Review
Cell Biology
Jing Peng, Wen Jie Zhang, Qi Zhang, Ying Hua Su, Li Ping Tang
Summary: Somatic cell reprogramming is the process of converting differentiated somatic cells into totipotent or pluripotent cells. Recent studies in plants or mammals have revealed the molecular mechanisms by which epigenetic modifications regulate the expression of totipotency or pluripotency genes by altering their chromatin states. This review provides a comprehensive overview of the dynamic changes in epigenetic modifications and chromatin states during somatic cell reprogramming, as well as the potential role of DNA methylation, histone modifications, histone variants, and chromatin remodeling in this process.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Article
Immunology
Ruo-Ran Wang, Xinyuan Qiu, Ran Pan, Hongxing Fu, Ziyin Zhang, Qintao Wang, Haide Chen, Qing-Qian Wu, Xiaowen Pan, Yanping Zhou, Pengfei Shan, Shusen Wang, Guoji Guo, Min Zheng, Lingyun Zhu, Zhuo-Xian Meng
Summary: This study establishes a mouse model to investigate the adaptation process of pancreatic beta cells in response to high-fat diet (HFD) feeding. The findings show that dietary intervention can rescue beta cell dysfunction and reverse the changes in islet chromatin accessibility and transcriptome induced by HFD. The study also identifies CTCF as a key candidate gene involved in preserving beta cell function.
JOURNAL OF EXPERIMENTAL MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Daniel C. Levings, Sarah E. Lacher, Juan Palacios-Moreno, Matthew Slattery
Summary: Oxidative stress has significant effects on gene expression, but minimal impact on chromatin accessibility. The large-scale transcriptional response to excess ROS is primarily constrained by the cell's preexisting chromatin landscape.
FREE RADICAL BIOLOGY AND MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Kee-Pyo Kim, Jinmi Choi, Juyong Yoon, Jan M. Bruder, Borami Shin, Jonghun Kim, Marcos J. Arauzo-Bravo, Dong Han, Guangming Wu, Dong Wook Han, Johnny Kim, Patrick Cramer, Hans R. Schoeler
Summary: A chemical screen targeting major epigenetic pathways can identify permissive epigenetic states that enhance reprogramming competence of transcription factors. In this study, inhibiting specific epigenetic roadblocks simultaneously was found to dramatically improve the reprogramming ability of most OCT factors and enable dismantling species-dependent reprogramming competence of certain transcription factors such as OCT6.
NATURE CHEMICAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Antoine Larrieu, Geraldine Brunoud, Aurore Guerault, Stephanie Laine, Lauriane Hennet, Arnaud Stigliani, Iris Gildea, Jeremy Just, Ludivine Soubigou-Taconnat, Sandrine Balzergue, Brendan Davies, Enrico Scarpella, Yka Helariutta, Francois Parcy, Teva Vernoux
Summary: This study reveals the transcriptional network induced by auxin at the early stage of flower development and suggests that auxin initiates growth through antagonistic regulation of growth-promoting and growth-repressive hormones, quasi-synchronously to floral fate specification. Additionally, two DNA-binding One Zinc Finger (DOF) transcription factors acting in an auxin-dependent network were identified to interface growth and cell fate from the early stages of flower development onward.
Article
Cell Biology
Zhihui Liu, Weiguo Wang, Yuhan Xia, Yuan Gao, Zhisong Wang, Mingyang Li, Giorgio Antonio Presicce, Liyou An, Fuliang Du
Summary: This study reveals the changes in the epigenetic modification pattern of H4K20me3 during fertilization and somatic cell nuclear transfer (NT). The results show that there are differences in the H4K20me3 pattern between fertilized embryos, NT embryos, and parthenogenetic activation (PA) embryos. H4K20me3 is only present in the maternal pronuclei of fertilized embryos. The intensity of H4K20me3 is significantly lower in fertilized embryos compared to NT and PA embryos. Knockdown of Suv4-20h2 improves the development and cloning efficiency of NT embryos by upregulating reprogramming factors and ZGA-related factors.
CELL PROLIFERATION
(2023)
Article
Biotechnology & Applied Microbiology
Sitara Persad, Zi-Ning Choo, Christine Dien, Noor Sohail, Ignas Masilionis, Ronan Chaligne, Tal Nawy, Chrysothemis C. C. Brown, Roshan Sharma, Itsik Pe'er, Manu Setty, Dana Pe'er
Summary: Metacells are identified using an algorithm called SEACells, which overcomes the sparsity and retains heterogeneity of single-cell data. SEACells outperforms existing algorithms in identifying comprehensive, compact, and well-separated metacells in both RNA and ATAC modalities across datasets. This method is particularly well suited for patient cohorts and allows for improved gene-peak associations, ATAC gene scores computation, and inference of critical regulators' activities during differentiation. Our metacells reveal expression dynamics and chromatin landscape reconfiguration during hematopoietic differentiation and identify CD4 T cell differentiation and activation states associated with COVID-19 disease onset and severity.
NATURE BIOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Jing Wang, Cai Zhou, Shuai Gao, Xiuling Song, Xinyan Yang, Jiaqi Fan, Shaofang Ren, Linzi Ma, Jiexiang Zhao, Manman Cui, Ke Song, Mei Wang, Chaohui Li, Yi Zheng, Fang Luo, Kai Miao, Xiaochun Bai, Andrew P. Hutchins, Lin Li, Gang Chang, Xiao-Yang Zhao
Summary: Round spermatid injection (ROSI) technique shows promise for treating infertility in some men. However, the developmental potential of ROSI embryos is compromised and the mechanisms are not fully understood. This study explores the transcriptome, chromatin accessibility, and DNA methylation patterns of ROSI embryos derived from early-stage round spermatids using single-cell multiomics sequencing. It identifies reprogramming defects in ROSI embryos at the pronuclear stages, primarily associated with misexpression of a group of minor zygotic genome activation genes. The study also discovers a small compound, A366, that can improve the developmental potential of ROSI embryos by correcting epigenetic and transcriptomic states.
Article
Cell Biology
Ah Reum Lee, Ji-Hoon Park, Sung Han Shim, Kwonho Hong, Hyeonwoo La, Kyung-Soon Park, Dong Ryul Lee
Summary: The study found that the activity of Rad 51 is lower in SCNT eggs and a significantly lower level of DSBs in SCNT embryos during reprogramming. Supplementation with RS-1 during the activation of SCNT embryos can increase RAD51 expression and DSB foci, thereby improving the efficiency of SCNT reprogramming. Through single-cell RNA-seq analysis, reactivation of genes and involvement of histone demethylase in reducing reprogramming-resistant regions were observed, which may contribute to overcoming developmental block and enhancing cell sources for regenerative medicine.
CELL PROLIFERATION
(2021)
Article
Immunology
Fabio F. Rosa, Cristiana F. Pires, Ilia Kurochkin, Evelyn Halitzki, Tasnim Zahan, Nejc Arh, Olga Zimmermannova, Alexandra G. Ferreira, Hongzhe Li, Stefan Karlsson, Stefan Scheding, Carlos-Filipe Pereira
Summary: Researchers have identified key gene regulatory networks driving the differentiation and reprogramming of human cDC1 cells, improving the efficiency of reprogramming and providing a new platform for generating patient-specific cDC1 cells for cancer immunotherapy vaccination strategies.
SCIENCE IMMUNOLOGY
(2022)
Article
Multidisciplinary Sciences
Marcella Pecora Milazzotto, Michael James Noonan, Marcia de Almeida Monteiro Melo Ferraz
Summary: Metaboloepigenetic regulation in early embryos is species-specific, varies with developmental stage, and can be disrupted by in vitro culture. Metabolic pathways and gene expressions are strongly associated with early embryo DNA methylation and are changed in in vitro culture.
Article
Genetics & Heredity
Per Johnsson, Christoph Ziegenhain, Leonard Hartmanis, Gert-Jan Hendriks, Michael Hagemann-Jensen, Bjorn Reinius, Rickard Sandberg
Summary: This study utilized allele-sensitive single-cell RNA sequencing to investigate the transcriptional dynamics of long noncoding RNAs (lncRNAs). The results showed that lncRNAs have a longer duration between two transcriptional bursts compared to messenger RNAs. The study also observed increased cell-to-cell variability in lncRNA expression, which is attributed to lower burst frequencies producing larger quantities of RNA molecules. Furthermore, the study identified lncRNAs with cell state-specific functions involved in cell cycle progression and apoptosis and demonstrated their regulatory effects on nearby protein-coding genes' transcriptional bursting.
Article
Biology
Joao C. Sabino, Madalena R. de Almeida, Patricia L. Abreu, Ana M. Ferreira, Paulo Caldas, Marco M. Domingues, Nuno C. Santos, Claus M. Azzalin, Ana Rita Grosso, Sergio Fernandes de Almeida
Summary: The activity of TET enzymes promotes the formation of R-loops, revealing new mechanisms of gene expression regulation.
Article
Biochemistry & Molecular Biology
Yuliangzi Sun, Woo Jun Shim, Sophie Shen, Enakshi Sinniah, Duy Pham, Zezhuo Su, Dalia Mizikovsky, Melanie D. White, Joshua W. K. Ho, Quan Nguyen, Mikael Boden, Nathan J. Palpant
Summary: This article introduces a method called TRIAGE-Cluster that utilizes genome-wide epigenetic data to identify genes that delineate cell diversity in scRNA-seq data. By integrating repressive chromatin patterns with weighted density estimation, TRIAGE-Cluster determines cell type clusters in a 2D UMAP space. The article also presents TRIAGE-ParseR, a machine learning method that evaluates gene expression rank lists to define gene groups governing the identity and function of cell types.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Reproductive Biology
Reza Moradi-Hajidavaloo, Farnoosh Jafarpour, Mehdi Hajian, Mohsen Rahimi Andani, Shiva Rouhollahi Varnosfaderani, Mohammad Hossein Nasr-Esfahani
Summary: This study demonstrated that supplementation of IVC medium with 1.5 μM OAC1 can accelerate SCNT reprogramming and improve the quality of derived blastocysts.
Article
Cell Biology
Abdullah Kaya, Sule Dogan, Peter Vargovic, Naseer Ahmad Kutchy, Pablo Ross, Einko Topper, Richard Oko, Frans van der Hoorn, Peter Sutovsky, Erdogan Memili
Summary: This study identified sperm proteins ODF2 and PAWP as biomarkers for assessing semen quality and predicting sire fertility, providing valuable insights for improving livestock reproductive performance in the cattle industry.
CELL AND TISSUE RESEARCH
(2022)
Article
Medicine, Research & Experimental
Nareg H. Roubinian, Sarah E. Reese, Hannah Qiao, Colleen Plimier, Fang Fang, Grier P. Page, Ritchard G. Cable, Brian Custer, Mark T. Gladwin, Ruchika Goel, Bob Harris, Jeanne E. Hendrickson, Tamir Kanias, Steve Kleinman, Alan E. Mast, Steven R. Sloan, Bryan R. Spencer, Steven L. Spitalnik, Michael P. Busch, Eldad A. Hod
Summary: Donor genetic and other factors, including the storage duration of RBC, have an impact on transfusion effectiveness. Addressing these factors can improve patient outcomes through a precision medicine approach.
Article
Computer Science, Artificial Intelligence
Chaitanya Baru, Michael Pozmantier, Ilkay Altintas, Stephen Baek, Jonathan Cohen, Laura Condon, Giulia Fanti, Raul Castro Fernandez, Ethan Jackson, Upmanu Lall, Bennett Landman, Hai Helen Li, Claudia Marin, Beatriz Martinez Lopez, Dimitris Metaxas, Bradley Olsen, Grier Page, Jingbo Shang, Yelda Turkan, Peng Zhang
Summary: This article provides a brief overview of 18 projects funded in Track D-Data and Model Sharing to Enable AI Innovation in the 2020 Cohort of the National Science Foundation's Convergence Accelerator program. These projects aim to deliver tools and technologies to facilitate data and model sharing, thereby driving AI innovation.
Article
Biotechnology & Applied Microbiology
Fang Fang, Kelsey Hazegh, Alan E. Mast, Darrell J. Triulzi, Bryan R. Spencer, Mark T. Gladwin, Michael P. Busch, Tamir Kanias, Grier P. Page
Summary: Through a study on 12,231 blood donors, it was found that males have a higher susceptibility to hemolysis than females. Genetic variants associated with sex-specific hemolysis susceptibility were identified at five loci that impact RBC function and hemolysis. The study suggests that there are genetic regulatory differences between sexes in the susceptibility of RBCs to hemolysis.
Article
Hematology
Hefei Liu, Robert T. Burns, Bryan R. Spencer, Grier P. Page, Alan E. Mast
Summary: This study investigated the factors associated with pica in high-intensity blood donors. The only independent predictor of pica was hematocrit. Although severe iron deficiency was more prevalent in high-intensity donors, pica behaviors were less common compared to less frequent donors.
TRANSFUSION MEDICINE
(2022)
Review
Cell Biology
Zhongde Wang, Robert T. Cormier
Summary: The golden Syrian hamster, with the application of CRISPR/Cas9 genetic engineering technology, can now be gene targeted as readily as mouse models. The phenotypes of gene-targeted knockout hamster cancer models TP53, KCNQ1, and IL2RG are described in this review, showing cancer phenotypes not observed in mouse KOs, such as aggressive acute myelogenous leukemia (AML) in TP53 KO hamsters. The strengths and weaknesses of mouse cancer models and hamster cancer models are discussed, highlighting the potential of genetically engineered hamster cancer models in developing new cancer therapies.
Article
Biology
Ravi Mathur, Fang Fang, Nathan Gaddis, Dana B. Hancock, Michael H. Cho, John E. Hokanson, Laura J. Bierut, Sharon M. Lutz, Kendra Young, Albert Smith, Edwin K. Silverman, Grier P. Page, Eric O. Johnson
Summary: This study developed and validated a protocol called GAWMerge, which combines genotypes from arrays and whole-genome sequencing to increase sample size and enhance discovery for understudied traits and ancestries. The protocol includes phasing, imputation, and filtering, and has been demonstrated to effectively control technology-driven artifacts and recover known disease-associated signals.
COMMUNICATIONS BIOLOGY
(2022)
Review
Agriculture, Dairy & Animal Science
Zulfi Nur Amrina Rosyada, Mokhamad Fakhrul Ulum, Ligaya I. T. A. Tumbelaka, Dedy Duryadi Solihin, Bambang Purwantara, Erdogan Memili
Summary: Heat shock protein 70 (HSP70) plays a crucial role in bull reproduction, particularly in sperm quality, sperm capacitation, sperm-egg recognition, and fertilization. The article highlights the importance of molecular analyses and omics methods in monitoring key aspects of sperm molecular morphology that influence fertilization success.
Review
Andrology
Arabela Guedes de Azevedo Viana, Iara Magalhaes Ribeiro, Renner Philipe Rodrigues Carvalho, Erdogan Memili, Arlindo de Alencar Moura, Mariana Machado-Neves
Summary: This meta-analytical study examines the effects of seminal fluid proteins on bovine fertility-related parameters and confirms that seminal proteins can improve sperm motility, quality, and protection. However, there is diversity in methodological strategies and limited research conducted in vivo.
Article
Hematology
Eric Jay Earley, Shannon Kelly, Fang Fang, Cecilia Salete Alencar, Daniela de Oliveira Werneck Rodrigues, Dahra Teles Soares Cruz, Jonathan M. Flanagan, Russell E. Ware, Xu Zhang, Victor Gordeuk, Mark Gladwin, Yingze Zhang, Mehdi Nouraie, Sergei Nekhai, Ester Sabino, Brian Custer, Carla Dinardo, Grier P. Page
Summary: This study performed a genome-wide association study on 1333 individuals with sickle cell disease (SCD) from Brazil and identified variants associated with early-onset ischaemic stroke. The study also found a shared genetic architecture between SCD individuals and non-SCD individuals younger than 65 years.
BRITISH JOURNAL OF HAEMATOLOGY
(2023)
Article
Public, Environmental & Occupational Health
Emily A. Knapp, Amii M. Kress, Corette B. Parker, Grier P. Page, Kristen McArthur, Kennedy K. Gachigi, Akram N. Alshawabkeh, Judy L. Aschner, Theresa M. Bastain, Carrie V. Breton, Casper G. Bendixsen, Patricia A. Brennan, Nicole R. Bush, Claudia Buss, Carlos A. Camargo, Diane Catellier, Jose F. Cordero, Lisa Croen, Dana Dabelea, Sean Deoni, Viren DSa, Cristiane S. Duarte, Anne L. Dunlop, Amy J. Elliott, Shohreh F. Farzan, Assiamira Ferrara, Jody M. Ganiban, James E. Gern, Angelo P. Giardino, Nissa R. Towe-Goodman, Diane R. Gold, Rima Habre, Ghassan B. Hamra, Tina Hartert, Julie B. Herbstman, Irva Hertz-Picciotto, Alison E. Hipwell, Margaret R. Karagas, Catherine J. Karr, Kate Keenan, Jean M. Kerver, Daphne Koinis-Mitchell, Bryan Lau, Barry M. Lester, Leslie D. Leve, Bennett Leventhal, Kaja Z. LeWinn, Johnnye Lewis, Augusto A. Litonjua, Kristen Lyall, Juliette C. Madan, Cindy T. McEvoy, Monica McGrath, John D. Meeker, Rachel L. Miller, Rachel Morello-Frosch, Jenae M. Neiderhiser, Thomas G. O'Connor, Emily Oken, Michael O'Shea, Nigel Paneth, Christina A. Porucznik, Sheela Sathyanarayana, Susan L. Schantz, Eliot R. Spindel, Joseph B. Stanford, Annemarie Stroustrup, Susan L. Teitelbaum, Leonardo Trasande, Heather Volk, Pathik D. Wadhwa, Scott T. Weiss, Tracey J. Woodruff, Rosalind J. Wright, Qi Zhao, Lisa P. Jacobson
Summary: The ECHO-Wide Cohort Study (EWC) is a collaborative research project funded by the National Institutes of Health (NIH) in 2016 to improve children's health in the United States. It includes 69 cohorts in 31 consortia and collects data using a standardized protocol. As of March 4, 2022, the EWC has gathered data from 60,553 children and obtained consent from 29,622 children for additional data and biospecimen collection. The study focuses on various health outcomes in children, including prenatal, perinatal, and postnatal outcomes, neurodevelopment, obesity, airways, and positive health.
AMERICAN JOURNAL OF EPIDEMIOLOGY
(2023)
Article
Obstetrics & Gynecology
Steven J. Ondersma, Amii M. Kress, Annemarie Stroustrup, Robert D. Annett, Lyndsay A. Avalos, Maria Talavera-Barber, Patricia A. Brennan, Carlos A. Camargo, Elisabeth Conradt, Anne L. Dunlop, Amy J. Elliott, Monique M. Hedderson, Ximin Li, Monica McGrath, Ruby H. N. Nguyen, Grier P. Page, Sheela Sathyanarayana, Barry Lester
JOURNAL OF PERINATOLOGY
(2023)
Article
Obstetrics & Gynecology
Michael W. Varner, Elizabeth A. Thom, C. Michael Cotten, Susan R. Hintz, Grier P. Page, Dwight J. Rouse, Brian M. Mercer, Maged M. Costantine, Yoram Sorokin, John M. Thorp Jr, Susan M. Ramin, Marshall W. Carpenter, Mary J. O'Sullivan, Alan M. Peaceman, George R. Saade, Donald J. Dudley, Steve N. Caritis
Summary: This study found genetic variants associated with adverse neurodevelopmental outcomes in extremely low birth weight infants, including a variant in the SERPINE1 gene that is associated with cerebral palsy or death.
AMERICAN JOURNAL OF PERINATOLOGY
(2023)
Article
Oncology
Fang Fang, Linran Zhou, Wei Perng, Carmen J. Marsit, Anna K. Knight, Andres Cardenas, Max T. Aung, Marie-France Hivert, Izzuddin M. Aris, Jaclyn M. Goodrich, Alicia K. Smith, Abigail Gaylord, Rebecca C. Fry, Emily Oken, George O'Connor, Douglas M. Ruden, Leonardo Trasande, Julie B. Herbstman, Carlos A. Camargo Jr, Nicole R. Bush, Anne L. Dunlop, Dana M. Dabelea, Margaret R. Karagas, Carrie V. Breton, Carole Ober, Todd M. Everson, Grier P. Page, Christine Ladd-Acosta
Summary: This study assessed the accuracy of pediatric epigenetic clocks in determining gestational and chronological age. The findings showed that different clocks performed differently in different tissue types, providing valuable guidance for future research and development of epigenetic clocks in pediatric samples.
CLINICAL EPIGENETICS
(2023)
Article
Agriculture, Dairy & Animal Science
Muhammet Rasit Ugur, Denise D. Guerreiro, Arlindo A. Moura, Erdogan Memili
Summary: Prediction of bull fertility is crucial for cattle production. Traditional methods are insufficient, thus a comprehensive approach is needed to understand the uncertainty in male subfertility. This review focuses on the molecular and functional signatures of bull sperm associated with fertility.
ANIMAL REPRODUCTION
(2022)