Article
Biochemistry & Molecular Biology
Yanis Zekri, Romain Guyot, Frederic Flamant
Summary: We have created a database that integrates RNA-seq and ChIP-seq data to better understand the target genes of thyroid hormone receptors in different cell types. This database serves as a resource for studying the mode of action of thyroid hormone and provides a user-friendly tool to access specific gene information and extract gene lists of interest.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Oncology
Ayman Osman, Malin Linden, Tobias Osterlund, Christoffer Vannas, Lisa Andersson, Mandy Escobar, Anders Stahlberg, Pierre Aman
Summary: DDIT3 is a transcription factor that plays a key role in cellular stress responses, cell cycle regulation, apoptosis, cell differentiation, and cancer development. It can bind to DNA and regulate target genes by forming heterodimers with other bZIP transcription factors. DDIT3 mainly binds to the promoter region of regulated genes and shows a strong overlap with H3K27 acetylation marks.
EXPERIMENTAL CELL RESEARCH
(2023)
Article
Biochemical Research Methods
Maria Osmala, Gokcen Eraslan, Harri Lahdesmaki
Summary: ChromDMM is a mixture model based on multiple chromatin features, which accurately clusters genomic regions and discovers distinctive patterns of epigenetic signals at regulatory elements. Validated with simulated data and ENCODE data, ChromDMM demonstrates higher accuracy and robustness.
Article
Neurosciences
Emily R. Brocato, Jennifer T. Wolstenholme
Summary: Adolescent binge ethanol use can lead to lasting changes in the prefrontal cortex and cognitive deficits, which may be linked to alterations in H3K36 methylation.
FRONTIERS IN MOLECULAR NEUROSCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Yuchao Jiang, Yuriko Harigaya, Zhaojun Zhang, Hongpan Zhang, Chongzhi Zang, Nancy R. Zhang
Summary: The epigenetic control of gene expression is highly cell-type and context specific, and can be broken down into modular components by a transcription factor activating or repressing the target gene expression. A new nonparametric approach, TRIPOD, is proposed to detect and characterize the relationships between TF, target gene, and TF binding site accessibility using single-cell RNA and ATAC multiomic data.
Article
Developmental Biology
Julie Gamart, Iros Barozzi, Frederic Laurent, Robert Reinhardt, Laurene Ramos Martins, Thomas Oberholzer, Axel Visel, Rolf Zeller, Aimee Zuniga
Summary: SMAD4 regulates gene expression in early limb buds, primarily mediating BMP signal transduction and playing a crucial role in upregulating target genes in anterior limb bud mesenchyme, while also repressing posterior gene expression. This study reveals opposing trans-regulatory inputs from SHH- and SMAD4-mediated BMP signal transduction during digit patterning and outgrowth in early limb buds.
Article
Plant Sciences
Heng Wei, Yunqing Cheng, Ying Sun, Xingzheng Zhang, Hongli He, Jianfeng Liu
Summary: This study identified the regulatory role of ChARF3 in hazel ovary development through analyzing its spatiotemporal expression and target genes, suggesting that ChARF3 may mediate genes related to auxin biosynthesis and transport, cell division and proliferation, and flower and fruit development to regulate ovary initiation and ovule development, providing new insights into the molecular mechanism of hazel yield formation.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Developmental Biology
Janani Ramachandran, Wanlu Chen, Rachel K. Lex, Kathryn E. Windsor, Hyunji Lee, Tingchang Wang, Weiqiang Zhou, Hongkai Ji, Steven A. Vokes
Summary: Transcriptional responses to the Hedgehog (HH) signaling pathway are primarily modulated by GLI repression in the mouse limb. The BAF chromatin remodeling complex has been suggested to play a role in mediating GLI repression. However, SMARCC1, a core BAF complex protein, maintains chromatin accessibility at most enhancers, including those bound by GLI, and its binding at GLI-regulated enhancers occurs independently of GLI3. SMARCC1 is not necessary for mediating constitutive GLI repression in HH mutant limb buds.
DEVELOPMENTAL BIOLOGY
(2023)
Article
Biology
Richard J. White, Eirinn Mackay, Stephen W. Wilson, Elisabeth M. Busch-Nentwich
Summary: In zebrafish, differentially expressed genes are often over-represented on the same chromosome as the mutation, due to different levels of expression of alleles from different genetic backgrounds. This has implications for interpreting the results and pathways in RNA-seq experiments.
Review
Cell Biology
Patricia A. Umberger, Stacey K. Ogden
Summary: SPOP protein serves as a guardian of genome integrity and controls transcriptional regulation by regulating the stability of GLI family members in the Hedgehog signaling pathway. In Drosophila, the protein HIB targets the GLI ortholog Ci for proteolysis through Cul3-directed degradation, but the molecular mechanisms of GLI/Ci targeting differ between Drosophila and vertebrates.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Cell Biology
Patricia A. Umberger, Stacey K. Ogden
Summary: SPOP plays a crucial role in maintaining cellular homeostasis by regulating DNA repair and gene expression-related DNA-binding proteins; within the Hedgehog signaling pathway, CUL3-SPOP activity influences stability of GLI transcription factors and the amplitude and duration of HH transcriptional responses; a similar mechanism exists in Drosophila, but HIB and SPOP have different molecular contributions to Drosophila and vertebrate HH signaling pathways.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Shengen Shawn Hu, Lin Liu, Qi Li, Wenjing Ma, Michael J. Guertin, Clifford A. Meyer, Ke Deng, Tingting Zhang, Chongzhi Zang
Summary: The authors develop a computational model, SELMA, to estimate and correct enzymatic cleavage biases in chromatin accessibility profiling data. SELMA accurately estimates the biases from both bulk and single-cell DNase-seq and ATAC-seq data, and improves transcription factor binding inference and cell clustering in single-cell ATAC-seq data. SELMA enhances the analysis of chromatin accessibility sequencing data.
NATURE COMMUNICATIONS
(2022)
Article
Biotechnology & Applied Microbiology
Junxiao Ren, Weihua Tian, Keren Jiang, Zhang Wang, Dandan Wang, Zhuanjian Li, Fengbin Yan, Yanbin Wang, Yadong Tian, Kepeng Ou, Hongjun Wang, Xiangtao Kang, Hong Li, Xiaojun Liu
Summary: Using RNA-Seq and ChIP-Seq, a total of 990 estrogen-responsive genes were identified in chicken liver, which are highly enriched in lipid metabolism and biological processes. Integrated analysis also revealed 191 genes directly targeted by estrogen, shedding light on the molecular mechanism of estrogen-related lipid metabolism.
Article
Biotechnology & Applied Microbiology
Rhys Newell, Richard Pienaar, Brad Balderson, Michael Piper, Alexandra Essebier, Mikael Boden
Summary: Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a primary protocol for detecting DNA-protein interactions, and the adapted ChIP-R method statistically evaluates reproducibility from experimental replicates, improving the identification of transcription factor binding events. By re-analyzing existing datasets, ChIP-R can reconstruct reproducible peaks from fragments with enhanced biological enrichment compared to current strategies.
Article
Entomology
Meng-Pei Guo, Wen-Liang Qian, Xue-Chuan He, Jian Peng, Peng Wang, Wei-Na Wang, Qing-You Xia, Dao-Jun Cheng
Summary: The study identified BR-C target genes in silkworm through ChIP-seq, revealing their involvement in biosynthetic, metabolic, and developmental pathways. Transcriptome analysis and real-time PCR confirmed similarities in expression patterns between some potential BR-C targets and BR-C. ChIP-PCR validation and luciferase assays further demonstrated BR-C's direct binding to target gene promoters and its regulatory role in insect growth and development.
Editorial Material
Biology
Timothy E. Saunders, Philip W. Ingham
Article
Biochemistry & Molecular Biology
Doria Filipponi, Alexander Emelyanov, Julius Muller, Clement Molina, Jennifer Nichols, Dmitry V. Bulavin
Article
Biochemistry & Molecular Biology
Yazi D. Ke, Gabriella Chan, Kristie Stefanoska, Carol Au, Mian Bi, Julius Mueller, Magdalena Przybyla, Astrid Feiten, Emmanuel Prikas, Glenda M. Halliday, Olivier Piguet, Matthew C. Kiernan, Michael Kassiou, John R. Hodges, Clement T. Loy, John S. Mattick, Arne Ittner, Jillian J. Kril, Greg T. Sutherland, Lars M. Ittner
JOURNAL OF BIOLOGICAL CHEMISTRY
(2019)
Article
Immunology
Mona O. Mohsen, Monique Vogel, Carsten Riether, Julius Muller, Silvia Salatinos, Nicola Ternette, Ariane C. Gomes, Gustavo Cabral-Miranda, Aadil El-Turabi, Christiane Ruedl, Thomas M. Kundig, Said Dermime, Alexander Knuth, Daniel E. Speiser, Martin F. Bachmann
FRONTIERS IN IMMUNOLOGY
(2019)
Editorial Material
Cell Biology
Philip W. Ingham, Bruno Reversade
CURRENT OPINION IN GENETICS & DEVELOPMENT
(2019)
Article
Medicine, Research & Experimental
Christoph J. Blohmke, Julius Muller, Malick M. Gibani, Hazel Dobinson, Sonu Shrestha, Soumya Perinparajah, Celina Jin, Harri Hughes, Luke Blackwell, Sabina Dongol, Abhilasha Karkey, Fernanda Schreiber, Derek Pickard, Buddha Basnyat, Gordon Dougan, Stephen Baker, Andrew J. Pollard, Thomas C. Darton
EMBO MOLECULAR MEDICINE
(2019)
Article
Immunology
Ariane C. Gomes, Mona O. Mohsen, Julius E. Mueller, Fabiana M. S. Leoratti, Gustavo Cabral-Miranda, Martin F. Bachmann
FRONTIERS IN IMMUNOLOGY
(2019)
Review
Infectious Diseases
Susanne H. Hodgson, Julius Muller, Helen E. Lockstone, Adrian V. S. Hill, Kevin Marsh, Simon J. Draper, Julian C. Knight
Article
Immunology
Paulo Bettencourt, Julius Muller, Annalisa Nicastri, Daire Cantillon, Meera Madhavan, Philip D. Charles, Carine B. Fotso, Rachel Wittenberg, Naomi Bull, Nawamin Pinpathomrat, Simon J. Waddell, Elena Stylianou, Adrian V. S. Hill, Nicola Ternette, Helen McShane
Article
Clinical Neurology
Magdalena Przybyla, Janet van Eersel, Annika van Hummel, Julia van der Hoven, Miheer Sabale, Anne Harasta, Julius Mueller, Mehul Gajwani, Emmanuel Prikas, Thomas Mueller, Claire H. Stevens, John Power, Gary D. Housley, Tim Karl, Michael Kassiou, Yazi D. Ke, Arne Ittner, Lars M. Ittner
Article
Biochemical Research Methods
Annalisa Nicastri, Hanqing Liao, Julius Muller, Anthony W. Purcell, Nicola Ternette
Article
Immunology
Ying Du, Ethan G. Thompson, Julius Muller, Joseph Valvo, Jackie Braun, Smitha Shankar, Robert A. van den Berg, Erik Jongert, Drew Dover, Jerald Sadoff, Jenny Hendriks, Malcolm J. Gardner, W. Ripley Ballou, Jason A. Regules, Robbert van der Most, Alan Aderem, Christian F. Ockenhouse, Adrian Hill, Ulrike Wale-Reece, Daniel E. Zak
FRONTIERS IN IMMUNOLOGY
(2020)
Article
Cell Biology
Josie F. Gibson, Tomasz K. Prajsnar, Christopher J. Hill, Amy K. Tooke, Justyna J. Serba, Rebecca D. Tonge, Simon J. Foster, Andrew J. Grierson, Philip W. Ingham, Stephen A. Renshaw, Simon A. Johnston
Summary: This study reveals the fate and location of Staphylococcus aureus within neutrophils, showing that recruitment of Lc3 and Sqstm1 to phagocytosed bacteria depends on bacterial location. Additionally, it demonstrates the key role of Sqstm1 in controlling cytosolic bacteria.
Article
Developmental Biology
Ilham J. J. Alshami, Yosuke Ono, Ana Correia, Christian Hacker, Anke Lange, Steffen Scholpp, Masashi Kawasaki, Philip W. Ingham, Tetsuhiro Kudoh
DEVELOPMENTAL BIOLOGY
(2020)
Article
Medicine, Research & Experimental
Julius Muller, Rachel Tanner, Magali Matsumiya, Margaret A. Snowden, Bernard Landry, Iman Satti, Stephanie A. Harris, Matthew K. O'Shea, Lisa Stockdale, Leanne Marsay, Agnieszka Chomka, Rachel Harrington-Kandt, Zita-Rose Manjaly Thomas, Vivek Naranbhai, Elena Stylianou, Stanley Kimbung Mbandi, Mark Hatherill, Gregory Hussey, Hassan Mahomed, Michele Tameris, J. Bruce McClain, Thomas G. Evans, Willem A. Hanekom, Thomas J. Scriba, Helen McShane, Helen A. Fletcher