Article
Plant Sciences
Rachel Schwope, Gabriele Magris, Mara Miculan, Eleonora Paparelli, Mirko Celii, Aldo Tocci, Fabio Marroni, Alice Fornasiero, Emanuele De Paoli, Michele Morgante
Summary: Research on Vitis vinifera using various sequencing techniques identified a large number of open chromatin regions which may serve as potential cis-regulatory regions associated with gene expression.
Article
Biochemistry & Molecular Biology
Yuqi Fang, Zhicheng Ji, Weiqiang Zhou, Jordi Abante, Michael A. Koldobskiy, Hongkai Ji, Andrew P. Feinberg
Summary: Epigenetic information, inherited through DNA methylation, plays a crucial role in defining tissue identity. This study reveals that methylation entropy, which represents stochastic changes in DNA methylation, is associated with specific DNA binding motifs, regulatory DNA, and CpG density. Additionally, the contribution of methylation entropy to developmental patterns is comparable to that of methylation mean, and it is associated with conserved sequence and chromatin features. Furthermore, methylation entropy is directly related to gene expression variability in development, suggesting its involvement in developmental plasticity.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Oncology
Nikhil Baban Ghate, Sangnam Kim, Erin Spiller, Sungmin Kim, Yonghwan Shin, Suhn K. Rhie, Goar Smbatyan, Heinz-Josef Lenz, Shannon M. Mumenthaler, Woojin An
Summary: This study reveals the role of VprBP in colon cancer, showing that it promotes proliferation of colon cancer cells by phosphorylating H2A and repressing growth regulatory genes. Inhibiting VprBP can impair colon tumor growth by blocking H2A phosphorylation and reactivating a transcriptional program resembling that of normal cells.
MOLECULAR ONCOLOGY
(2021)
Article
Multidisciplinary Sciences
Evan W. Weber, Kevin R. Parker, Elena Sotillo, Rachel C. Lynn, Hima Anbunathan, John Lattin, Zinaida Good, Julia A. Belk, Bence Daniel, Dorota Klysz, Meena Malipatlolla, Peng Xu, Malek Bashti, Sabine Heitzeneder, Louai Labanieh, Panayiotis Vandris, Robbie G. Majzner, Yanyan Qi, Katalin Sandor, Ling-Chun Chen, Snehit Prabhu, Andrew J. Gentles, Thomas J. Wandless, Ansuman T. Satpathy, Howard Y. Chang, Crystal L. Mackall
Summary: This study showed that transient cessation of chimeric antigen receptor (CAR) signaling can enhance the efficacy of CAR-T cells, reactivating their anti-tumor functions, and challenging the notion that exhaustion is an epigenetically fixed state.
Article
Cell Biology
Hee-Sook Kim
Summary: In Trypanosoma brucei, genes are arranged in polycistronic transcription units, with transcription termination sites being crucial for controlling mRNA production. Three chromatin factors, H3v, H4v, and base J, contribute to the regulation of transcription termination sites in a coordinated manner, with H4v playing a major role in this process.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biophysics
Adrienne K. Scott, Eduard Casas, Stephanie E. Schneider, Alison R. Swearingen, Courtney L. Van Den Elzen, Benjamin Seelbinder, Jeanne E. Barthold, Jennifer F. Kugel, Josh Lewis Stern, Kyla J. Foster, Nancy C. Emery, Justin Brumbaugh, Corey P. Neu
Summary: Understanding mechanical memory of cells is crucial for designing biomaterials and therapies in medicine. The limit of mechanical priming for cartilage regeneration procedures and the influence of physical environments on cell potential remain poorly understood. This study reveals a threshold to mechanical priming and identifies the correlation between chromatin architecture and the phenotype of chondrocytes.
BIOPHYSICAL JOURNAL
(2023)
Review
Biochemistry & Molecular Biology
Nguyen Xuan Thang, Seonho Yoo, Hyeonwoo La, Hyeonji Lee, Chanhyeok Park, Kyoung Sik Park, Kwonho Hong
Summary: Luminal breast cancer is characterized by high steroid hormone receptor activity and aberrant gene expression profiles. Recent studies have shown that epigenetic factors play critical roles in tumorigenesis and drug resistance of luminal breast cancer. Epigenetic modulators are potential therapeutic agents for breast cancer, inhibiting tumor cell invasiveness and endocrine therapy resistance.
Article
Genetics & Heredity
Qiao Liu, Kui Hua, Xuegong Zhang, Wing Hung Wong, Rui Jiang
Summary: DeepCAGE is a deep learning framework that accurately predicts chromatin accessible regions in a variety of cell types, and exhibits superior performance in the classification and regression of chromatin accessibility signals.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Article
Biology
Teresa Romeo Luperchio, Leandros Boukas, Li Zhang, Genay Pilarowski, Jenny Jiang, Allison Kalinousky, Kasper D. Hansen, Hans T. Bjornsson
Summary: The study reveals shared epigenetic alterations in different MDEM diseases, primarily localized in gene promoters, which may disrupt gene expression and contribute to specific phenotypes, such as IgA deficiency. Joint study of MDEMs offers a systematic approach for mapping functional epigenetic variation in mammals.
Article
Biochemistry & Molecular Biology
Hiroto S. Fukushima, Hiroyuki Takeda, Ryohei Nakamura
Summary: Epigenetic modifications undergo erasure and reestablishment after fertilization, with some histone modifications escaping reprogramming. In nonmammalian vertebrates, most histone modifications are thought to be intensively erased and reestablished. However, the histone modifications that escape reprogramming in nonmammalian vertebrates and their potential functional roles remain unknown.
Article
Biology
Andrea Cipriano, Martina Macino, Giulia Buonaiuto, Tiziana Santini, Beatrice Biferali, Giovanna Peruzzi, Alessio Colantoni, Chiara Mozzetta, Monica Ballarino
Summary: This study identified a novel lncRNA, Lnc-Rewind, which regulates MuSC proliferation and expansion by influencing the expression of skeletal muscle genes and components of the WNT signaling pathway in mouse. The interaction of Lnc-Rewind with the G9a histone lysine methyltransferase mediates the repression of the Wnt7b gene, providing insights into the epigenetic regulation of adult muscle stem cells fate by lncRNAs.
Article
Cell Biology
Alexandre Segelle, Yaiza Nunez-Alvarez, Andrew J. Oldfield, Kimberly M. Webb, Philipp Voigt, Reini F. Luco
Summary: Histone modifications play a role in final splicing decisions. In this study, researchers used CRISPR epigenome editing tools and found that a single change in H3K27ac or H3K27me3 levels at the alternatively spliced exon is sufficient to induce splicing changes associated with epithelial-to-mesenchymal transition (EMT). These findings suggest that the dynamic nature of chromatin and its histone marks can rapidly and reversibly regulate alternative splicing in response to cell-extrinsic cues like EMT induction.
Article
Plant Sciences
Konstantin O. Kutashev, Michal Franek, Klev Diamanti, Jan Komorowski, Marie Olsinova, Martina Dvorackova
Summary: Arabidopsis thaliana's 45S ribosomal genes are located on the termini of chromosomes 2 and 4, encoding rRNA. Not all intranucleolar rDNA is active, with some forming condensed foci marked with repressive histone marks. The condensed foci relate to rDNA folding and contain typical modifications of inactive rDNA.
Article
Biochemistry & Molecular Biology
Roser Zaurin, Roberto Ferrari, Ana Silvina Nacht, Jose Carbonell, Francois Le Dily, Jofre Font-Mateu, Lara Isabel de Llobet Cucalon, Enrique Vidal, Antonios Lioutas, Miguel Beato, Guillermo P. Vicent
Summary: In T47D breast cancer cells, 50 pM progestin can activate cell cycle entry and the progesterone gene expression program. Highly accessible sites (HAs) are enriched in RAD21 and CTCF, but PR binding is the driving force for the most robust interactions with hormone-regulated genes, indicating their potential usefulness as targets for therapeutic intervention.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Tongwen Han, Fang Wang, Qingxin Song, Wenxue Ye, Tieshan Liu, Liming Wang, Z. Jeffrey Chen
Summary: Inbreeding depression in maize is associated with epigenetic modifications including hypermethylation and changes in chromatin accessibility, leading to down-regulation of hundreds of genes involved in plant growth and development. Random mating can reverse these epigenetic changes and restore growth vigor.
Article
Genetics & Heredity
Tasnim H. Beacon, Wayne Xu, James R. Davie
Review
Biotechnology & Applied Microbiology
Tasnim H. Beacon, Genevieve P. Delcuve, James R. Davie
Summary: ACE2 is the receptor for three coronaviruses and involved in regulating the renin-angiotensin system and blood pressure, as well as various signaling pathways. Its expression is regulated by two promoters, with tissue-specific differences, and is highest in the small intestine, kidney, and heart.
Review
Biochemistry & Molecular Biology
Genevieve P. Delcuve, Ted M. Lakowski, Ruey-Chyi Su, Tasnim H. Beacon, James R. Davie
Review
Biotechnology & Applied Microbiology
Tasnim H. Beacon, James R. Davie
Summary: The chicken model organism has made significant advancements in various fields and has aided in the study of human diseases. Recent advances in high-throughput sequencing and bioinformatic tools have enabled researchers to better understand the chicken genome. Chickens play a crucial role in basic and pre-clinical research.
Review
Biotechnology & Applied Microbiology
Wenxia Luo, Olufola O. Ige, Tasnim H. Beacon, Ruey-Chyi Su, Shujun Huang, James R. Davie, Ted M. Lakowski
Summary: This article discusses antiviral treatments for SARS-CoV2 and treatment strategies for the CSS. It compares antivirals with in vitro activity against SARS-CoV2, SARS-CoV1 and MERS-CoV, and discusses medications that reduce the effects or expression of cytokines involved in the CSS. It also explores how some medications influence enzymes involved in epigenetic processes.
Editorial Material
Biotechnology & Applied Microbiology
Tasnim H. Beacon, James R. Davie, Michael J. Hendzel
Review
Oncology
Tasnim H. Beacon, Genevieve P. Delcuve, Camila Lopez, Gino Nardocci, Igor Kovalchuk, Andre J. van Wijnen, James R. Davie
Summary: The broad epigenetic domain, marked by H3K4me3, is associated with cell identity, essential cell functions, and the metastatic potential of cancer cells. It interacts with various histone modifications and forms a hub of interactions involving transcription factors, enhancers, and super-enhancers. This dynamic chromatin structure supports frequent transcription bursts and may act as a transcription factory.
CLINICAL EPIGENETICS
(2021)
Review
Cell Biology
Tasnim H. Beacon, James R. Davie
Summary: The chicken erythrocyte model system is valuable for studying chromatin structure and function, with unique features allowing the separation of transcriptionally active chromatin and silenced chromatin. Recent studies have mapped transcriptionally active chromosomal domains in the chicken erythrocyte genome and reported detailed landscapes of histone modifications in relation to chromatin structural features.
Article
Genetics & Heredity
Kiran L. Sharma, Shuo Jia, Tasnim H. Beacon, Ifeoluwa Adewumi, Camila Lopez, Pingzhao Hu, Wayne Xu, James R. Davie
Summary: Activation of the RAS-MAPK pathway in serum-starved human cells drives cells towards proliferation by initiating a transcriptional program. The kinase MSK phosphorylates histone H3 at specific sites to initiate a series of chromatin remodeling events and transcription initiation. Transcriptome analysis of cells stimulated with EGF or TPA revealed that MSK modulates the induction levels of immediate-early genes, with some genes being independent of MSK activity. Utilizing inhibitors H89 and Rp-cAMPS can impact the induction levels of these genes.
Article
Biochemistry & Molecular Biology
Zahra Sepehri, Archana Banerjee, Frederick S. Vizeacoumar, Andrew Freywald, Franco J. Vizeacoumar, Vernon W. Dolinsky, James R. Davie
Summary: HNF1A-AS1 is a long non-coding RNA expressed in multiple types of cancer and associated with poor clinical prognosis and oncogenic properties. This study reveals the epigenetic features of HNF1A gene locus in colorectal cancer cells and suggests that HNF1A-AS1 may contribute to oncogenic properties by interacting with specific proteins and forming RNA-DNA triplexes.
Article
Genetics & Heredity
Camila Lopez, Mohammad T. T. Barnon, Tasnim H. H. Beacon, Gino Nardocci, James R. R. Davie
Summary: Epigenetic processes are altered in cancer cells, with specific genes showing broad histone modifications associated with breast cancer subtypes. These genes play critical roles in breast cancer and have been targeted in therapeutic treatments.
Article
Endocrinology & Metabolism
Prasoon Agarwal, Brandy A. Wicklow, Allison B. Dart, Nikho A. Hizon, Elizabeth A. C. Sellers, Jonathan M. McGavock, Charlotte P. J. Talbot, Mario A. Fonseca, Wayne Xu, James R. Davie, Meaghan J. Jones, Animesh Acharjee, Vernon W. Dolinsky
Summary: We identified DNA methylation changes and serum metabolites associated with T2D in adolescents, suggesting their potential significance in gene expression and metabolism control.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Article
Cell Biology
Prerna Sharma, Hedieh Sattarifard, Narges Fatemiyan, Ted M. Lakowski, James R. Davie
Summary: This study investigated the broad distribution of the H3K79me2 associated with cancer, highlighting the importance of this binding feature in the diagnosis and treatment of leukemia.
Review
Biochemistry & Molecular Biology
Hedieh Sattarifard, Akram Safaei, Enzhe Khazeeva, Mojgan Rastegar, James R. Davie
Summary: The mitogen- and stress-activated protein kinases (MSK) are epigenetic modifiers that regulate gene expression in normal and disease cell states. MSK1/2 phosphorylate histone H3 at multiple sites, resulting in chromatin remodeling and gene expression induction. They can stimulate genes involved in cell proliferation, inflammation, innate immunity, neuronal function, and neoplastic transformation. Abrogation of the MSK-involved signaling pathway is a mechanism used by pathogenic bacteria to subdue the host's innate immunity. MSK overexpression can either promote or hinder metastasis depending on the type of cancer and genes involved.
BIOCHEMISTRY AND CELL BIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Narges Fatemiyan, James R. Davie
Summary: H4K20me1 is a modification that is broadly distributed along genes and is associated with expressed and repressed genes. In contrast, H3K4me3 is a modification that is localized to the 5' end of most expressed genes in vertebrate cells. This study found that H4K20me1 is associated with expressed genes in estrogen receptor-positive breast cancer MCF7 cells and erythroleukemic K562 cells. The broad H4K20me1 domain marks the gene bodies of expressed genes, but not the promoter or enhancer regions. There is little overlap between the genes marked with H4K20me1 and those marked with H3K4me3. The distribution of H4K20me1 and H3K79me2 along expressed gene bodies is similar, suggesting a relationship between the enzymes involved in these histone modifications.