Review
Genetics & Heredity
Martha L. Bulyk, Jacques Drouin, Melissa M. Harrison, Jussi Taipale, Kenneth S. Zaret
Summary: This article discusses the important roles of pioneer factors in gene regulation, including their unique ability to bind to chromatin and promote its remodeling for gene expression. It highlights the unique insights that exploring these proteins can offer in understanding gene regulation and cellular identity.
NATURE REVIEWS GENETICS
(2023)
Review
Cell Biology
Aurelio Balsalobre, Jacques Drouin
Summary: Pioneer factors are transcription factors that can initiate the opening of closed chromatin. They play crucial roles in determining cell fate and cellular reprogramming, but their misexpression can have pathological consequences.
NATURE REVIEWS MOLECULAR CELL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Daisuke Kurotaki, Kenta Kikuchi, Kairong Cui, Wataru Kawase, Keita Saeki, Junpei Fukumoto, Akira Nishiyama, Kisaburo Nagamune, Keji Zhao, Keiko Ozato, Pedro P. Rocha, Tomohiko Tamura
Summary: This study comprehensively determined higher-order chromatin structures by Hi-C in DC progenitors and cDC subpopulations. The results showed that chromatin activation was initially induced at the MDP stage during cDC differentiation, followed by a shift from inactive to active nuclear compartments in CDPs. This study also identified the transcription factor IRF8 as a mediator of chromatin activation and changes in the active compartments in DC progenitors. Furthermore, the study found preestablished chromatin structures of host defense-related gene loci in unstimulated cDCs, which may contribute to the rapid responses to pathogens.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Benjamin D. Sunkel, Benjamin Z. Stanton
Summary: Transcription factors play a crucial role in epigenetic regulation by remodeling chromatin states through nucleosomal motif recognition. Pioneer factor class of transcription factors are significant in epigenetic initiation and may have implications in human cancers.
Article
Cell Biology
Yihao Yang, Nicholas Gomez, Nicole Infarinato, Rene C. Adam, Megan Sribour, Inwha Baek, Melanie Laurin, Elaine Fuchs
Summary: This study reveals the crucial role of SOX9 in diverting embryonic epidermal stem cells into hair follicle stem cells. By re-activating SOX9 in adult epidermal stem cells, the researchers induce fate switching. They show that SOX9 binds and opens hair follicle enhancers in epidermal stem cells, while recruiting epigenetic factors away from epidermal enhancers, leading to their silencing. This sustained expression of SOX9 subsequently activates oncogenic transcriptional regulators and contributes to the development of cancer.
NATURE CELL BIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Benjamin Edginton-White, Constanze Bonifer
Summary: The development of multicellular organisms involves differential usage of genetic information to generate various cell types that form specialized tissues. A shift from studying single genes to a global view of gene expression control has revolutionized our understanding of gene functions and cell communication. The paradigm of blood cell development highlights how transcription factors and chromatin components work together in shaping gene regulatory networks and driving differentiation, as well as how this process is altered in blood cancers. Emerging concepts place these processes within subnuclear structures, adding another layer of control to differential gene expression.
Review
Genetics & Heredity
Mary Attaway, Tzippora Chwat-Edelstein, Bao Q. Vuong
Summary: The article discusses the role of non-coding RNAs, such as miRNAs and lncRNAs, in regulating the expression and activity of transcriptional regulators during B lymphocyte development, highlighting the complex gene regulatory networks and identifying new regulatory RNAs that require further investigation.
FRONTIERS IN GENETICS
(2021)
Review
Endocrinology & Metabolism
Juliette Harris, Arthur Gouhier, Jacques Drouin
Summary: Pioneer transcription factors play crucial roles in cell fate specification by accessing closed heterochromatin, remodeling chromatin, and activating new gene subsets. Pax7 is the only well-documented pioneer factor in pituitary development, specifying the fate of melanotrope cells in the intermediate lobe. The potent activity of pioneer factors in reprogramming gene expression has been associated with tumor development, with overexpression or chromosomal translocations leading to the production of chimeric pioneers in different cancers.
EUROPEAN JOURNAL OF ENDOCRINOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Fulong Yu, Liam D. Cato, Chen Weng, L. Alexander Liggett, Soyoung Jeon, Keren Xu, Charleston W. K. Chiang, Joseph L. Wiemels, Jonathan S. Weissman, Adam J. de Smith, Vijay G. Sankaran
Summary: Genome-wide association studies combined with single-cell genomic atlases can reveal the mechanisms of disease-causal genetic variations. However, sparse and noisy single-cell epigenomic data analysis often hinders the identification of disease-relevant cell types. To overcome this, the SCAVENGE algorithm uses network propagation to map causal variants to their relevant cellular context at a single-cell resolution, successfully identifying key biological mechanisms in various blood traits and diseases.
NATURE BIOTECHNOLOGY
(2022)
Article
Pharmacology & Pharmacy
Kannan Harithpriya, Ravichandran Jayasuriya, Trishla Adhikari, Awantika Rai, Kunka Mohanram Ramkumar
Summary: Transcription factors play crucial roles in regulating gene expression and development of pancreatic B-cells. Hyperglycemia can reduce the expression and/or activities of these transcription factors, leading to loss of B-cell function. Activating transcription factors using small molecules has shown promising results in regenerating and maintaining B-cell function and survival. This review discusses the various transcription factors involved in pancreatic B-cell development and the regulation of their activities in normal and pathological states, as well as the potential pharmacological effects of natural and synthetic compounds on these transcription factors.
EUROPEAN JOURNAL OF PHARMACOLOGY
(2023)
Review
Immunology
Eva Neugebauer, Aura M. Bastidas-Quintero, Daniel Weidl, Florian Full
Summary: This article reviews the current research progress on how viruses utilize pioneer factors for viral replication and persistence in the host, as well as for the development of viral cancer.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Cell Biology
Yuting Liu, Xin Wan, Hu Li, Yingxi Chen, Xiaodi Hu, Hebing Chen, Dahai Zhu, Cheng Li, Yong Zhang
Summary: CTCF cooperates with lineage-specific pioneer transcription factors to control cell identity genes, facilitating CTFC occupancy and forming regulatory hubs at both 1D and 3D levels.
Article
Biochemistry & Molecular Biology
Xuelei Lai, Romain Blanc-Mathieu, Loic GrandVuillemin, Ying Huang, Arnaud Stigliani, Jeremy Lucas, Emmanuel Thevenon, Jeanne Loue-Manifel, Laura Turchi, Hussein Daher, Eugenia Brun-Hernandez, Gilles Vachon, David Latrasse, Moussa Benhamed, Renaud Dumas, Chloe Zubieta, Francois Parcy
Summary: As a pioneer transcription factor, LFY has the ability to bind both methylated and non-methylated DNA, modify chromatin state to initiate gene expression, and induce chromatin accessibility in target genes APETALA1 and AGAMOUS in plant seedling tissues. This study suggests that LFY possesses key pioneer TF features contributing to launching the floral gene expression program.
Article
Multidisciplinary Sciences
Ryan J. Geusz, Allen Wang, Dieter K. Lam, Nicholas K. Vinckier, Konstantinos-Dionysios Alysandratos, David A. Roberts, Jinzhao Wang, Samy Kefalopoulou, Araceli Ramirez, Yunjiang Qiu, Joshua Chiou, Kyle J. Gaulton, Bing Ren, Darrell N. Kotton, Maike Sander
Summary: FOXA plays a dual role in endodermal organ development: facilitating signal-dependent lineage initiation via enhancer priming, and enforcing organ cell type-specific gene expression via indirect recruitment by lineage-specific TFs. Only a small subset of organ-specific enhancers are bound and primed by FOXA prior to lineage induction, whereas the majority engage FOXA upon lineage induction without undergoing chromatin priming.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Vivekanandan Ramalingam, Xinyang Yu, Brian D. Slaughter, Jay R. Unruh, Kaelan J. Brennan, Anastasiia Onyshchenko, Jeffrey J. Lange, Malini Natarajan, Michael Buck, Julia Zeitlinger
Summary: Lola-I, a Drosophila zinc finger transcription factor, can regulate the promoter state independently of gene activation. It makes the target promoters accessible and acquire paused RNA polymerase II throughout the embryo. This promoter transition is crucial for tissue-specific target gene activation. Lola-I mediates this function by depleting promoter nucleosomes.
NATURE COMMUNICATIONS
(2023)