Review
Biochemistry & Molecular Biology
Dongwei Li, Xiaodong Shu, Ping Zhu, Duanqing Pei
Summary: Recent research has shown that chromatin dynamics are closely linked to cell fate control, with a binary off/on switch occurring during iPSC reprogramming. This implies that similar mechanisms may also be present in normal development, suggesting potential for further approaches to directing cell fate changes.
Article
Genetics & Heredity
Tsunetoshi Nakatani, Jiangwei Lin, Fei Ji, Andreas Ettinger, Julien Pontabry, Mikiko Tokoro, Luis Altamirano-Pacheco, Jonathan Fiorentino, Elmir Mahammadov, Yu Hatano, Capucine Van Rechem, Damayanti Chakraborty, Elias R. Ruiz-Morales, Paola Y. Arguello Pascualli, Antonio Scialdone, Kazuo Yamagata, Johnathan R. Whetstine, Ruslan Sadreyev, Maria-Elena Torres-Padilla
Summary: Totipotent cells in early mouse embryos and 2-cell-like cells have slow DNA replication fork speed. Slowing replication fork speed promotes the emergence of 2-cell-like cells and improves the efficiency of somatic cell nuclear transfer reprogramming and the formation of induced pluripotent stem cell colonies.
Review
Cell Biology
Amritha Sreekumar, Sharanjot Saini
Summary: Therapy-induced neuroendocrine prostate cancer (NEPC) is a highly aggressive variant of prostate cancer that arises through a reversible process called neuroendocrine differentiation (NED). NED involves decreased expression of androgen receptor (AR) and increased expression of neuroendocrine lineage markers. This article reviews the role of transcription factors and chromatin modifiers in driving lineage reprogramming and discusses the potential for better therapeutic strategies to target NEPC.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Article
Medicine, Research & Experimental
Chunshen Long, Hanshuang Li, Pengfei Liang, Lemuge Chao, Yan Hong, Junping Zhang, Qilemuge Xi, Yongchun Zuo
Summary: Single-cell studies have revealed that somatic cell reprogramming is a continuous process of cell fate transition. The activation of pluripotency networks and the mesenchymal-epithelial transition are crucial for successful reprogramming. By reconstructing cellular trajectory, we identified key factors and genes driving cell fate bifurcations, and found several drivers for successful reprogramming and alternative fates.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2023)
Article
Cardiac & Cardiovascular Systems
Glynnis A. Garry, Eric N. Olson
Summary: Direct reprogramming of resident cardiac fibroblasts to induced cardiomyocytes is a promising therapy for restoring heart function and repairing injured heart. Traditional cardiac transcription factors Gata4, Mef2c, and Tbx5 have been widely used in direct cardiac reprogramming strategies. However, recent discoveries have identified alternative epigenetic factors that can reprogram human cells without using these canonical factors. Single-cell genomics studies have provided insights into the cellular maturation and epigenetics during reprogramming after injury, pointing towards potential areas of discovery in the field. These findings enhance the effectiveness of reprogramming as a means of promoting cardiac regeneration following myocardial infarction and heart failure.
JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY
(2023)
Article
Medicine, Research & Experimental
Guizhen Zhao, Yang Zhao, Haocheng Lu, Ziyi Chang, Hongyu Liu, Huilun Wang, Wenying Liang, Yuhao Liu, Tianqing Zhu, Oren Rom, Yanhong Guo, Lin Chang, Bo Yang, Minerva T. Garcia-Barrio, Jiandie D. Lin, Y. Eugene Chen, Jifeng Zhang
Summary: The study demonstrates that BAF60c plays a crucial role in preventing and treating abdominal aortic aneurysm (AAA). It maintains the contractile phenotype of vascular smooth muscle cells (VSMCs), suppresses inflammation, and prevents apoptosis to maintain VSMC homeostasis.
JOURNAL OF CLINICAL INVESTIGATION
(2022)
Article
Biochemistry & Molecular Biology
Xiao-Min Liu, Yuanhui Mao, Shen Wang, Jun Zhou, Shu-Bing Qian
Summary: Transcriptional programming plays a key role in determining cell state. This study identifies METTL3 as a crucial modulator of dynamic transcription and chromatin accessibility during embryonic stem cell differentiation.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Review
Immunology
Olga Zimmermannova, Ines Caiado, Alexandra G. Ferreira, Carlos-Filipe Pereira
Summary: The development of cancer immunotherapy is based on advances in understanding the interaction between cancer cells and the immune system, with cell fate reprogramming providing new alternatives for personalized immunotherapy. Technologies such as induced pluripotent stem cells (iPSCs) enable the study and generation of clinically useful immune cells, offering potential for enhancing anti-tumor properties and addressing challenges in cellular immunotherapy. Advances in in vivo reprogramming and gene delivery mechanisms are opening exciting avenues for direct manipulation of immune or tumor cells in situ, providing new tools for overcoming obstacles in cancer immunotherapy.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biochemical Research Methods
Jennifer Hammelman, Tulsi Patel, Michael Closser, Hynek Wichterle, David Gifford
Summary: This study compares nine computational methods for identifying reprogramming factors for cell differentiation. The researchers found that methods using chromatin accessibility performed the best, with an average identification rate of 50-60% of reprogramming factors in the top ten candidates. Among the chromatin accessibility methods, DeepAccess and diffTF showed the highest correlation with the ranked significance of transcription factor candidates. AME and diffTF were identified as optimal methods for transcription factor recovery, allowing for systematic prioritization of candidates in the design of new reprogramming protocols.
Article
Biochemistry & Molecular Biology
Daisylyn Senna Tan, Yanpu Chen, Ya Gao, Anastasia Bednarz, Yuanjie Wei, Vikas Malik, Derek Hoi-Hang Ho, Mingxi Weng, Sik Yin Ho, Yogesh Srivastava, Sergiy Velychko, Xiaoxiao Yang, Ligang Fan, Johnny Kim, Johannes Graumann, Gary D. Stormo, Thomas Braun, Jian Yan, Hans R. Schoeler, Ralf Jauch
Summary: Transcription factor-driven cell fate engineering requires efficiency, speed, and maturity for clinical translation. Directed evolution led to the discovery of an artificially evolved POU factor (ePOU) that surpasses Oct4 in reprogramming efficacy. ePOU can induce pluripotency with or without Sox2, has altered DNA binding preferences, and accelerates pluripotency network establishment.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Review
Cell Biology
Aurelio Balsalobre, Jacques Drouin
Summary: Pioneer factors are transcription factors that can initiate the opening of closed chromatin. They play crucial roles in determining cell fate and cellular reprogramming, but their misexpression can have pathological consequences.
NATURE REVIEWS MOLECULAR CELL BIOLOGY
(2022)
Review
Oncology
Emily Zboril, Hannah Yoo, Lizhen Chen, Zhijie Liu
Summary: This review explores the dynamics of tumor progression-associated enhancers, their transcription factor drivers, and how enhancer reprogramming modulates gene expression during cancer invasive progression. Recent advancements in technology such as single-cell sequencing, spatial transcriptomics, and CUT&RUN have enabled integrated studies of enhancer reprogramming in vivo. Understanding these changes in enhancer dynamics and its drivers will be crucial in controlling cancer progression and treatment outcomes.
FRONTIERS IN ONCOLOGY
(2021)
Article
Cardiac & Cardiovascular Systems
Haofei Wang, Yuchen Yang, Yunzhe Qian, Jiandong Liu, Li Qian
Summary: Direct conversion of cardiac fibroblast into induced cardiomyocytes by cardiac transcription factors shows promise for regenerative medicine. Transcriptome remodelling during cardiac reprogramming is driven by chromatin landscape alteration. The study used single-cell ATAC-seq to identify early chromatin accessibility changes and discovered Smad3 as a bimodal TF in cardiac reprogramming. Integrative analysis with scRNA-seq data revealed active TFs important for iCM conversion and global rewiring of cis-regulatory interactions of cardiac genes along the reprogramming trajectory.
JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY
(2022)
Review
Multidisciplinary Sciences
Jason H. Brickner
Summary: This article discusses the mechanisms by which histone modifications can be inherited and relates them to the phenomenon of epigenetic transcriptional memory. Recent studies have found that the histone H3 lysine 4 dimethylation associated with this memory plays a critical role in sustaining memory and can be stably maintained through multiple mitoses. This chromatin-mediated inheritance mechanism involves a physical interaction between an H3K4me2 reader, SET3C, and an H3K4me2 writer, Spp1(-) COMPASS. This is the first example of chromatin-mediated inheritance of a mark that promotes transcription.
ANNALS OF THE NEW YORK ACADEMY OF SCIENCES
(2023)
Article
Chemistry, Multidisciplinary
Meiyan Wang, Yuanxiao Liu, Ziwei Wang, Longliang Qiao, Xiaoding Ma, Lingfeng Hu, Deqiang Kong, Yuan Wang, Haifeng Ye
Summary: The LIRE system utilizes light-inducible control over endogenous transcription factor expression to achieve cell reprogramming. It offers the ability to manipulate cell fate and tissue function through light. In mouse experiments, the system successfully generated optogenetic chimeric mice, providing a valuable tool for controlled gene expression studies.
Review
Developmental Biology
Jan Hendrik van Weerd, Vincent M. Christoffels
Article
Cell Biology
Ryo Nakamura, Kazuko Koshiba-Takeuchi, Megumi Tsuchiya, Mizuyo Kojima, Asuka Miyazawa, Kohei Ito, Hidesato Ogawa, Jun K. Takeuchi
DEVELOPMENT GROWTH & DIFFERENTIATION
(2016)
Article
Cardiac & Cardiovascular Systems
Yuika Morita, Peter Andersen, Akitsu Hotta, Yuko Tsukahara, Noriko Sasagawa, Naoko Hayashida, Chizuko Koga, Misato Nishikawa, Yumiko Saga, Sylvia M. Evans, Kazuko Koshiba-Takeuchi, Ryuichi Nishinakamura, Yoshinori Yoshida, Chulan Kwon, Jun K. Takeuchi
JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY
(2016)
Article
Multidisciplinary Sciences
Masato Tsuji, Takanori Kawasaki, Takeru Matsuda, Tomio Arai, Satoshi Gojo, Jun K. Takeuchi
Article
Multidisciplinary Sciences
Masao Takeuchi, Atsunori Higashino, Kikuko Takeuchi, Yutaro Hori, Kazuko Koshiba-Takeuchi, Hatsune Makino, Yoko Monobe, Marina Kishida, Jun Adachi, Jun Takeuchi, Takeshi Tomonaga, Akihiro Umezawa, Yosuke Kameoka, Ken-ichi Akagi
Article
Biotechnology & Applied Microbiology
Yutaro Hori, Yoko Tanimoto, Satoru Takahashi, Tetsushi Furukawa, Kazuko Koshiba-Takeuchi, Jun K. Takeuchi
Article
Cell Biology
Malou van den Boogaard, Jan Hendrik van Weerd, Amira C. Bawazeer, Ingeborg B. Hooijkaas, Harmen J. G. van de Werken, Federico Tessadori, Wouter de Laat, Phil Barnett, Jeroen Bakkers, Vincent M. Christoffels
Article
Multidisciplinary Sciences
Rajiv A. Mohan, Fernanda M. Bosada, Jan H. van Weerd, Karel van Duijvenboden, Jianan Wang, Mathilda T. M. Mommersteeg, Ingeborg B. Hooijkaas, Vincent Wakker, Corrie de Gier-de Vries, Ruben Coronel, Gerard J. J. Boink, Jeroen Bakkers, Phil Barnett, Bas J. Boukens, Vincent M. Christoffels
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Biology
Jan Hendrik van Weerd, Rajiv A. Mohan, Karel van Duijvenboden, Ingeborg B. Hooijkaas, Vincent Wakker, Bastiaan J. Boukens, Phil Barnett, Vincent M. Christoffels
Article
Cardiac & Cardiovascular Systems
Xiaoxi Yang, Tetsuo Sasano, Yusuke Ebana, Jun K. Takeuchi, Kensuke Ihara, Masahiro Yamazoe, Tetsushi Furukawa
CIRCULATION JOURNAL
(2020)
Article
Multidisciplinary Sciences
Joongoo Lee, Kevin J. Schwarz, Do Soon Kim, Jeffrey S. Moore, Michael C. Jewett
NATURE COMMUNICATIONS
(2020)
Article
Multidisciplinary Sciences
Jiyoung Lee, Akito Sutani, Rin Kaneko, Jun Takeuchi, Tetsuo Sasano, Takashi Kohda, Kensuke Ihara, Kentaro Takahashi, Masahiro Yamazoe, Tomohiro Morio, Tetsushi Furukawa, Fumitoshi Ishino
NATURE COMMUNICATIONS
(2020)
Article
Multidisciplinary Sciences
Masao Takeuchi, Kikuko Takeuchi, Tomoyo Takai, Ritsuko Yamaguchi, Tetsushi Furukawa, Ken-ichi Akagi, Jun K. Takeuchi
Summary: GPC5, a heparan sulfate proteoglycan, is localized to multiple subcellular regions and colocalizes with FGFR, Rab11, and ARF6, implicating its involvement in regulating cell migration. The delivery of GPC5 to different cellular locations via recycling endosomes suggests its key role in FGF2-stimulated cell migration.
Article
Cardiac & Cardiovascular Systems
Doris Skoric-Milosavljevic, Rafik Tadros, Fernanda M. Bosada, Federico Tessadori, Jan Hendrik van Weerd, Odilia Woudstra, Fleur V. Y. Tjong, Najim Lahrouchi, Fanny Bajolle, Heather J. Cordell, A. J. Agopian, Gillian M. Blue, Daniela Q. C. M. Barge-Schaapveld, Marc Gewillig, Christoph Preuss, Elisabeth M. Lodder, Phil Barnett, Aho Ilgun, Leander Beekman, Karel van Duijvenboden, Regina Bokenkamp, Martina Muller-Nurasyid, Hubert W. Vliegen, Thelma C. Konings, Joost P. van Melle, Arie P. J. van Dijk, Roland R. J. van Kimmenade, Jolien W. Roos-Hesselink, Gertjan Sieswerda, Folkert Meijboom, Hashim Abdul-Khaliq, Felix Berger, Sven Dittrich, Marc-Phillip Hitz, Julia Moosmann, Frank-Thomas Riede, Stephan Schubert, Pilar Galan, Mark Lathrop, Hans Markus Munter, Ammar Al-Chalabi, Christopher E. Shaw, Pamela J. Shaw, Karen E. Morrison, Jan H. Veldink, Leonard H. van den Berg, Sylvia Evans, Marcelo A. Nobrega, Ivy Aneas, Milena Radivojkov-Blagojevic, Thomas Meitinger, Erwin Oechslin, Tapas Mondal, M. Lynn Bergin, John F. Smythe, Luis Altamirano-Diaz, Jane Lougheed, Berto J. Bouma, Marie A. Chaix, Jennie Kline, Anne S. Bassett, Gregor Andelfinger, Roel L. F. van der Palen, Patrice Bouvagnet, Sally-Ann B. Clur, Jeroen Breckpot, Wilhelmina S. Kerstjens-Frederikse, David S. Winlaw, Ulrike M. M. Bauer, Seema Mital, Elizabeth Goldmuntz, Bernard Keavney, Damien Bonnet, Barbara J. Mulder, Michael W. T. Tanck, Jeroen Bakkers, Vincent M. Christoffels, Cornelis J. Boogerd, Alex Postma, Connie R. Bezzina
Summary: This study reveals the genetic mechanism of dextro-transposition of the great arteries (D-TGA), identifies a susceptibility locus near the WNT5A gene, and confirms the role of WNT5A in D-TGA. The findings provide important insights for the treatment of D-TGA.
CIRCULATION RESEARCH
(2022)
Review
Cell Biology
Baoxu Pang, Jan H. van Weerd, Feija L. Hamoen, Michael P. Snyder
Summary: Cell type- and differentiation-specific gene expression is controlled by genomic non-coding regulatory elements (NCREs), including promoters, enhancers, silencers, and insulators. Recent studies have focused on identifying and characterizing silencers, which repress gene transcription, and have highlighted their importance in homeostasis and disease. Understanding silencers has potential implications for genome research and therapeutic applications.
NATURE REVIEWS MOLECULAR CELL BIOLOGY
(2023)
