Article
Multidisciplinary Sciences
Lorenzo Rinaldi, Gregory Fettweis, Sohyoung Kim, David A. Garcia, Saori Fujiwara, Thomas A. Johnson, Theophilus T. Tettey, Laurent Ozbun, Gianluca Pegoraro, Michele Puglia, Blagoy Blagoev, Arpita Upadhyaya, Diana A. Stavreva, Gordon L. Hager
Summary: This study reveals that the interaction between a transcription factor and the cohesin loader NIPBL regulates gene activity, and this mechanism is achieved by promoting loop extrusion and long-range gene regulation at the chromatin level. Additionally, it is discovered that patients with cohesin mutations exhibit a reduced response to glucocorticoids.
Article
Computer Science, Artificial Intelligence
Qiao Liu, Shengquan Chen, Rui Jiang, Wing Hung Wong
Summary: Recent advances in single-cell technologies have enabled large-scale profiling of chromatin accessibility at the single-cell level, but computational analysis faces challenges due to high dimensionality and sparsity of data. Researchers propose a computational tool, scDEC, based on deep generative neural networks for scATAC-seq analysis, showing superior performance in multiple datasets and experimental settings. The generative power of scDEC helps infer cell trajectory and state during differentiation, potentially revealing cell types and within-cell-type variations.
NATURE MACHINE INTELLIGENCE
(2021)
Article
Biochemistry & Molecular Biology
Anushua Biswas, Leelavati Narlikar
Summary: cisDIVERSITY is a new statistical framework that analyzes various gene regulation activities by modeling regions as diverse modules characterized by combinations of motifs while simultaneously learning the motifs themselves.
Article
Biochemistry & Molecular Biology
Paola Cornejo-Paramo, Kathrein Roper, Sandie M. Degnan, Bernard M. Degnan, Emily S. Wong
Summary: The study reveals three major developmental periods in the embryonic development of the sponge Amphimedon queenslandica, involving activating and repressive chromatin in early development, similar to bilaterian embryogenesis, and an increase in transcriptionally repressive elements during late embryogenesis.
Article
Biochemistry & Molecular Biology
Jaegeon Joo, Sunghyun Cho, Sukbum Hong, Sunwoo Min, Kyukwang Kim, Rajeev Kumar, Jeong-Mo Choi, Yongdae Shin, Inkyung Jung
Summary: This study introduces a novel computational method to systematically characterize inter-chromosomal interactions using in situ Hi-C results. The research identifies two hub-like inter-chromosomal contacts associated with nuclear speckles and nucleoli, respectively, and finds that speckle-associated inter-chromosomal interactions are highly cell-type invariant with a marked enrichment of cell-type common super-enhancers (CSEs). The study also demonstrates the importance of MAZ binding in regulating speckle-associated inter-chromosomal contacts.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
David A. Gallegos, Melyssa Minto, Fang Liu, Mariah F. Hazlett, S. Aryana Yousefzadeh, Luke C. Bartelt, Anne E. West
Summary: This study found that amphetamine regulates the transcription of PV+ interneurons in the NAc and the regulation program is distinct from that of other GABAergic neurons in the NAc. Chromatin accessibility at enhancers predicts cell-type specific gene regulation, providing insight into transcriptional mechanisms. The functional importance of this transcriptional program was explored through expression assessment in a mouse strain with heightened behavioral sensitivity.
MOLECULAR PSYCHIATRY
(2023)
Article
Biochemistry & Molecular Biology
Tian Lu, Cheen Euong Ang, Xiaowei Zhuang
Summary: The recent development of spatial omics methods has advanced our understanding of spatial regulation of cell and tissue functions. In this study, a new method for spatially resolved epigenomic profiling of single cells was introduced, allowing for high-resolution spatial mapping. This approach has the potential to enhance our understanding of how gene expression is temporally and spatially regulated.
Article
Biochemistry & Molecular Biology
Xiao-Min Liu, Yuanhui Mao, Shen Wang, Jun Zhou, Shu-Bing Qian
Summary: Transcriptional programming plays a key role in determining cell state. This study identifies METTL3 as a crucial modulator of dynamic transcription and chromatin accessibility during embryonic stem cell differentiation.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Gastroenterology & Hepatology
Noga Korenfeld, Maya Finkel, Nufar Buchshtab, Meirav Bar-Shimon, Meital Charni-Natan, Ido Goldstein
Summary: The study reveals that glucagon and glucocorticoids play a role in the transcriptional regulation of amino acid catabolism genes, and their synergistic effect can enhance gluconeogenesis.
CELLULAR AND MOLECULAR GASTROENTEROLOGY AND HEPATOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Yuchao Jiang, Yuriko Harigaya, Zhaojun Zhang, Hongpan Zhang, Chongzhi Zang, Nancy R. Zhang
Summary: The epigenetic control of gene expression is highly cell-type and context specific, and can be broken down into modular components by a transcription factor activating or repressing the target gene expression. A new nonparametric approach, TRIPOD, is proposed to detect and characterize the relationships between TF, target gene, and TF binding site accessibility using single-cell RNA and ATAC multiomic data.
Article
Multidisciplinary Sciences
Lewis Taylor, Steven Walsh, Anna Ashton, Norbert Varga, Sejal Kapoor, Charlotte George, Aarti Jagannath
Summary: In this study, the accessibility of the Mycoplasma hyorhinis genome was profiled using ATAC-Seq technology. The differential and highly reproducible chromatin accessibility landscape was found to be associated with the bacteria's life cycle and infectivity. These results highlight the importance of differential chromatin accessibility in the regulation of gene expression in bacteria.
Article
Immunology
Francesco Cilenti, Giulia Barbiera, Nicoletta Caronni, Dario Iodice, Elisa Montaldo, Simona Barresi, Eleonora Lusito, Vincenzo Cuzzola, Francesco Maria Vittoria, Luca Mezzanzanica, Paolo Miotto, Pietro Di Lucia, Dejan Lazarevic, Daniela Maria Cirillo, Matteo Iannacone, Marco Genua, Renato Ostuni
Summary: Tightly controlling inflammatory gene expression by antagonistic environmental signals is crucial for immune protection and tissue damage prevention. PGE(2) modulates macrophage activation and interferes with LPS-induced gene expression through targeting the MEF2A-ERK5 interaction, impacting IFN I induction.
Review
Cell Biology
Christopher M. Uyehara, Effie Apostolou
Summary: The spatiotemporal control of gene expression depends on the activity of regulatory sequences known as enhancers, which regulate target genes over varying distances in the genome. Recent advancements in genomics and imaging technologies have revealed complex networks of enhancer-promoter interactions. This review summarizes our current understanding of enhancer-promoter communication and discusses highly connected enhancer-promoter hubs and their functions in signal integration and gene regulation.
Review
Immunology
Nilisha Fernando, Giuseppe Sciume, John J. O'Shea, Han-Yu Shih
Summary: This study focuses on unraveling the regulatory mechanisms of cytokine production in ILCs and T cells, including DNA methylation, transcription factor binding, histone modification, and other epigenetic mechanisms. ILCs are programmed to rapidly respond to environmental signals in a polarized manner without the need for T cell receptor signaling.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Oncology
Ling Wei, Jiaxin Chen, Chao Song, Yuexin Zhang, Yimeng Zhang, Mingcong Xu, Chenchen Feng, Yu Gao, Fengcui Qian, Qiuyu Wang, Desi Shang, Xinyuan Zhou, Jiang Zhu, Xiaopeng Wang, Yijie Jia, Jiaqi Liu, Yanbing Zhu, Chunquan Li
Summary: A core transcriptional regulatory circuit (CRC) consists of interconnected auto-regulating transcription factors (TFs) that play a crucial role in defining cellular identity and fate. The Cancer CRC platform has documented 94,108 cancer CRCs and 325 core TFs, offering SE active core TFs analysis and TF enrichment analysis tools for identifying key TFs in cancer. Additionally, a comprehensive analysis of core TFs in various cancer types has revealed conserved and cancer-specific TFs.
FRONTIERS IN ONCOLOGY
(2021)
