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.
Article
Biology
Vivek Kumar Raxwal, Somya Singh, Manu Agarwal, Karel Riha
Summary: The study revealed that new genes in rice have relatively low expression levels, possibly controlled by distal enhancers and chromatin conformation at their TSS; the chromatin in TSS regions may be remodeled in response to abiotic stress, indicating conditional expression of young genes. Furthermore, transcripts of young genes in Arabidopsis are prone to nonsense-mediated RNA decay, restricting their expression.
Article
Multidisciplinary Sciences
Jiankang Wang, Masashige Bando, Katsuhiko Shirahige, Ryuichiro Nakato
Summary: This study comprehensively characterizes cohesin binding sites in different human cell types and identifies a subset of cohesin binding sites, DICs, which are negatively correlated with transcriptional regulation. These findings suggest a previously unidentified function of cohesin on intragenic regions for transcriptional regulation.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Rachel A. Keuls, Young Sun Oh, Ivanshi Patel, Ronald J. Parchem
Summary: Developmental potential is restricted after germ layer specification, but cranial neural crest cells challenge this by giving rise to both ectodermal and ectomesenchymal lineages. The mechanism behind this cell differentiation is poorly understood. This study demonstrates that cranial neural crest cells have a transient state of increased chromatin accessibility, and the deletion of miR-302 leads to premature specification of the ectomesenchymal lineage.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Review
Plant Sciences
Takuya Sakamoto, Sachihiro Matsunaga
Summary: Plants exhibit diverse characteristics and functions of chromatin organization, with similarities and differences to animals. The relationship between chromatin organization and transcriptional regulation in response to environmental stresses is becoming clearer. The regulation of specific chromatin positions in the nuclear space plays a crucial role in transcription, and recent findings suggest that local chromatin interactions have a greater impact on gene expression regulation than large-scale chromatin organization. The study highlights the importance of chromatin dynamics and transcriptional regulation in plants and discusses future directions in this field.
CURRENT OPINION IN PLANT BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Adriana K. Alexander, Edward J. Rice, Jelena Lujic, Leah E. Simon, Stephanie Tanis, Gilad Barshad, Lina Zhu, Jyoti Lama, Paula E. Cohen, Charles G. Danko
Summary: During meiotic prophase I, balance between transcriptional activation and homologous recombination is crucial. We investigated the interplay between chromatin accessibility and transcription through prophase I and found that Pol II is initially in a paused state and later released in a burst mediated by transcription factors A-MYB and BRDT. This transcriptional activity is separate from meiotic recombination, which shows earlier chromatin accessibility and distinct loci from transcriptional activation. Our findings reveal mechanisms underlying chromatin specialization in transcription or recombination during meiosis.
NATURE COMMUNICATIONS
(2023)
Article
Plant Sciences
Marleny Garcia-Lozano, Purushothaman Natarajan, Amnon Levi, Ramesh Katam, Carlos Lopez-Ortiz, Padma Nimmakayala, Umesh K. Reddy
Summary: The study revealed that 88% of genes in tetraploid watermelon followed a >1:1 dosage effect, with most genes being upregulated. A large number of hypomethylated regions were identified in an isogenic tetraploid watermelon, localized near transcriptional start sites of upregulated genes, highlighting the importance of methylation in gene regulation. Genome doubling caused changes in higher-order chromatin structures and led to switching of compartments harboring genes associated with growth, development, and stress responses.
Article
Multidisciplinary Sciences
Philippe J. Batut, Xin Yang Bing, Zachary Sisco, Joao Raimundo, Michal Levo, Michael S. Levine
Summary: Past studies have provided contradictory claims about the role of genome organization in gene activity regulation. This study demonstrates that the Drosophila genome is organized by two independent classes of regulatory sequences, tethering elements and insulators. These two levels of genome organization operate independently to ensure precise transcriptional dynamics and reliable complex patterning processes.
Review
Biochemistry & Molecular Biology
Talha Ijaz, Michael A. Burke
Summary: Heart failure is a complex disease process with neurohormonal system aberrations leading to dysregulated cellular signaling and gene transcription. The BET family epigenetic reader proteins play a key role in regulating gene transcription, influencing cardiac fibrosis and systolic dysfunction. Recent studies also highlight the importance of BRD4 in maintaining cardiomyocyte mitochondrial respiration and define BET bromodomain-independent processes involved in cardiac homeostasis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Immunology
Chenshen Huang, Na Zhang, Hao Xiong, Ning Wang, Zhizhong Chen, Zhizhan Ni, Xiaohong Liu, Boxu Lin, Bujun Ge, Bing Du, Qi Huang
Summary: This study aims to explore a novel method for transcriptional regulation and proposes a new pipeline for analyzing the role of GPRC5B in COAD. By using RNA-seq, ATAC-seq, and ChIP-seq, researchers found the correlation between GPRC5B and macrophages and identified TF GATA4 as a key upstream factor.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Immunology
Noam Kadouri, Tal Givony, Shir Nevo, Joschka Hey, Shifra Ben Dor, Golda Damari, Bareket Dassa, Jan Dobes, Dieter Weichenhan, Marion Bahr, Michelle Paulsen, Rebecca Haffner-Krausz, Marcus A. Mall, Christoph Plass, Yael Goldfarb, Jakub Abramson
Summary: This study reveals the importance of FOXN1 in the development of thymic epithelial cells and hair follicle cells, and identifies key regulatory regions and transcription factors involved in its expression.
SCIENCE IMMUNOLOGY
(2022)
Article
Cell Biology
Xin Li, Shanshan Wang, Xilan Yu, Shanshan Li
Summary: Autophagy is a catabolic process that maintains homeostasis and is involved in cell differentiation and development. The chromatin remodeling complex INO80 and histone variant H2A.Z have been identified as new regulators of autophagy, and the histone deacetylase Rpd3L complex plays a role in repressing autophagy by deacetylating Ino80 and H2A.Z. These findings highlight the importance of chromatin remodelers and histone variants in regulating autophagy in response to nutrient availability.
Article
Cell Biology
Wei Yu, V. Praveen Chakravarthi, Shaon Borosha, Iman Dilower, Eun Bee Lee, Anamika Ratri, Rebekah R. Starks, Patrick E. Fields, Michael W. Wolfe, M. Omar Faruque, Geetu Tuteja, M. A. Karim Rumi
Summary: The study reveals that trophoblast-specific Satb1 expression is regulated by long-range chromatin looping mediated by an enhancer that interacts with ELF5 and SATB proteins, contributing to the maintenance of cell state.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Mathias Boulanger, Mehuli Chakraborty, Denis Tempe, Marc Piechaczyk, Guillaume Bossis
Summary: SUMO plays a crucial role in transcriptional control by modifying various transcriptional factors, coregulators, chromatin components, and transcriptional machineries. Recent large-scale studies have significantly advanced our understanding of the role of SUMO in gene expression control, shedding light on its impact on transcription and chromatin organization.
Article
Multidisciplinary Sciences
Ester Marina-Zarate, Ana Rodriguez-Ronchel, Manuel J. Gomez, Fatima Sanchez-Cabo, Almudena R. Ramiro
Summary: CTCF is a DNA-binding protein that plays important roles in chromatin structure organization and transcriptional regulation; however, the functional determinants of different CTCF-binding sites (CBS) are not well characterized. Using a conditional mouse model, we identified a set of CBSs that are lost upon CTCF depletion (lost CBSs) and another set that persists (retained CBSs). Retained CBSs are more similar to the consensus CTCF-binding sequence and usually span tandem CTCF peaks. Lost CBSs are enriched at enhancers and promoters and associated with active chromatin marks and higher transcriptional activity. In contrast, retained CBSs are enriched at TAD and loop boundaries, acting as chromatin barriers between distinct chromatin states.
Article
Oncology
Egle Ramelyte, Aizhan Tastanova, Zsolt Balazs, Desislava Ignatova, Patrick Turko, Ulrike Menzel, Emmanuella Guenova, Christian Beisel, Michael Krauthammer, Mitchell Paul Levesque, Reinhard Dummer
Summary: The study found that intralesional T-VEC treatment in primary cutaneous B cell lymphoma patients led to significant tumor response, rapid eradication of malignant cells, activation of the interferon pathway, and early influx of various immune cells, ultimately resulting in enhanced cellular immunity.
Editorial Material
Oncology
Anja Irmisch, Ximena Bonilla, Stephane Chevrier, Kjong-Van Lehmann, Franziska Singer, Nora C. Toussaint, Cinzia Esposito, Julien Mena, Emanuele S. Milani, Ruben Casanova, Daniel J. Stekhoven, Rebekka Wegmann, Francis Jacob, Bettina Sobottka, Sandra Goetze, Jack Kuipers, Jacobo Sarabia del Castillo, Michael Prummer, Mustafa A. Tuncel, Ulrike Menzel, Andrea Jacobs, Stefanie Engler, Sujana Sivapatham, Anja L. Frei, Gabriele Gut, Joanna Ficek, Nicola Miglino, Rudolf Aebersold, Marina Bacac, Niko Beerenwinkel, Christian Beisel, Bernd Bodenmiller, Reinhard Dummer, Viola Heinzelmann-Schwarz, Viktor H. Koelzer, Markus G. Manz, Holger Moch, Lucas Pelkmans, Berend Snijder, Alexandre P. A. Theocharides, Markus Tolnay, Andreas Wicki, Bernd Wollscheid, Gunnar Ratsch, Mitchell P. Levesquel
Summary: The Tumor Profiler Study combines a prospective diagnostic approach with an exploratory strategy to assess the relevance of in-depth tumor profiling in supporting clinical decision-making and improving the biological understanding of the disease.
Article
Hematology
Tata Nageswara Rao, Nils Hansen, Jan Stetka, Damien Luque Paz, Milena Kalmer, Julian Hilfiker, Max Endele, Nouraiz Ahmed, Lucia Kubovcakova, Margareta Rybarikova, Hui Hao-Shen, Florian Geier, Christian Beisel, Stefan Dirnhofer, Timm Schroeder, Tim H. Brummendorf, Dominik Wolf, Steffen Koschmieder, Radek C. Skoda
Summary: The study revealed a bias of CD41(hi) HSCs towards megakaryocyte differentiation and aberrant function in relation to MPN and JAK2-V617F mutation. CD41(hi) HSCs exhibited higher cell cycle activity and gene expression levels related to oxidative phosphorylation.
Article
Biochemical Research Methods
Tobias Kockmann, Christian Panse
Summary: The Bioconductor project has shown that R is valuable for genomics data analysis, but infrastructure for proteomics data analysis in R is lacking. The rawDiag and rawrr packages provide access to mass spectrometry raw files for metadata analysis and visualization, with rawrr now offering complete access to spectral data in Thermo Fisher Scientific raw files. Two use cases demonstrate the application of the package for real-world research tasks.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Genetics & Heredity
Mireia Coscolla, Sebastien Gagneux, Fabrizio Menardo, Chloe Loiseau, Paula Ruiz-Rodriguez, Sonia Borrell, Isaac Darko Otchere, Adwoa Asante-Poku, Prince Asare, Leonor Sanchez-Buso, Florian Gehre, C. N'Dira Sanoussi, Martin Antonio, Dissou Affolabi, Janet Fyfe, Patrick Beckert, Stefan Niemann, Abraham S. Alabi, Martin P. Grobusch, Robin Kobbe, Julian Parkhill, Christian Beisel, Lukas Fenner, Erik C. Bottger, Conor J. Meehan, Simon R. Harris, Bouke C. de Jong, Dorothy Yeboah-Manu, Daniela Brites
Summary: This study sheds new light on the genomic diversity and evolutionary history of M. africanum, revealing that the most likely ancestral distribution of L9 is East Africa, while L5 and L6 are most likely from the Eastern part of West Africa, with important differences in their phylogeographical substructure and genetic diversity. The study also indicates that previous associations of drug resistance with lineage are likely influenced by sample bias or geography.
MICROBIAL GENOMICS
(2021)
Article
Virology
Julia Klaus, Marina L. Meli, Barbara Willi, Sarah Nadeau, Christian Beisel, Tanja Stadler, Herman Egberink, Shan Zhao, Hans Lutz, Barbara Riond, Nina Rosinger, Hanspeter Stalder, Sandra Renzullo, Regina Hofmann-Lehmann
Summary: This study reports the first SARS-CoV-2 infection in a cat from a COVID-19-affected household in Switzerland. The infected cat showed upper respiratory tract infection symptoms, while the cohabiting cat remained asymptomatic. Furthermore, the study confirmed contamination of the cats' fur and bed with viral RNA.
Article
Oncology
Ariane L. Moore, Aashil A. Batavia, Jack Kuipers, Jochen Singer, Elodie Burcklen, Peter Schraml, Christian Beisel, Holger Moch, Niko Beerenwinkel
Summary: Intra-tumour heterogeneity is a key feature of renal cancer, with different tumour clones evolving over time. Analysis of 178 tumour samples from 89 clear cell renal cell carcinoma patients revealed frequent subclonal mutations and both shared and private mutations contribute to the complexity of differential gene expression and pathway interaction. Multi-regional sequencing is essential for identifying subclones within clear cell renal cell carcinoma.
Article
Biochemistry & Molecular Biology
Jeremias N. Brand, Gudrun Viktorin, R. Axel W. Wiberg, Christian Beisel, Lukas Schaerer
Summary: This study reports on a global sampling campaign aimed at increasing taxon sampling and geographic representation of the genus Macrostomum. Using extensive transcriptome and single-locus data, the researchers generated phylogenomic hypotheses including 145 species. The results show consistent clades across different phylogenetic methods, but the exact grouping is unclear, possibly due to a radiation early in Macrostomum evolution. Additionally, the study reveals a large undescribed diversity, with 94 of the studied species likely being new to science, and identifies multiple novel morphological traits.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Microbiology
Helen Cox, Galo A. Goig, Zubeida Salaam-Dreyer, Anzaan Dippenaar, Anja Reuter, Erika Mohr-Holland, Johnny Daniels, Patrick G. T. Cudahy, Mark P. Nicol, Sonia Borrell, Miriam Reinhard, Anna Doetsch, Christian Beisel, Sebastien Gagneux, Robin M. Warren, Jennifer Furin
Summary: Treatment of multidrug-resistant or rifampicin-resistant tuberculosis could be improved by using whole-genome sequencing to predict drug resistance and provide more effective individualized treatment regimens.
JOURNAL OF CLINICAL MICROBIOLOGY
(2022)
Article
Biochemical Research Methods
Jack Kuipers, Ariane L. Moore, Katharina Jahn, Peter Schraml, Feng Wang, Kiyomi Morita, P. Andrew Futreal, Koichi Takahashi, Christian Beisel, Holger Moch, Niko Beerenwinkel
Summary: Tumour progression involves the evolutionary process of different clones within the same tumor, leading to intra-tumour heterogeneity. The interactions between these clones can impact tumor evolution, disease progression, and treatment outcomes. Identifying gene pairs altered in distinct subclones using a statistical testing framework like GeneAccord is crucial for understanding the cooperative effects between different clones.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Alexander Yermanos, Kai-Lin Hong, Andreas Agrafiotis, Jiami Han, Sarah Nadeau, Cecilia Valenzuela, Asli Azizoglu, Roy Ehling, Beichen Gao, Michael Spahr, Daniel Neumeier, Ching-Hsiang Chang, Andreas Dounas, Ezequiel Petrillo, Ina Nissen, Elodie Burcklen, Mirjam Feldkamp, Christian Beisel, Annette Oxenius, Miodrag Savic, Tanja Stadler, Fabian Rudolf, Sai T. Reddy
Summary: DeepSARS is a high-throughput platform that enables simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2. It combines multiple techniques to achieve highly sensitive viral detection and capture genomic diversity and viral evolution.
Article
Multidisciplinary Sciences
Lukas M. von Ziegler, Amalia Floriou-Servou, Rebecca Waag, Rebecca R. Das Gupta, Oliver Sturman, Katharina Gapp, Christina A. Maat, Tobias Kockmann, Han-Yu Lin, Sian N. Duss, Mattia Privitera, Laura Hinte, Ferdinand von Meyenn, Hanns U. Zeilhofer, Pierre-Luc Germain, Johannes Bohacek
Summary: This study investigates the molecular events in the mouse hippocampus induced by acute stress through the use of swim exposure. The results reveal the complexity and specificity of the acute stress response, highlighting changes in protein phosphorylation, gene transcription, and protein translation. These molecular events efficiently resolve within four hours after stress initiation.
NATURE COMMUNICATIONS
(2022)
Article
Biology
Barbara Pfister, Jessica M. Shields, Tobias Kockmann, Jonas Grossmann, Melanie R. Abt, Martha Stadler, Samuel C. Zeeman
Summary: This study used Saccharomyces cerevisiae as a testbed to investigate the functions of plant starch biosynthetic enzymes and create diverse starch-like polymers. The results revealed unexpected effects of glucan biosynthesis on protein abundances and demonstrated that different enzyme ratios influenced glucan structure and solubility.
Article
Dermatology
Michael Koch, Tobias Kockmann, Elke Rodriguez, Ulrike Wehkamp, Paul Hiebert, Maya Ben-Yehuda Greenwald, Dora Stoelzl, Hans-Dietmar Beer, Erwin Tschachler, Stephan Weidinger, Sabine Werner, Ulrich Auf Dem Keller
Summary: Atopic dermatitis is a common inflammatory skin disease characterized by a compromised epidermal barrier and cutaneous inflammation. This study identified the molecular alterations in the epidermis of patients with atopic dermatitis, revealing an impaired NRF2-antioxidant pathway and reduced abundance of mitochondrial proteins involved in key metabolic pathways. These findings provide insights into the pathogenesis of atopic dermatitis and potential targets for pharmaceutical intervention.
JOURNAL OF INVESTIGATIVE DERMATOLOGY
(2023)
Article
Biology
Ulrike Lischetti, Aizhan Tastanova, Franziska Singer, Linda Grob, Matteo Carrara, Phil F. F. Cheng, Julia M. Martinez M. Gomez, Federica Sella, Veronika Haunerdinger, Christian Beisel, Mitchell P. Levesque
Summary: CITE-seq technology bridges the gap between RNA and protein in single-cell analysis, but its application to solid biopsies is limited. Applying CITE-seq to clinically relevant solid biopsies is an essential step in single-cell translational studies.
COMMUNICATIONS BIOLOGY
(2023)
