Article
Genetics & Heredity
Adam W. Turner, Shengen Shawn Hu, Jose Verdezoto Mosquera, Wei Feng Ma, Chani J. Hodonsky, Doris Wong, Gaelle Auguste, Yipei Song, Katia Sol-Church, Emily Farber, Soumya Kundu, Anshul Kundaje, Nicolas G. Lopez, Lijiang Ma, Saikat Kumar B. Ghosh, Suna Onengut-Gumuscu, Euan A. Ashley, Thomas Quertermous, Aloke Finn, Nicholas J. Leeper, Jason C. Kovacic, Johan L. M. Bjoerkgren, Chongzhi Zang, Clint L. Miller
Summary: This study applied single-nucleus technology to analyze nuclei from patients with coronary artery disease, identifying elements and transcription factors associated with the disease and proposing key driver transcription factors. This research is of great significance for understanding the regulatory mechanisms of coronary artery disease risk.
Article
Multidisciplinary Sciences
Chang Ge, Zheng Yu, Huakang Sheng, Xiaolin Shen, Xinxiao Sun, Yifei Zhang, Yajun Yan, Jia Wang, Qipeng Yuan
Summary: Quorum sensing is a widespread cell-cell communication mechanism that can regulate metabolic fluxes. The regulatory roles of CRP-binding site and lux box to -10 region in controlling QS promoters have been discovered. By varying the numbers of CRP-binding site and redesigning the lux box to -10 site sequence, a library of QS variants with high dynamic ranges and low leakiness has been created.
NATURE COMMUNICATIONS
(2022)
Review
Plant Sciences
Courtney E. Dresden, Quratulayn Ashraf, Aman Y. Husbands
Summary: The StARkin domain is an evolutionarily conserved structure with a deep hydrophobic pocket capable of binding lipophilic ligands. Dysregulation of StARkin proteins has significant effects on disease and development. Recent studies highlight the diversity of regulatory mechanisms employed by the StARkin module, providing valuable insights for researchers.
CURRENT OPINION IN PLANT BIOLOGY
(2021)
Article
Cell Biology
Magdalena Malachowicz, Aleksei Krasnov, Roman Wenne
Summary: Adaptation to environmental variation caused by global climate change is an important aspect of fisheries management and ecology. The study found that the western and eastern Baltic cod subpopulations respond differently to salinity changes, with 400 differentially expressed genes involved in various processes.
Article
Biochemistry & Molecular Biology
Meghan D. J. Bragdon, Nikit Patel, James Chuang, Ethan Levien, Caleb J. Bashor, Ahmad S. Khalil
Summary: This study demonstrates that high regulatory specificity can be achieved through cooperative multivalent interactions among artificial zinc-finger-based transcription factors. This mechanism effectively prevents aberrant misregulation of the host cell genome, resulting in genetic and functional stability of synthetic gene circuits.
Article
Multidisciplinary Sciences
Jian Han, Omer An, Xi Ren, Yangyang Song, Sze Jing Tang, Haoqing Shen, Xinyu Ke, Vanessa Hui En Ng, Daryl Jin Tai Tay, Hui Qing Tan, Dennis Kappei, Henry Yang, Leilei Chen
Summary: DAP3 acts as a splicing modulator in cancer by coordinating splicing regulatory networks and causing mis-splicing events, which are associated with poor prognosis in multiple cancers.
NATURE COMMUNICATIONS
(2022)
Article
Cell Biology
Xiaojuan Zhou, Fengge Ma, Jun Xie, Meng Yuan, Yunqiao Li, Namir Shaabani, Fangzhu Zhao, Deli Huang, Nicholas C. Wu, Chang-Chun D. Lee, Hejun Liu, Jiali Li, Zhonghui Chen, Yazhen Hong, Wen-Hsien Liu, Nengming Xiao, Dennis R. Burton, Haijian Tu, Hang Li, Xin Chen, John R. Teijaro, Ian A. Wilson, Changchun Xiao, Zhe Huang
Summary: The study found that neutralizing antibody responses to SARS-CoV-2 have diverse B cell receptor repertoires and convergent epitope targeting, providing important guidance for effective vaccine design.
Review
Zoology
Hai-Yan Lin, Gang Song, Fumin Lei, Dongming Li, Yanhua Qu
Summary: CBG is a high-affinity plasma protein that plays a crucial role in birds by regulating the biological activities of glucocorticoids and helping them adapt to various stresses and environments. The structural and functional properties of CBG are important for understanding the biological actions of glucocorticoids in mediating stress responses and adaptive mechanisms in birds.
FRONTIERS IN ZOOLOGY
(2021)
Article
Multidisciplinary Sciences
Xingyu Wang, Jianming Chen, Sachiko T. Zamojski, Yinhang Wang, Gregory R. Smith, Frederique Ruf-Zamojski, Stuart C. Sealfon, Lan Zhou
Summary: Fibrosis is observed in the diaphragm of mdx5cv mouse model for DMD, but not in the limb muscles. Single-cell RNA sequencing reveals that fibro/adipogenic progenitors (FAPs) are the main source of ECM and also express important ECM regulatory genes. FAPs are more abundant in the diaphragm than in the quadriceps, suggesting that anti-fibrotic therapy for DMD should target ECM production and the regulatory functions of FAPs.
Article
Multidisciplinary Sciences
Charles Sackerson, Vivian Garcia, Nicole Medina, Jessica Maldonado, John Daly, Rachel Cartwright
Summary: Cetacea, including the minke whale, have evolved high levels of myoglobin gene expression in skeletal muscles. Contrary to previous assumptions, the study found that the myoglobin gene from the minke whale shows a low level of expression compared to humans. The study also identified key regulatory elements in the gene that differ from those in humans.
Article
Biotechnology & Applied Microbiology
Yang Liu, Wenzhi Yang, Tao Su, Chengchuan Che, Guizhi Li, Can Chen, Meiru Si
Summary: This study revealed that CssR in C. glutamicum mediates stress response through ligand-induced conformational changes of the protein, rather than cysteine oxidation-based thiol modification. CssR negatively controls the expression of the ncgl1576-ncgl1577 operon, its structural gene, and/or redox homeostasis-related genes, showing its crucial role in stress response.
MICROBIAL CELL FACTORIES
(2021)
Review
Biochemistry & Molecular Biology
Goutham V. Ganesh, Kumar Ganesan, Baojun Xu, Kunka Mohanram Ramkumar
Summary: Studying the role of macrophages in diabetic foot ulcers is important for understanding wound healing and repair mechanisms as well as other pathological conditions.
Review
Genetics & Heredity
M. Brandon Titus, Adeline W. Chang, Eugenia C. Olesnicky
Summary: Alternative splicing is a fundamental mechanism of eukaryotic RNA regulation that increases complexity in transcriptomes and proteomes. Understanding aberrant splicing has shed light on developmental and neurodegenerative diseases, leading to innovative therapeutic treatments. Research on distinct protein-coding spliceforms and the use of noncoding exons in alternative splicing can provide insights into physiological roles and specific functions of gene spliceforms.
FRONTIERS IN GENETICS
(2021)
Article
Medicine, Research & Experimental
Carsten Schwarz, Patience Eschenhagen, Henrijette Schmidt, Thordis Hohnstein, Christina Iwert, Claudia Grehn, Jobst Roehmel, Eva Steinke, Mirjam Stahl, Laura Lozza, Ekaterina Tikhonova, Elisa Rosati, Ulrik Stervbo, Nina Babel, Jochen G. Mainz, Hilmar Wisplinghoff, Frank Ebel, Lei-Jie Jia, Matthew G. Blango, Peter Hortschansky, Sascha Brunke, Bernhard Hube, Axel A. Brakhage, Olaf Kniemeyer, Alexander Scheffold, Petra Bacher
Summary: This study investigated fungus-specific Th cells in the peripheral blood of patients with cystic fibrosis (pwCF) and healthy controls. It was found that high-avidity A. fumigatus-specific effector Th cells developed in pwCF, targeting different A. fumigatus proteins. Patients with allergic bronchopulmonary aspergillosis (ABPA) exhibited high frequencies of Th2 cells that could cross-recognize various filamentous fungi.
JOURNAL OF CLINICAL INVESTIGATION
(2023)
Article
Genetics & Heredity
Daniel S. Kim, Viviana I. Risca, David L. Reynolds, James Chappell, Adam J. Rubin, Namyoung Jung, Laura K. H. Donohue, Vanessa Lopez-Pajares, Arwa Kathiria, Minyi Shi, Zhixin Zhao, Harsh Deep, Mahfuza Sharmin, Deepti Rao, Shin Lin, Howard Y. Chang, Michael P. Snyder, William J. Greenleaf, Anshul Kundaje, Paul A. Khavari
Summary: By analyzing multiomic data and using a deep learning framework, cooperative DNA sequence rules that regulate gene modules during epidermal differentiation were identified. The temporal dynamics and cis-regulatory logic were validated through massively parallel reporter assay analysis.
Review
Cell Biology
Bas van Steensel, Eileen E. M. Furlong
NATURE REVIEWS MOLECULAR CELL BIOLOGY
(2019)
Article
Biochemistry & Molecular Biology
Olga M. Sigalova, Amirreza Shaeiri, Mattia Forneris, Eileen E. M. Furlong, Judith B. Zaugg
MOLECULAR SYSTEMS BIOLOGY
(2020)
Editorial Material
Genetics & Heredity
Amy L. McGuire, Stacey Gabriel, Sarah A. Tishkoff, Ambroise Wonkam, Aravinda Chakravarti, Eileen E. M. Furlong, Barbara Treutlein, Alexander Meissner, Howard Y. Chang, Nuria Lopez-Bigas, Eran Segal, Jin-Soo Kim
NATURE REVIEWS GENETICS
(2020)
Article
Cell Biology
James P. Reddington, David A. Garfield, Olga M. Sigalova, Aslihan Karabacak Calviello, Raquel Marco-Ferreres, Charles Girardot, Rebecca R. Viales, Jacob F. Degner, Uwe Ohler, Eileen E. M. Furlong
DEVELOPMENTAL CELL
(2020)
Article
Biochemistry & Molecular Biology
Swann Floc'hlay, Emily S. Wong, Bingqing Zhao, Rebecca R. Viales, Morgane Thomas-Chollier, Denis Thieffry, David A. Garfield, Eileen E. M. Furlong
Summary: Genetic variation (allelic imbalance) more frequently impacts gene expression, especially metabolic and environmental response genes. Allelic imbalance in cis-regulatory elements is common and highly heritable, but generally does not propagate to gene expression. Genetic variation affects RNA levels through mechanisms involving H3K4me3 or chromatin accessibility and H3K27ac.
Review
Cell Biology
Gabriel R. Cavalheiro, Tim Pollex, Eileen E. M. Furlong
Summary: The past decade has witnessed significant advancements in understanding the three-dimensional properties of the genome, particularly in terms of chromatin structures and their impact on gene expression. However, there is still much to learn about the underlying mechanisms and functional roles of genome topology. Recent studies utilizing genetic manipulations have provided new insights into the relationship between genome topology and gene expression, with a focus on enhancer function.
CURRENT OPINION IN GENETICS & DEVELOPMENT
(2021)
Article
Cell Biology
Anna C. Koegler, Yacine Kherdjemil, Katharina Bender, Adam Rabinowitz, Raquel Marco-Ferreres, Eileen E. M. Furlong
Summary: Many developmental regulators have complex and context-specific roles in different tissues and stages, making the dissection of their function extremely challenging. The improved light-inducible nuclear export system (iLEXY) enables rapid, efficient, and reversible nuclear protein depletion in embryos, and is generalizable to proteins of diverse sizes and functions, highlighting its power in dissecting the function of pleiotropic factors during embryogenesis with unprecedented temporal precision.
DEVELOPMENTAL CELL
(2021)
Article
Biochemistry & Molecular Biology
Jialin Liu, Rebecca R. Viales, Pierre Khoueiry, James P. Reddington, Charles Girardot, Eileen E. M. Furlong, Marc Robinson-Rechavi
Summary: Inter-species comparisons reveal an hourglass expression pattern during embryogenesis, with a higher proportion of conserved enhancers at the phylotypic period. Positive selection is detected on developmental enhancers at early and late stages, with a depletion at the phylotypic period, suggesting positive selection as an evolutionary mechanism underlying the hourglass pattern of animal evolution.
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
Charalampos Chrysovalantis Galouzis, Eileen E. M. Furlong
Summary: Enhancers are cis-regulatory elements that can activate transcription remotely to regulate a specific pattern of gene expression. Mechanisms of enhancer-promoter communication, including the role of cohesin and the Mediator complex, as well as the genetic dissection and genome-wide approaches, highlight key components such as core promoter sequence and genomic context.
CURRENT OPINION IN CELL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Diego Calderon, Ronnie Blecher-Gonen, Xingfan Huang, Stefano Secchia, James Kentro, Riza M. Daza, Beth Martin, Alessandro Dulja, Christoph Schaub, Cole Trapnell, Erica Larschan, Kate M. O'Connor-Giles, Eileen E. M. Furlong, Jay Shendure
Editorial Material
Biochemistry & Molecular Biology
Blanca Pijuan-Sala, Eileen E. M. Furlong
Article
Multidisciplinary Sciences
Gabriel R. Cavalheiro, Charles Girardot, Rebecca R. Viales, Tim Pollex, T. B. Ngoc Cao, Perrine Lacour, Songjie Feng, Adam Rabinowitz, Eileen E. M. Furlong
Summary: During early Drosophila embryogenesis, most TAD boundaries are established by a combination of CTCF, BEAF-32, and CP190, although a subset of boundaries show higher dependence on specific insulators. Weakened boundaries result in aberrant gene expression due to unconstrained enhancer activity.
Article
Biotechnology & Applied Microbiology
Tobias Heinen, Stefano Secchia, James P. Reddington, Bingqing Zhao, Eileen E. M. Furlong, Oliver Stegle
Summary: In this paper, the authors developed a computational framework called scDALI to characterize the genetic effects specific to certain cell states. Application of scDALI to single-cell sequencing data from fruit fly embryos and human iPSCs revealed heterogeneous genetic effects in specific lineages, developmental stages, or cell types.
Review
Multidisciplinary Sciences
Liesbeth Minnoye, Georgi K. Marinov, Thomas Krausgruber, Lixia Pan, Alexandre P. Marand, Stefano Secchia, William J. Greenleaf, Eileen E. M. Furlong, Keji Zhao, Robert J. Schmitz, Christoph Bock, Stein Aerts
Summary: This article discusses the characteristics and biochemical methods of chromatin accessibility, emphasizing its importance in identifying candidate regulatory genomic regions. It also mentions the use of bioinformatics tools for data interpretation and discovery of key regulators, as well as the maintenance of data quality and reproducibility. Lastly, it points out that while chromatin accessibility profiling is valuable, it needs to be complemented with orthogonal assays to explain the complex gene regulation process.
NATURE REVIEWS METHODS PRIMERS
(2021)