Article
Cell Biology
Yanqing Wu, Juan Dong, Shenglei Feng, Qiang Zhao, Peng Duan, Mengneng Xiong, Yujiao Wen, Chunyu Lv, Xiaoli Wang, Shuiqiao Yuan
Summary: The study reveals that maternal UHRF1 plays a critical role in establishing the correct epigenetic chromatin reprogramming of early embryos, regulating essential genes during MZT, and preserving genome integrity that drives early embryonic development in mice.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Cell Biology
Pooja Bhat, Luis E. Cabrera-Quio, Veronika A. Herzog, Nina Fasching, Andrea Pauli, Stefan L. Ameres
Summary: The maternal-to-zygotic transition (MZT) is a crucial process in embryonic development, involving the activation of zygotic transcription (ZGA) and degradation of maternal transcripts. Using metabolic mRNA sequencing (SLAMseq) in zebrafish embryos, researchers identified spurious transcription of short and intron-poor genes as early as the 2-cell stage. Upon ZGA, most zygotic transcripts originated from maternal-zygotic (MZ) genes and replenished maternal mRNAs at different timescales. This process involved transcript decay features unrelated to major degradation pathways and promoted the synthesis of the core gene expression machinery. SLAMseq provided insights into the regulation and molecular features of MZT in zebrafish embryogenesis.
Article
Agriculture, Dairy & Animal Science
Yu Shi, Mingcheng Cai, Kun Du, Xue Bai, Lipeng Tang, Xianbo Jia, Shiyi Chen, Jie Wang, Songjia Lai
Summary: This study revealed the expression and function of long non-coding RNAs (lncRNAs) during pre-implantation development in rabbits, suggesting their involvement in regulating embryo cleavage and development. The study also found that the maternal and zygotic pathways play a crucial role in the degradation of lncRNAs.
Article
Multidisciplinary Sciences
Chunxia Zhang, Meng Wang, Yisi Li, Yi Zhang
Summary: Transcriptional regulation is important in early mouse embryo development. Using a new technique, the mRNA translation landscape of mouse preimplantation embryos was revealed, showing the critical role of active translation of maternal mRNAs in maternal-to-zygotic transition. The study also identified two maternal factors required for chromatin reprogramming and zygotic genome activation.
Review
Microbiology
Mengwen Zhang, Shu Zheng, Jessie Qiaoyi Liang
Summary: Human endogenous retroviruses (HERVs) originated from ancient retroviral infections of germline cells millions of years ago and have evolved as part of the host genome. HERVs not only retain the capacity as retroelements but also regulate host gene expression. Domesticated copies of HERVs in normal cells play important roles in genome regulation and transcription processes.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Xiaoqing Nie, Qianhua Xu, Chengpeng Xu, Fengling Chen, Qizhi Wang, Dandan Qin, Rui Wang, Zheng Gao, Xukun Lu, Xinai Yang, Yu Wu, Chen Gu, Wei Xie, Lei Li
Summary: This study reveals that TDP-43, a maternal factor, is crucial for mouse embryonic development by regulating RNA Pol II and mediating zygotic genome activation. The authors demonstrate that TDP-43 forms large foci with RNA Pol II in the nucleus and co-occupies the promoters of zygotic genome activation genes. Depletion of maternal TDP-43 leads to defective zygotic genome activation and arrested development at the two-cell stage.
NATURE COMMUNICATIONS
(2023)
Article
Plant Sciences
Jacobo Perez-Pastrana, Pilar S. Testillano, Ivett Barany, Adriana Canto-Flick, Dulce Alvarez-Lopez, Gema Pijeira-Fernandez, Susana A. Aviles-Vinas, Laura Pena-Yam, Liliana Munoz-Ramirez, Sara Nahuat-Dzib, Ignacio Islas-Flores, Nancy Santana-Buzzy
Summary: Zygotic and somatic embryogenesis in plants are finely regulated by a specific group of genes and dynamic levels of plant hormones, with levels of indole-3-acetic acid (IAA) increasing as embryogenesis progresses. The distribution of IAA changes dynamically throughout different stages of embryo development, showing a correlation between IAA levels and cell differentiation in Capsicum chinense species.
JOURNAL OF PLANT PHYSIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Huan Ou-Yang, Shinn-Chih Wu, Li-Ying Sung, Shiao-Hsuan Yang, Shang-Hsun Yang, Kowit-Yu Chong, Chuan-Mu Chen
Summary: The study identified maternal factors that regulate Gzmg promoter activity in mouse embryos from zygotes to the two-cell stage. Different-sized Gzmg promoters were tested, showing that Delta 4-pGzmg promoted the highest expression of the reporter gene. Transcription factor binding sites predicted in the -417 to +28 nt Gzmg promoter region included STAT3 and GABP alpha, with STAT3 being crucial for Gzmg upregulation and early embryonic development.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Reproductive Biology
Mingtian Deng, Baobao Chen, Yingnan Yang, Yongjie Wan, Zifei Liu, Jun Fu, Feng Wang
Summary: This study utilized RNA sequencing to analyze the transcriptional activity of SCNT embryos during ZGA/EGA in goats, mice, humans, and cattle. The research identified differentially expressed genes that failed to be reprogrammed during SCNT embryo development, as well as key players in histone methylation and N6-methyladenosine modifiers that were differentially expressed in SCNT embryos of all species. Furthermore, the study identified critical genes potentially essential for SCNT reprogramming using weighted gene correlation network analysis, providing valuable insights for future studies.
BIOLOGY OF REPRODUCTION
(2021)
Article
Biology
Markus Frederik Schliffka, Anna Francesca Tortorelli, Ozge Ozguc, Ludmilla de Plater, Oliver Polzer, Diane Pelzer, Jean-Leon Maitre
Summary: Studies have shown that actomyosin contractility plays a crucial role in driving mammalian embryo development, and even in cases of failed cell division, morphogenesis and fate specification can still take place in the embryo.
Article
Biotechnology & Applied Microbiology
Matthew T. Chang, Frances Shanahan, Thi Thu Thao Nguyen, Steven T. Staben, Lewis Gazzard, Sayumi Yamazoe, Ingrid E. Wertz, Robert Piskol, Yeqing Angela Yang, Zora Modrusan, Benjamin Haley, Marie Evangelista, Shiva Malek, Scott A. Foster, Xin Ye
Summary: Transcriptional mechanisms of drug response are identified using TraCe-seq, which captures differential clonal responses at the single-cell level. Targeted degradation of EGFR protein is associated with a loss of antigrowth activity, highlighting the essential role of the endoplasmic reticulum protein processing pathway in anti-EGFR therapeutic efficacy. TraCe-seq is established as a useful approach to study how preexisting transcriptional programs impact treatment responses.
NATURE BIOTECHNOLOGY
(2022)
Article
Reproductive Biology
Hengye Zhang, Ke Yan, Lumin Sui, Pan Li, Ya Du, Jiahao Hu, Mengqi Li, Xiaogan Yang, Xingwei Liang
Summary: The study reveals that reducing pyruvate levels in mouse embryos leads to arrest at the 2-cell stage, affecting transcriptional activity and mRNA clearance. These findings highlight the crucial role of energy substrates in maternal mRNA clearance during embryogenesis.
Article
Pharmacology & Pharmacy
Xumiao Li, Wencheng Zhu, Yi Shen, Qinqin Wang, Wenjun Liu, Junfeng Zhang, Huiping Zhang, Jingquan Li, Ziyi Li, Zhen Liu, Chen Li, Hui Wang
Summary: Single-cell or low-input multi-omics techniques have revolutionized the study of pre-implantation embryo development. However, the single-cell or low-input proteomic research in this field is relatively underdeveloped. In this study, a comprehensive solution of ultrasensitive proteome technology (CS-UPT) was developed for single-cell or low-input mouse oocyte/ embryo samples. The deep coverage and high-throughput routes significantly reduced the starting material and provided rich insights into minor zygotic genome activation.
JOURNAL OF PHARMACEUTICAL ANALYSIS
(2023)
Article
Environmental Sciences
Zhi-Ming Ding, Shang-Ke Wang, Shou-Xin Zhang, Yang-Wu Chen, Yong-Sheng Wang, Sheng-Ji Yang, Yun-Xia Cao, Yi-Liang Miao, Li-Jun Huo
Summary: Triclocarban (TCC) is a harmful chemical that is used globally as a broad-spectrum antibacterial agent and is present in high concentrations in the environment. The exposure to TCC can occur through skin contact, diet, and inhalation, leading to its accumulation in the human body. The impact of TCC on human health, specifically its reproductive toxicity, needs to be evaluated due to the lack of clear understanding about its safety profile. This study examined the effect of TCC on the early embryonic development of mice and identified the mechanisms involved.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2023)
Article
Biochemistry & Molecular Biology
Xiaona Zhao, Bo Feng, Qian Wang, Lili Tang, Qian Liu, Wenxiu Ma, Chenghua Li, Changwei Shao
Summary: This study identified the org gene and its associated lncRNA ORG-AS in Chinese tongue sole. The results showed that org is involved in early embryonic development and oogenesis, and is negatively regulated by lncRNA ORG-AS. These findings expand the understanding of the functions of MEGs in bony fish embryonic development and oogenesis, and highlight the importance of lncRNAs in regulating org.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
T. Lohoff, S. Ghazanfar, A. Missarova, N. Koulena, N. Pierson, J. A. Griffiths, E. S. Bardot, C. -H. L. Eng, R. C. V. Tyser, R. Argelaguet, C. Guibentif, S. Srinivas, J. Briscoe, B. D. Simons, A. -K. Hadjantonakis, B. Gottgens, W. Reik, J. Nichols, L. Cai, J. C. Marioni
Summary: Improved integration of spatial and single-cell transcriptomic data through the seqFISH method provides insights into mouse development, revealing cell types across the embryo and uncovering axes of cell differentiation that are not apparent from scRNA-seq data. This approach offers a high-resolution spatial map for studying cell fate decisions in complex tissues and development.
NATURE BIOTECHNOLOGY
(2022)
Article
Cell Biology
Hahn Nahmgoong, Yong Geun Jeon, Eun Seo Park, Yoon Ha Choi, Sang Mun Han, Jeu Park, Yul Ji, Jee Hyung Sohn, Ji Seul Han, Ye Young Kim, Injae Hwang, Yun Kyung Lee, Jin Young Huh, Sung Sik Choe, Tae Jung Oh, Sung Hee Choi, Jong Kyoung Kim, Jae Bum Kim
Summary: This study characterized adipose stem cells (ASCs) in two different types of white adipose tissues (EAT and IAT) and investigated the effects of intrinsic and tissue micro-environmental factors on ASC features. The results showed that ASC subpopulations in EAT and IAT exhibited different molecular features and adipogenic potential. Furthermore, ASCs in these two depots responded differently to obesogenic stimuli, influencing the characteristics of the adipose tissues.
Article
Biotechnology & Applied Microbiology
Emma Dann, Neil C. Henderson, Sarah A. Teichmann, Michael D. Morgan, John C. Marioni
Summary: Milo is a scalable statistical framework that performs differential abundance testing by assigning cells to partially overlapping neighborhoods on a k-nearest neighbor graph. It can identify perturbations obscured by discretizing cells into clusters and outperforms alternative testing strategies. Milo is based on cell-cell similarity structure and may be applicable to various single-cell data beyond scRNA-seq.
NATURE BIOTECHNOLOGY
(2022)
Article
Oncology
Sung-Ill Jang, Jae-Hee Cho, So-Young Kim, In-Young Hong, Joon-Seong Park, Hye-Sun Lee, Goeun Park, Jong-Kyoung Kim, Hyung-Keun Lee, Dong-Ki Lee
Summary: This study identified IL-7R as a potential early diagnostic biomarker for PDAC and demonstrated that the combination of IL-7R and CA19-9 can improve diagnostic performance.
Article
Cell & Tissue Engineering
Ji-Hyun Lee, Somi Kim, Seungmin Han, Jimin Min, Brianna Caldwell, Aileen-Diane Bamford, Andreia Sofia Batista Rocha, JinYoung Park, Sieun Lee, Szu-Hsien Sam Wu, Heetak Lee, Juergen Fink, Sandra Pilat-Carotta, Jihoon Kim, Manon Josserand, Reka Szep-Bakonyi, Yohan An, Young Seok Ju, Anna Philpott, Benjamin D. Simons, Daniel E. Stange, Eunyoung Choi, Bon-Kyoung Koo, Jong Kyoung Kim
Summary: This study identified p57 as a molecular switch for maintaining the reserve stem cell state in chief cells of the stomach. p57 expression is constantly maintained in chief cells during homeostasis but rapidly diminishes after injury, leading to robust proliferation. Overexpression of p57 induces a long-term reserve stem cell state accompanied by altered niche requirements and a mature chief cell phenotype. However, constitutive expression of p57 impairs the injury response of chief cells.
Article
Biochemistry & Molecular Biology
Valentina Carlini, Cristina Policarpi, Jamie A. Hackett
Summary: This study utilized an epigenetic editing strategy and forced Xist activity to investigate the inheritance of chromatin states in mammalian development. It was found that ectopic domains of heterochromatin are systematically erased during the naive pluripotent phases, but acquired chromatin states can be probabilistically inherited upon lineage specification. The study also identified molecular factors that restrict heritable memory and demonstrated the potential for epigenetic inheritance uncoupled from DNA sequence.
Article
Cell Biology
Walfred W. C. Tang, Aracely Castillo-Venzor, Wolfram H. Gruhn, Toshihiro Kobayashi, Christopher A. Penfold, Michael D. Morgan, Dawei Sun, Naoko Irie, M. Azim Surani
Summary: In this study, Tang et al. investigate the epigenetic principles underlying the development of human primordial germ cells (hPGCs). They show that sequential epigenetic remodelling of mesendoderm enhancers is crucial for the segregation of hPGC and mesendodermal cell fates. The researchers identify key transcription factors and enhancers involved in the establishment of a core germline programme in hPGCs. Furthermore, they demonstrate that activation of upstream cis-regulatory elements is sufficient for specifying hPGCs. These findings provide insights into the molecular mechanisms underlying germline-soma segregation and the evolution of mammalian germlines.
NATURE CELL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Dong-il Kwon, Eun Seo Park, Mingyu Kim, Yoon Ha Choi, Myeong-seok Lee, Si-hyung Joo, Yeon-Woo Kang, Minji Lee, Saet-byeol Jo, Seung-Woo Lee, Jong Kyoung Kim, You Jeong Lee
Summary: This study demonstrates that plasma cells in the thymus secrete IgE and other immunoglobulins, and their development is induced by IL-4 and related to mast cell survival. Thymic B cells go through transitional, mature, memory, and plasma cell stages. Thymic plasma cells produce polyclonal antibodies without somatic hypermutation and regulate mast cell homeostasis in the gut and skin, which is linked to the severity of anaphylaxis.
NATURE COMMUNICATIONS
(2022)
Review
Cell Biology
David Pladevall-Morera, Jan J. Zylicz
Summary: Cellular metabolism and epigenetics play crucial roles in early mammalian embryo development, interacting with each other to influence cell fate and the epigenome. Recent studies have revealed the non-canonical functions of metabolism when re-localized to the nucleus, along with the challenges and future prospects in advancing the field of epi-metabolomics.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Jong-Wan Kwon, Sang-Hyuk Seok, Somi Kim, Hyeok-Won An, Anahita Dev Choudhury, Sang-Ho Woo, Jeong-Seop Oh, Jong Kyoung Kim, Dominic C. Voon, Dae-Yong Kim, Jun Won Park
Summary: The study reveals the important role of ST2 and IL-33 in gastric cancer progression, with their expression levels clinically correlated to cancer progression. The IL-33/ST2 axis enhances the self-renewal and survival of gastric cancer stem cells, and cooperates with the canonical Wnt pathway to promote cancer stem cell activity. Inhibiting Bcl-xL can suppress the activity of the IL-33/ST2 axis, offering a novel therapeutic strategy for gastric cancer.
Article
Multidisciplinary Sciences
Wolfram H. Gruhn, Walfred W. C. Tang, Sabine Dietmann, Joao P. Alves-Lopes, Christopher A. Penfold, Frederick C. K. Wong, Navin B. Ramakrishna, M. Azim Surani
Summary: Epigenetic resetting in the mammalian germ line involves acute DNA demethylation, resulting in reduced repressive histone modifications and acquisition of a neutral or paused epigenetic state in hypomethylated human primordial germ cells (hPGCs). Transcriptional repression in hPGCs relies on local maintenance of heterochromatic features and a lack of inductive cues, with a subset of genomic loci requiring specific histone modifications for efficient repression.
Review
Biochemistry & Molecular Biology
Nikolaos Stamidis, Jan Jakub Zylicz
Summary: The failure to repress transcription of repetitive genomic elements can lead to genome instability and human diseases. Multiple parallel mechanisms cooperate to ensure repression and heterochromatinization of these elements, especially during germline development and early embryogenesis. Recent evidence suggests a role of RNA methylation, piRNAs, and other localized satellite RNAs in targeting repressive histone marks and DNA methylation to repetitive elements in mammals.
Article
Biochemistry & Molecular Biology
Arianne C. Richard, Claire Y. Ma, John C. Marioni, Gillian M. Griffiths
Summary: This study investigates the impact of transcriptomic changes on the killing ability of effector cytotoxic T lymphocytes (CTLs). The results show that while transcription is required for the expression of cytokines/chemokines and transcriptional machinery, it is relatively robust to transcription blockade for cytotoxic protein expression and cytolytic activity. Additionally, the study reveals a cell-intrinsic transcriptional requirement for infiltration.
Article
Genetics & Heredity
Emma Dann, Ana-Maria Cujba, Amanda J. Oliver, Kerstin B. Meyer, Sarah A. Teichmann, John C. Marioni
Summary: Joint analysis of diseased tissues and healthy reference data can reveal altered cell states. Using a reference atlas for latent space learning followed by differential analysis against controls improves identification of disease-associated cells, especially with multiple perturbed cell types. Reducing control sample numbers does not increase false discovery rates.
Article
Biochemistry & Molecular Biology
Deivendran Rengaraj, Dong Gon Cha, Hong Jo Lee, Kyung Youn Lee, Yoon Ha Choi, Kyung Min Jung, Young Min Kim, Hee Jung Choi, Hyeon Jeong Choi, Eunhui Yoo, Seung Je Woo, Jin Se Park, Kyung Je Park, Jong Kyoung Kim, Jae Yong Han
Summary: This study used a novel method to trace and isolate chicken germ cells at different stages of development, and revealed the dynamic transcriptional landscape of avian germ cells through single-cell RNA sequencing. The study identified sex-specific developmental stages and trajectories of chicken germ cells, as well as the gradual acquisition of stage-specific transcription factor activities. Additionally, the study discovered evolutionary conserved and species-specific gene expression programs during both chicken and human germ-cell development.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)