Review
Neurosciences
Erick Sousa, Nuria Flames
Summary: Neuronal diversity is an intrinsic feature of the nervous system, with transcription factors playing key roles in establishing different neuronal identities. Common features in transcription factor categories can be identified in both mammals and nematodes, highlighting their pleiotropic functions. Transcriptional repression is crucial in controlling neuronal diversity, and the acquisition of neuronal identities is considered a metastable process.
EUROPEAN JOURNAL OF NEUROSCIENCE
(2022)
Review
Cell Biology
Qianhui Li, Xin Liu, Jingtao Wen, Xi Chen, Bumin Xie, Yang Zhao
Summary: With the advancement of high-throughput sequencing technology, an increasing number of non-coding RNAs have been discovered, including miRNAs, lncRNAs, circRNAs, snoRNAs, and piRNAs. The identification of eRNAs in 2010 has expanded the diversity of non-coding RNAs. eRNAs are non-coding RNA molecules transcribed from enhancer fragments of DNA cis-acting elements. Recent studies have revealed that eRNA transcription may serve as a biological marker for enhancer activity and can participate in the regulation of coding gene transcription. This review discusses the biological characteristics of eRNAs, their functions in transcriptional regulation, the factors regulating eRNA production, and the research progress of eRNAs in different diseases.
CELL COMMUNICATION AND SIGNALING
(2023)
Article
Genetics & Heredity
Amarni L. Thomas, Judith Marsman, Jisha Antony, William Schierding, Justin M. O'Sullivan, Julia A. Horsfield
Summary: This study used bioinformatic methods and functional data to characterize the regulatory landscape of vertebrate Runx1 gene. It identified conserved REs between human and mouse, some of which have single nucleotide polymorphisms associated with gene expression. The study suggests that REs may be variant in haematological malignancies.
Review
Biochemistry & Molecular Biology
Yanna Shi, Bai-Jun Li, Guanqing Su, Mengxue Zhang, Donald Grierson, Kun-Song Chen
Summary: Fleshy fruit texture is an important quality characteristic of ripe fruit, and softening is an irreversible process mainly caused by changes in cell wall, starch degradation, and flavonoid levels. Lignification of certain fruits negatively affects eating quality, and excessive softening can lead to physical damage and infection. Transcription factors play a crucial role in regulating fruit texture by controlling genes related to cell wall and starch metabolism. This review focuses on the transcriptional regulatory mechanisms governing fruit textural change and discusses potential targets for breeding and future research directions.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2022)
Review
Immunology
Shengbo Zhang, Cindy Audiger, Michael Chopin, Stephen L. Nutt
Summary: This review summarizes recent advances in understanding the transcriptional networks that regulate the development of different subsets of dendritic cells (DCs). It discusses the heterogeneity of cDC2s, the ontogeny of pDCs, and the newly described DC subset, DC3. The review also examines critical transcription factors such as IRF8, PU.1, and E2-2, and highlights their regulatory mechanisms and downstream targets. The complex interplay between these transcription factors shapes the DC transcriptome and influences their function in response to environmental stimuli. The information presented in this review provides essential insights into the regulation of DC development and function, with potential implications for developing novel therapeutic strategies for immune-related diseases.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Pharmacology & Pharmacy
Jie Zeng, Jiahong Chen, Maozhang Li, Chuanfan Zhong, Zezhen Liu, Yan Wang, Yuejiao Li, Funeng Jiang, Shumin Fang, Weide Zhong
Summary: This study identified super enhancers (SE) and associated genes that play a critical role in the progression of metastatic castration-resistant prostate cancer (mCRPC). The analysis showed that 142 overlapping SE-associated differentially expressed genes (DEGs) had strong predictive power in recurrence risk prediction. Additionally, FKBP5 activity was significantly inhibited by the BET inhibitor JQ1.
FRONTIERS IN PHARMACOLOGY
(2023)
Article
Genetics & Heredity
Hang Li, Caiping Zhao, Zeli Li, Kainan Yao, Jingjing Zhang, Wenwen Si, Xiaohong Liu, Yong Jiang, Meiling Zhu
Summary: Abnormal fibroblast differentiation into myofibroblast is a crucial mechanism of pulmonary fibrosis. Super-enhancers are believed to regulate cell identity and their abnormal activation may be involved in the pathogenesis of PF. This study aimed to identify potential pathogenic super-enhancer-driven genes in PF, and identified overlap genes that are predicted to play a role in the disease's pathology. LTBP2, a predicted super-enhancer-driven pathogenic gene, was validated to be upregulated in PF mouse models and TGF-beta stimulated fibroblasts. It was found that interference with super-enhancers could decrease the expression of LTBP2, suggesting a potential new therapeutic avenue for PF.
FRONTIERS IN GENETICS
(2021)
Article
Multidisciplinary Sciences
Anil K. Panigrahi, David M. Lonard, Bert W. O'Malley
Summary: This study demonstrates the interdependence of transcription between enhancers and target promoters. The results suggest that transcriptional concurrence and coordination throughout the genome are based on the transcriptional interdependence of enhancers and promoters. The study proposes a model where enhancers and promoters are entangled in the form of enhancer-promoter contact, reside in a proteinaceous bubble, and utilize shared transcriptional resources and regulatory inputs.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Cell Biology
Tiegh Taylor, Natalia Sikorska, Virlana M. Shchuka, Sanjay Chahar, Chenfan Ji, Neil N. Macpherson, Sakthi D. Moorthy, Marit A. C. de Kort, Shanelle Mullany, Nawrah Khader, Zoe E. Gillespie, Lida Langroudi, Ian C. Tobias, Tineke L. Lenstra, Jennifer A. Mitchell, Tom Sexton
Summary: The connection between transcriptional control and chromatin architecture is not clearly understood. This study using genome editing and chromatin interaction analysis in mouse embryonic stem cells found a disconnect where Sox2 transcriptional activation is traced back to a few key transcription factor binding sites that have no effect on promoter-enhancer interaction frequencies or topological domain organization. Maintenance of local chromatin architecture, including at the topologically associating domain boundary downstream from the Sox2 enhancer, is distributed across multiple transcription factor-bound regions and is independent of CTCF. Additionally, disruption of promoter-enhancer interactions has no effect on Sox2 transcription. These findings suggest that many transcription factors can modulate chromatin architecture independently of CTCF.
GENES & DEVELOPMENT
(2022)
Article
Developmental Biology
James D. Price, Susan Lindtner, Athena Ypsilanti, Fadya Binyameen, Jeffrey R. Johnson, Billy W. Newton, Nevan J. Krogan, John L. R. Rubenstein
Summary: This study reveals the crucial role of transcription factors Dlx1/2 and Olig1/2 in determining the fate of subpallium cells. Dlx1/2 interacts with the NuRD complex to regulate gene transcription and cell differentiation. Loss of Dlx1/2 leads to dysregulation of regulatory elements near genes such as Olig2, resulting in increased production of OLIG2(+) cells.
Article
Urology & Nephrology
Jingping Yang, Difei Zhang, Masaru Motojima, Tsutomu Kume, Qing Hou, Yu Pan, Aiping Duan, Mingchao Zhang, Song Jiang, Jinhua Hou, Jingsong Shi, Zhaohui Qin, Zhihong Liu
Summary: This study identified potential TFs in human glomerulus cells through analysis of superenhancer distribution, and elucidated the regulatory roles of FOXC1/2 in podocyte maintenance using transcriptomics and cistromics. The results suggest that FOXC1/2 maintain podocyte differentiation through transcriptional stabilization, with overexpression protecting podocytes from injury. The genome-wide chromatin resources support further investigation of TFs' regulatory roles in glomeruli transcription programs.
JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY
(2021)
Editorial Material
Genetics & Heredity
Gerd A. Blobel, Douglas R. Higgs, Jennifer A. Mitchell, Dimple Notani, Richard A. Young
Summary: In this Viewpoint, five experts discuss our biological understanding of super-enhancers, how we can responsibly study their functions, and their opinions on whether names for enhancer clusters are an informative reflection of their functional properties.
NATURE REVIEWS GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Yuan Jiang, Yan-Yi Jiang, De-Chen Lin
Summary: This review summarizes the methods for identifying super-enhancers and core regulatory circuits in cancer cells, as well as the mechanisms by which master transcription factors and super-enhancers cooperatively regulate cancer-specific expression programs. It also discusses the cancer type and subtype specificity of core regulatory circuits and their significance in cancer biology.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Review
Immunology
Audrey Dauba, Ahmed Amine Khamlichi
Summary: CSR is a crucial mechanism in adaptive immune responses, triggered by both T-cell-dependent and T-cell-independent antigens. Transcription of switch sequences and regulation within dynamic chromatin domains play key roles in controlling CSR.
FRONTIERS IN IMMUNOLOGY
(2021)
Review
Immunology
Anna A. Korchagina, Sergey A. Shein, Ekaterina Koroleva, Alexei V. Tumanov
Summary: Innate lymphoid cells (ILCs) are diverse innate immune cells that play a role in host defense, mucosal repair, and immunopathology by producing effector cytokines. The development of ILC subsets is controlled by core transcription factors, and ILCs can undergo plasticity and change into other subsets in response to invading pathogens and changes in local tissue environment. The regulation of ILCs involves a balance between various transcription factors, but the exact mechanisms behind ILC plasticity and identity maintenance are still hypothetical. This review discusses recent advancements in understanding the transcriptional regulation of ILCs in different conditions.
FRONTIERS IN IMMUNOLOGY
(2023)
