Article
Cell & Tissue Engineering
Hanwen Yu, Manqi Chen, Yuanlang Hu, Songbang Ou, Xiu Yu, Shiqi Liang, Niannian Li, Mingzhu Yang, Xuhui Kong, Chuanbo Sun, Shiqi Jia, Qingxue Zhang, Lin Liu, Laurence D. Hurst, Ruiqi Li, Wenjun Wang, Jichang Wang
Summary: Reprogramming of H3K9me3-dependent heterochromatin plays an important role in early human development, affecting the interaction between specific promoters and enhancers, regulating zygotic genome activation and transcription of inner cell mass-specific genes.
Article
Biochemistry & Molecular Biology
Sebastian Canovas, Elena Ivanova, Meriem Hamdi, Fernando Perez-Sanz, Dimitrios Rizos, Gavin Kelsey, Pilar Coy
Summary: The study found that in vitro culture affects DNA methylation, and the sex-specific methylation differences in blastocysts vary in embryos from different sources. Methylation differences were more frequent in the first intron than in CpGi in promoters, and sex produced a stronger bias in the results than embryo origin.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Ji-Yun Shang, Xue-Wei Cai, Yin-Na Su, Zhao-Chen Zhang, Xin Wang, Nan Zhao, Xin-Jian He
Summary: This study reveals a previously unknown mechanism for the regulation of DNA methylation, showing that ATX1-5 proteins play a crucial role in plant development, survival, and the regulation of DNA methylation. The redundant ATX paralogues promote the expression and H3K4me3 levels of both RNA-directed DNA methylation genes and active DNA demethylation genes to regulate DNA methylation.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Pan Liu, Wen-Feng Nie, Xiansong Xiong, Yuhua Wang, Yuwei Jiang, Pei Huang, Xueqiang Lin, Guochen Qin, Huan Huang, Qingfeng Niu, Jiamu Du, Zhaobo Lang, Rosa Lozano-Duran, Jian-Kang Zhu
Summary: A protein complex containing ROS1 in Arabidopsis has been discovered, which regulates ROS1 gene expression and targets the ROS1 protein to specific genomic regions. This complex plays a crucial role in active DNA demethylation at several endogenous loci in Arabidopsis.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2021)
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
Biology
Diljeet Gill, Aled Parry, Fatima Santos, Hanneke Okkenhaug, Christopher D. Todd, Irene Hernando-Herraez, Thomas M. Stubbs, Ines Milagre, Wolf Reik
Summary: Ageing is a gradual decline in organismal fitness that is associated with reduced cellular function and altered gene expression. Recent research has shown that the epigenome can be rejuvenated during somatic cell reprogramming, suggesting that full reprogramming may not be necessary to reverse ageing. In this study, the researchers developed a method called maturation phase transient reprogramming (MPTR), which selectively expresses reprogramming factors until a rejuvenation point and then withdraws them. They found that this method rejuvenated multiple cellular attributes, including the transcriptome and epigenome, to a larger extent than previous protocols. Overall, this work demonstrates the possibility of separating rejuvenation from complete pluripotency reprogramming and may facilitate the discovery of anti-ageing genes and therapies.
Review
Genetics & Heredity
Dongdong Lu, Jixian Zhai, Mengli Xi
Summary: The endosperm is a crucial storage tissue in plant seeds, providing nutrients for embryos or seedlings during seed development and germination. Although genetic information in the endosperm cannot be directly passed on, its inherited epigenetic marks have an impact on gene expression and subsequently influence embryo and seed growth. Understanding the effects of endosperm DNA methylation on crop yield and traits is highly significant.
FRONTIERS IN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Octavio Morante-Palacios, Gerard Godoy-Tena, Josep Calafell-Segura, Laura Ciudad, Eva M. Martinez-Caceres, Jose Luis Sardina, Esteban Ballestar
Summary: This study investigates the epigenomic and transcriptomic reprogramming induced by vitamin C in monocyte-derived dendritic cell (DC) differentiation and maturation. Vitamin C triggers extensive demethylation and upregulation of antigen-presentation and immune response-related genes during DC maturation. It also enhances TNF beta production in DCs and improves their ability to stimulate antigen-specific T cells.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Adda-Lee Graham-Paquin, Deepak Saini, Jacinthe Sirois, Ishtiaque Hossain, Megan S. Katz, Qinwei Kim-Wee Zhuang, Sin Young Kwon, Yojiro Yamanaka, Guillaume Bourque, Maxime Bouchard, William A. Pastor
Summary: Zmym2(-/-) mice exhibit embryonic lethality and fail to undergo proper DNA methylation, resulting in upregulation of germline genes and abnormal expression of transposon-gene fusion transcripts. It suggests that ZMYM2 plays a crucial role in early embryonic development and DNA methylation patterning.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Plant Sciences
Lucija Markulin, Andreja Skiljaica, Mirta Tokic, Mateja Jagic, Tamara Vuk, Natasa Bauer, Dunja Leljak Levanic
Summary: The article discusses the importance of DNA methylation during plant embryogenesis, with a focus on the regulatory role of RNA-directed DNA methylation (RdDM) and its involvement in both zygotic and somatic embryogenesis. It highlights the mechanism of RdDM in silencing transposons and establishing genome stability in developing embryos, as well as its potential global mechanism of transcription control during developmental transitions.
FRONTIERS IN PLANT SCIENCE
(2021)
Review
Biochemistry & Molecular Biology
Marcelo T. Moura, Lais B. Latorraca, Fabiola E. Paula-Lopes
Summary: Mammals have developed mechanisms to cope with environmental stressors throughout their lifespan, including the autophagy pathway, which helps repair damage and reallocates resources for long-term survival. Autophagy plays a key role in mammalian gametogenesis, fertilization, and preimplantation embryonic development, affecting physiological processes and responses to stressors.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Xiao Tang, Yonglei Zhang, Hong-Mei Yuan, Jinling Zhai, Xi Huang
Summary: This study found that cold treatment induces global genomic DNA demethylation and alters the sequence contexts of methylated cytosines in Hevea brasiliensis. DNA demethylation in the upstream region of genes correlates with higher gene expression, whereas demethylation in the gene body has less association.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Veterinary Sciences
Lijing Shi, Yanhui Zhai, Yuanshen Zhao, Xiangjie Kong, Daoyu Zhang, Hao Yu, Ziyi Li
Summary: The effects of ELF4 on porcine embryonic development are not well understood, but knocking down ELF4 was shown to decrease the developmental competency and blastocyst quality of embryos while inducing DNA damage at the 4-cell stage. ELF4 affects pig embryo development by maintaining genome integrity and regulating epigenetic modifications, as well as activating Zygotic gene activation-related genes.
FRONTIERS IN VETERINARY SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Rebecca Shepherd, Bowon Kim, Richard Saffery, Boris Novakovic
Summary: This study investigates the effects of triiodothyronine (T3) on the transcriptome and methylome of human monocytes in vitro. The results indicate that T3 induces limited transcriptional and DNA methylation remodeling in genes enriched in metabolism and immune processes, as well as alters the normal LPS response.
Article
Multidisciplinary Sciences
Julio C. Flores, Simone Sidoli, Meelad M. Dawlaty
Summary: Tet2 is a member of the Ten-eleven translocation (Tet1/2/3) family of enzymes and plays a role in DNA demethylation and gene regulation in embryonic stem cells. Its catalytic and noncatalytic functions regulate DNA demethylation and Sin3a recruitment at active enhancers in ESCs.
Article
Oncology
Sandra Cristea, Garry L. Coles, Daniel Hornburg, Maya Gershkovitz, Julia Arand, Siqi Cao, Triparna Sen, Stuart C. Williamson, Jun W. Kim, Alexandros P. Drainas, Andrew He, Laurent Le Cam, Lauren Averett Byers, Michael P. Snyder, Kevin Contrepois, Julien Sage
Article
Multidisciplinary Sciences
Rajini Srinivasan, Nataliya Nady, Neha Arora, Laura J. Hsieh, Tomek Swigut, Geeta J. Narlikar, Mark Wossidlo, Joanna Wysocka
Article
Oncology
Garry L. Coles, Sandra Cristea, James T. Webber, Rebecca S. Levin, Steven M. Moss, Andy He, Jaya Sangodkar, Yeonjoo C. Hwang, Julia Arand, Alexandros P. Drainas, Nancie A. Mooney, Janos Demeter, Jessica N. Spradlin, Brandon Mauch, Vicky Le, Yan Ting Shue, Julie H. Ko, Myung Chang Lee, Christina Kong, Daniel K. Nomura, Michael Ohlmeyer, Danielle L. Swaney, Nevan J. Krogan, Peter K. Jackson, Goutham Narla, John D. Gordan, Kevan M. Shokat, Julien Sage
Article
Biochemistry & Molecular Biology
Mirjam A. Beck, Heinz Fischer, Lisa M. Grabner, Tamara Groffics, Mircea Winter, Simone Tangermann, Tina Meischel, Barbara Zaussinger-Haas, Patrick Wagner, Carina Fischer, Christina Folie, Julia Arand, Christian Schoefer, Bernard Ramsahoye, Sabine Lagger, Georg Machat, Gregor Eisenwort, Stephanie Schneider, Alexandra Podhornik, Michael Kothmayer, Ursula Reichart, Martin Gloesmann, Ido Tamir, Michael Mildner, Raheleh Sheibani-Tezerji, Lukas Kenner, Peter Petzelbauer, Gerda Egger, Maria Sibilia, Andrea Ablasser, Christian Seiser
Summary: DNA methylation is crucial in biological processes and the absence of DNMT1 disrupts epidermal structure and homeostasis, triggering a massive innate immune response. DNA hypomethylation in keratinocytes leads to transposon derepression, causing inflammation.
Article
Biochemistry & Molecular Biology
Julia Arand, H. Rosaria Chiang, David Martin, Michael P. Snyder, Julien Sage, Renee A. Reijo Pera, Mark Wossidlo
Summary: Tet enzymes play crucial roles in mouse embryonic development, with Tet2 deficiency showing the most severe phenotype. They function in the consecutive oxidation of 5-methylcytosine to 5-carboxylcytosine, necessary for embryonic genome activation and expression of transposable elements.
Article
Genetics & Heredity
Alex Doan, Julia Arand, Diana Gong, Alexandros P. Drainas, Yan Ting Shue, Myung Chang Lee, Shuyuan Zhang, David M. Walter, Andrea C. Chaikovsky, David M. Feldser, Hannes Vogel, Lukas E. Dow, Jan M. Skotheim, Julien Sage
Summary: The RB tumor suppressor is inactivated in various human tumors promoting tumorigenesis. A new mouse model was used to study the consequences of RB depletion and re-activation, showing that continuous RB loss is required for maintaining tumor phenotypes and re-expressing RB leads to cell cycle arrest in cancer cells.
Review
Obstetrics & Gynecology
Fang Fang, Phillip J. Iaquinta, Ninuo Xia, Lei Liu, Lei Diao, Renee A. Reijo Pera
Summary: This article discusses the important role of transcription factors in reproductive development, focusing specifically on the transcriptional mechanisms of human reproductive development. By studying the transcriptional network components of human germ cells, deeper insights into human infertility and reproductive disorders can be gained, potentially contributing to the development of novel treatments for infertility.
HUMAN REPRODUCTION UPDATE
(2022)
Article
Cell Biology
Shuyuan Zhang, Evgeny Zatulovskiy, Julia Arand, Julien Sage, Jan M. M. Skotheim
Summary: Every type of cell in an animal maintains a specific size, and the RB-dilution mechanism plays a role in controlling cell size by linking cell growth to the G1/S transition, as demonstrated in the mouse liver.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biology
Kristeli Eleftheriou, Antonia Peter, Ivanna Fedorenko, Katy Schmidt, Mark Wossidlo, Julia Arand
Summary: A well-organized program of oocyte growth and differentiation leads to the development of a mature oocyte. The study found that in mice, germinal vesicle oocytes undergo chromatin remodeling and nuclear rearrangements during the transition from a non-surrounded nucleolus chromatin state to a surrounded nucleolus chromatin state. This transition is accompanied by changes in DNA methylation and Tet enzyme-catalyzed DNA modifications. The study suggests that a successful transition from NSN to SN state is crucial for the establishment of a developmentally competent oocyte.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biochemical Research Methods
Charalampos Kyriakopoulos, Karl Nordstroem, Paula Linh Kramer, Judith Yumiko Gottfreund, Abdulrahman Salhab, Julia Arand, Fabian Mueller, Ferdinand von Meyenn, Gabriella Ficz, Wolf Reik, Verena Wolf, Joern Walter, Pascal Giehr
Summary: GwEEP is a versatile approach that uses genome-wide hairpin datasets to infer dynamic efficiencies of DNA modifying enzymes, accurately predicting epigenetic changes in the genome.
CELL REPORTS METHODS
(2022)