in vertebrates and invertebrates were revealed through comparison of cell-type-specific transcription factors. This work provides a valuable resource and a new strategy for studying regulatory grammar in diverse biological systems.
Article
Biology
Honggang Wu, Nannan Zhu, Jiyong Liu, Jun Ma, Renjie Jiao
Summary: The Hippo pathway, which is evolutionarily conserved, regulates cell proliferation, differentiation, and apoptosis. This study identifies Shaggy as a novel regulator of the Hippo pathway in Drosophila, which promotes the expression of Hippo target genes through negative regulation of the protein Expanded.
SCIENCE CHINA-LIFE SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Yun-Fei Li, Tao Cheng, Ying-Jie Zhang, Xin-Xin Fu, Jing Mo, Guo-Qin Zhao, Mao-Guang Xue, Ding-Hao Zhuo, Yan-Yi Xing, Ying Huang, Xiao-Zhi Sun, Dan Wang, Xiang Liu, Yang Dong, Xiao-Sheng Zhu, Feng He, Jun Ma, Dong Chen, Xi Jin, Peng-Fei Xu
Summary: Through the development of a zebrafish model for Feingold syndrome type 1, it was discovered that disturbance of ribosomal biogenesis and blockage of protein synthesis are the main causes of intestinal defects in this syndrome. Furthermore, leucine supplementation may be a feasible and easy treatment option for this disease.
Article
Nutrition & Dietetics
Huanju Liu, Jiajun Li, Xinyue Chang, Feng He, Jun Ma
Summary: We conducted a quantitative study to examine the impact of a high-calorie diet on Drosophila oogenesis. Our findings demonstrate that the interaction between sucrose and protein has complex effects on body fat and fertility when considering them as an integrated physiological response. By experimentally verifying our quantitative modeling approach, we confirmed the expected physiological responses, such as increased body fat, reduced fertility, and ovarian insulin insensitivity. Additionally, under a specific treatment condition, we discovered a Drosophila oogenesis phenotype resembling key aspects of polycystic ovary syndrome in humans. Our research provides insights into the dynamics of diet-induced pathophysiology and the order of onset for obesity, ovarian dysfunction, and insulin resistance.
Article
Multidisciplinary Sciences
Xin-Xin Fu, Ding-Hao Zhuo, Ying-Jie Zhang, Yun-Fei Li, Xiang Liu, Yan-Yi Xing, Ying Huang, Yi-Fan Wang, Tao Cheng, Dan Wang, Si-Han Chen, Yi-Jian Chen, Guan-Nan Jiang, Fu- Lu, Yu Feng, Xiao Huang, Jun Ma, Wei Liu, Ge Bai, Peng-Fei Xu
Summary: The emergence of left-right (LR) asymmetry in a patterning field along the anterior-posterior axis is still an unresolved problem in developmental biology. This study identifies Follistatin (Fst) as a regulator that restricts the propagation of Nodal ortholog Southpaw (Spaw) in the right lateral plate mesoderm (LPM) and facilitates the establishment of a robust LR asymmetric Nodal patterning. Furthermore, Fst inhibits the Activin-Nodal signaling pathway in the forebrain, contributing to the orderly propagation of asymmetric Nodal activation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Dianpeng Zheng, Yaowen Mao, Yinglong Gao, Feng He, Jun Ma
Summary: The cellular response to nutrient deprivation is not well known, but it has been observed that glucose withdrawal does not immediately halt the cell cycle like the removal of amino acids or glutamine does. Daughter cells from mother cells experiencing glucose withdrawal in S phase have the choice of proliferation or quiescence, while those experiencing it in G1 phase predominantly enter quiescence. This difference is due to the accumulation of p21 protein during G2/M in the latter cells, which can be degraded to allow daughter cells to enter S phase but with increased DNA damage.
Article
Multidisciplinary Sciences
Ruoqing Xu, Fei Dai, Honggang Wu, Renjie Jiao, Feng He, Jun Ma
Summary: In this study, we investigate the formation of patterns in the embryo of Drosophila along the anterior-posterior axis. By analyzing the dynamic movements of gap gene expression boundaries in relation to embryo length and the Bicoid gradient, we observe the emergence of a global scaling landscape and convergence of pattern scaling characteristics. We demonstrate the contributions of Bicoid input and regulatory dynamics in shaping the embryonic pattern's scaling characteristics.
Article
Cell Biology
Maoguang Xue, Fei Cong, Wanling Zheng, Ruoqing Xu, Xiaoyu Liu, Hongcun Bao, Ying Ying Sung, Yongmei Xi, Feng He, Jun Ma, Xiaohang Yang, Wanzhong Ge
Summary: Loss of Paip1 leads to reduced protein translation and pupal lethality. Knockdown of Paip1 specifically in wing imaginal disc results in apoptotic cell death. Paip1 depletion activates the integrated stress response pathway and leads to increased phosphorylation of eIF2α.
CELL DEATH DISCOVERY
(2023)