Article
Multidisciplinary Sciences
Joana Esteves de Lima, Reem Bou Akar, Leo Machado, Yuefeng Li, Bernadette Drayton-Libotte, F. Jeffrey Dilworth, Frederic Relaix
Summary: The authors demonstrate that HIRA, a H3.3 histone chaperone, establishes the chromatin landscape required for skeletal muscle cell identity.
NATURE COMMUNICATIONS
(2021)
Article
Cell Biology
Guillaume Giraud, Rachel Paul, Marilyne Duffraisse, Soumen Khan, L. S. Shashidhara, Samir Merabet
Summary: Developmental processes must be robust and flexible to cope with genetic and environmental variations. A self-sufficient molecular model is proposed to explain the development of a specific flight organ in the fruit fly, indicating a potential molecular strategy for Hox proteins to innovate and stabilize new forms during evolution.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Liqiang Shen, Giorgio Lai, Linlin You, Jing Shi, Xiaoxian Wu, Maria Puiu, Zhanxi Gu, Yu Feng, Yulia Yuzenkova, Yu Zhang
Summary: This study presents the cryo-EM structures of cyanobacterial transcription initiation complexes, revealing the role of SI3-& sigma; arch interaction in transcription initiation of cyanobacteria. Disruption of this structure affects the growth and stress response of cyanobacteria.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Genetics & Heredity
Siqian Feng, Shan Lu, Wesley B. Grueber, Richard S. Mann
Summary: The technique described in the study offers a simple and efficient method for scarless engineering of Drosophila genomic sequences near any landing site containing an inverted attP cassette. It combines phiC31 integrase-mediated site-specific integration and homing nuclease-mediated resolution of local duplications, allowing for efficient modification of alleles in a scarless manner. This method may also be applicable to other species.
Article
Genetics & Heredity
Anita Hermann, Dave Kosman, William McGinnis, Ella Tour
Summary: The study investigates the function of a lncRNA, lncRNA:PS4, which shows complementary expression to Ubx in the thoracic primordia and undergoes significant changes in a Ubx(Cbx-1) mutation background. Deletion of lncRNA:PS4 promoters does not impact Ubx expression in embryos.
G3-GENES GENOMES GENETICS
(2022)
Review
Genetics & Heredity
Vallari Shukla, Anna Cetnarowska, Mette Hyldahl, Susanne Mandrup
Summary: This article reviews recent advances in the understanding of the interplay between chromatin topology and transcription, revealing that lineage determination and differentiation depend on the dynamic chromatin topology, forming transcriptional hubs.
TRENDS IN GENETICS
(2022)
Article
Multidisciplinary Sciences
Masaru Shimizu, Yuya Kondo, Reona Tanimura, Kotona Furuyama, Masahiro Yokosawa, Hiromitsu Asashima, Hiroto Tsuboi, Isao Matsumoto, Takayuki Sumida
Summary: The lack of T-bet can exacerbate autoimmune arthritis, while the expression of T-bet in CD4+ T cells can suppress arthritogenic Th17 cells and CIA.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Siqian Feng, Richard S. Mann
Summary: Chromatin immunoprecipitation (ChIP) is a crucial technique for studying protein-DNA interactions, but lacks cell type-specificity in complex tissues. SpyChIP overcomes this limitation by utilizing a specific isopeptide bond to identify cell type-specific transcription factor (TF) binding sites, offering insights into TF mechanisms in different cell types.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Immunology
Kalina T. Belcheva, Jayanta Chaudhuri
Summary: The maintenance of B cell identity relies on active transcriptional control, and disruptions to this regulatory network can compromise cell function and induce cell fate plasticity. B lymphocytes serve as an insightful case study for understanding cellular plasticity and the role of master regulators in maintaining cell lineage stability.
JOURNAL OF IMMUNOLOGY
(2022)
Article
Immunology
Xianzhi Gao, Xin Shen, Kuai Liu, Chenyu Lu, Ying Fan, Qianying Xu, Xiaoyu Meng, Shenghui Hong, Zhengwei Huang, Xia Liu, Linrong Lu, Lie Wang
Summary: This study revealed the critical role of ThPOK in regulating the homeostasis and functions of ILC3 subsets.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Cell Biology
Stefano Secchia, Mattia Forneris, Tobias Heinen, Oliver Stegle, Eileen E. M. Furlong
Summary: This study combines single-cell regulatory genomics with loss-of-function mutants to systematically evaluate the functional input of transcription factors (TFs) and uncover cellular and molecular phenotypes. By performing experiments at different time points during Drosophila embryo development, the researchers reconstruct the developmental trajectories and identify the TFs and enhancers involved in major muscle types. They also develop a single-nucleus genotyping strategy to assess mutant phenotypes and discover new ones while revealing regulatory input and mode of action.
DEVELOPMENTAL CELL
(2022)
Article
Cell Biology
Han Han, Hiroki J. Nakaoka, Line Hofmann, Jeff Jiajing Zhou, Clinton Yu, Lisha Zeng, Junyu Nan, Gayoung Seo, Rebecca Elizabeth Vargas, Bing Yang, Ruxi Qi, Lee Bardwell, Dmitry A. Fishman, Ken W. Y. Cho, Lan Huang, Ray Luo, Rahul Warrior, Wenqi Wang
Summary: The Hippo pathway was found to regulate heavy metal homeostasis by phosphorylating and inhibiting MTF1, thus attenuating the transcription of heavy metal response genes and protecting cells from heavy metal-induced toxicity. The activity of the Hippo pathway kinase LATS is also inhibited by heavy metal treatment, suggesting an interplay between heavy metals and the Hippo pathway.
NATURE CELL BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Henry A. Ertl, Mark S. Hill, Patricia J. Wittkopp
Summary: This study reveals the role of chromatin remodeling factors and their relationship with gene expression and chromatin structure in gene regulatory mechanisms. The findings suggest that variations in chromatin accessibility and Grainy head binding contribute to the evolution of gene expression, shedding light on the complex interactions among molecular layers in gene regulation.
Article
Biochemistry & Molecular Biology
Jin Zhang, Jiankai Wei, Haiyan Yu, Bo Dong
Summary: The study identified 553 transcription factors classified into 60 families from Styela clava based on whole genome data, particularly focusing on their expression during early embryonic development. Analysis of transcription factors among different tunicate species revealed significant differences in the zinc finger superfamily, suggesting its potential role in species differentiation and environmental adaptation. The discovery of eight Hox genes located on one chromosome and 23 forkhead box genes in Styela clava provided insights into their potential functions in neurodevelopment and sensory organ development.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Eliana Toren, Yanping Liu, Maigen Bethea, Alexa Wade, Chad S. Hunter
Summary: Pancreatic islet cell development is regulated by transcription factors, and the interaction between Isl1 and Ldb1 is crucial for the maturation and function of islet cells. Ldb1 is expressed in multipotent progenitor cells and endocrine progenitor cells, affecting the formation and function of islets. The loss of Ldb1 leads to a reduction in endocrine cells and dysglycemia, which may have important implications for improving cell-based diabetes therapies.
Article
Multidisciplinary Sciences
Julie Carnesecchi, Gianluca Sigismondo, Katrin Domsch, Clara Eva Paula Baader, Mahmoud-Reza Rafiee, Jeroen Krijgsveld, Ingrid Lohmann
NATURE COMMUNICATIONS
(2020)
Article
Cell Biology
Marilyne Duffraisse, Rachel Paul, Julie Carnesecchi, Bruno Hudry, Agnes Banreti, Jonathan Reboulet, Leiore Ajuria, Ingrid Lohmann, Samir Merabet
JOURNAL OF CELL SCIENCE
(2020)
Article
Multidisciplinary Sciences
Rachel Paul, Guillaume Giraud, Katrin Domsch, Marilyne Duffraisse, Frederic Marmigere, Soumen Khan, Solene Vanderperre, Ingrid Lohmann, Robby Stoks, L. S. Shashidhara, Samir Merabet
Summary: The authors demonstrate that the Hox genes Antennapedia (Antp) and Ultrabithorax (Ubx) play a role in controlling flight appendage morphology in Drosophila, with a particular spatial expression profile and dosage. Interestingly, this phenomenon is also found in evolutionary distant four-winged insect species.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Ioannis Sarropoulos, Mari Sepp, Robert Fromel, Kevin Leiss, Nils Trost, Evgeny Leushkin, Konstantin Okonechnikov, Piyush Joshi, Peter Giere, Lena M. Kutscher, Margarida Cardoso-Moreira, Stefan M. Pfister, Henrik Kaessmann
Summary: This study investigated the regulatory basis of mouse cerebellum development from early neurogenesis to adulthood using snATAC-seq profiles. The research revealed spatiotemporal heterogeneity among progenitor cells and gradual divergence in the regulatory programs of cerebellar neurons during differentiation. Comparison to vertebrate genomes showed a shared decrease in CRE conservation during development and differentiation, as well as differences in constraint between cell types. The study provides insights into mammalian organ development dynamics and evolutionary gene regulation in cerebellar cells.
Article
Biochemistry & Molecular Biology
Julie Carnesecchi, Panagiotis Boumpas, Patrick van Nierop Y. Sanchez, Katrin Domsch, Hugo Daniel Pinto, Pedro Borges Pinto, Ingrid Lohmann
Summary: This study reveals a novel role of the Drosophila Hox transcription factor at the RNA level, by regulating mRNA expression and splicing to promote cell fate decisions. The interaction between the transcription factor and active RNA Polymerase II is crucial for its splicing activity.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Jessica Velten, Xuefan Gao, Patrick Van Nierop Y. Sanchez, Katrin Domsch, Rashi Agarwal, Lena Bognar, Malte Paulsen, Lars Velten, Ingrid Lohmann
Summary: The correct wiring of neuronal circuits is a complex process in development. In our study of Drosophila embryonic motoneurons, we found that a combination of homeodomain transcription factors and immunoglobulin molecules plays an important role in determining connections between neurons and target muscles.
MOLECULAR SYSTEMS BIOLOGY
(2022)
Review
Cell Biology
Panagiotis Boumpas, Samir Merabet, Julie Carnesecchi
Summary: Transcription factors play a crucial role in orchestrating gene expression and splicing, promoting tissue-specific functions and cell fate. Despite the lack of clear understanding of the mechanisms, recent studies have shed light on the importance of transcription factors in these processes and proposed several possible models.
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2023)
Article
Multidisciplinary Sciences
Pedro B. Pinto, Katrin Domsch, Xuefan Gao, Michaela Woelk, Julie Carnesecchi, Ingrid Lohmann
Summary: Hox proteins have similar binding specificities in vitro but control different morphologies in vivo. This paradox has been partially resolved with the discovery of low-affinity binding sites. The specificity of anterior Hox proteins, which are more promiscuous than posterior Hox proteins, is achieved through a precise balance of transcription factors and binding site affinities. Small variations in affinity change the enhancer's sensitivity to different Hox levels, resulting in perturbed gene expression and morphogenesis.
NATURE COMMUNICATIONS
(2022)
Article
Developmental Biology
Laura Folkendt, Ingrid Lohmann, Katrin Domsch
Summary: The study reveals that the broadly expressed Drosophila Hox TF Ultrabithorax (Ubx) interacts with multiple tissue-specific chromatin sites in the mesoderm and neuronal tissues, showing differences in the distribution of active and repressive histone marks between tissue-specific Ubx chromatin sites.
JOURNAL OF DEVELOPMENTAL BIOLOGY
(2021)
