Article
Developmental Biology
Ha T. H. Vu, Regan L. Scott, Khursheed Iqbal, Michael J. Soares, Geetu Tuteja
Summary: In this study, the chromatin accessibility and gene regulation patterns of invasive trophoblast cells in rat and human were compared using single-nucleus ATAC-seq and single-cell RNA-seq data. Similarities in gene regulation and enriched motifs were found between the two species, and a conserved gene regulatory network in invasive trophoblast cells was identified.
Review
Biochemistry & Molecular Biology
Ryo Onishi, Soichiro Yamanaka, Mikiko C. Siomi
Summary: The piRNA pathway is a self-defense mechanism essential for maintaining germline genome integrity, suppressing transposons through RNA degradation and heterochromatinization. While showing conservation across species, there is clear biodiversity in the overall schemes of nuclear events.
Article
Biochemical Research Methods
Mohammed Eslami, Amin Espah Borujeni, Hamed Eramian, Mark Weston, George Zheng, Joshua Urrutia, Carolyn Corbet, Diveena Becker, Paul Maschhoff, Katie Clowers, Alexander Cristofaro, Hamid Doost Hosseini, D. Benjamin Gordon, Yuval Dorfan, Jedediah Singer, Matthew Vaughn, Niall Gaffney, John Fonner, Joe Stubbs, Christopher A. Voigt, Enoch Yeung
Summary: The Host Response Model (HRM) combines high-throughput sequencing and machine learning to accurately predict the directionality of gene dysregulation to a combination of inducers. The use of prior knowledge of cell regulatory networks doubles the predictive performance of the HRM.
Article
Biochemistry & Molecular Biology
Arnulf Hertweck, Maria Vila de Mucha, Paul R. Barber, Robert Dagil, Hayley Porter, Andres Ramos, Graham M. Lord, Richard G. Jenner
Summary: This study reveals that lineage-determining transcription factors (LD-TFs) can drive specific cell fate choices by redistributing another transcription factor, even in the presence of other factors driving alternative differentiation pathways.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Immunology
Tom Sidwell, Ellen V. Rothenberg
Summary: Bcl11b, a critical transcription factor, plays context-dependent roles in the development of different cell types. Its chromatin binding activity is largely guided by interactions with other transcription factors, and it recruits multiple families of chromatin-modifying enzyme complexes to induce changes in regional suites of epigenetic modifications.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Immunology
Boyoung Shin, Wen Zhou, Jue Wang, Fan Gao, Ellen V. Rothenberg
Summary: Runx factors regulate lineage specification of hematopoietic cells, including T lymphocytes, by binding to specific genomic regions. In early T cell development, dynamic Runx binding shifts are regulated by Runx dosage and functional partners rather than local chromatin state. Limited Runx protein availability leads to premature Runx occupancy at post-commitment binding sites, accelerating T cell lineage development. This regulation involves the activation of T cell-identity and innate lymphoid cell programs by Runx and other transcription factors. Overall, Runx proteins play a crucial role in directing lineage-fate decisions in various cell types.
Article
Cell Biology
Ramesh Yelagandula, Karin Stecher, Maria Novatchkova, Luca Michetti, Georg Michlits, Jingkui Wang, Pablo Hofbauer, Gintautas Vainorius, Carina Pribitzer, Luke Isbel, Sasha Mendjan, Dirk Schuebeler, Ulrich Elling, Julius Brennecke, Oliver Bell
Summary: ZNF462 haploinsufficiency is associated with Weiss-Kruszka syndrome, which is characterized by neurodevelopmental defects including autism. However, the molecular functions of ZNF462 have remained unclear. This study identifies ZFP462 as the murine homologue of ZNF462 and demonstrates its role in regulating neural lineage specification in mouse embryonic stem cells (ESCs) by interacting with the H3K9-specific histone methyltransferase complex G9A/GLP to silence meso-endodermal genes.
NATURE CELL BIOLOGY
(2023)
Review
Oncology
Alastair Davies, Amina Zoubeidi, Himisha Beltran, Luke A. Selth
Summary: Lineage plasticity is a crucial process in cancer progression and therapy resistance, mainly regulated by transcriptional and epigenetic dysregulation. This review explores the regulators of lineage plasticity and their interaction with other malignant features. Strategies for detecting and treating highly plastic tumors are also discussed.
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)
Review
Biology
Vina D. L. Putra, Kristopher A. Kilian, Melissa L. Knothe Tate
Summary: This review discusses the biomechanical, biophysical, and biochemical factors that regulate cytoskeletal remodeling during tissue neogenesis for targeted tissue regeneration. It highlights the effects of cytoskeletal remodeling on stem cell mechanoadaptation and lineage commitment. The review also summarizes findings on cytoskeletal remodeling in tissue neogenesis and its relevance in guiding tissue regeneration, as well as methods for visualizing and measuring cytoskeletal remodeling and its effects on cell mechanics.
COMMUNICATIONS BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Ka Lung Cheung, Anbalagan Jaganathan, Yuan Hu, Feihong Xu, Alannah Lejeune, Rajal Sharma, Cristina I. Caescu, Jamel Meslamani, Adam Vincek, Fan Zhang, Kyung Lee, Nilesh Zaware, Amina Abdul Qayum, Chunyan Ren, Mark H. Kaplan, John Cijiang He, Huabao Xiong, Ming-Ming Zhou
Summary: This study uncovers a previously unrecognized mechanism of self-directed cell type-specific regulation of the master transcription factor Stat3 through its own transcriptional target Hipk2 in Th17 cell differentiation. These findings provide insights into the regulation of Th17 cell immune functions and suggest a therapeutic strategy for developing targeted therapies for Th17-associated inflammatory disorders.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Zhifen Zhou, Yujing Li, Huimin Xu, Xiaowei Xie, Zibin He, Song Lin, Ruofei Li, Shouheng Jin, Jun Cui, Hai Hu, Feng Liu, Su Wu, Wenbin Ma, Zhou Songyang
Summary: This study identified multiple positive regulators, including the E3 ligase DTX2, through an inducible CRISPR/Cas9 KO screen. Depletion of DTX2 in telomerase-positive cancer cells resulted in downregulation of hTERT transcription and telomerase activity, leading to progressive telomere shortening, growth arrest, and increased apoptosis. BioID analysis revealed that DTX2 interacts with multiple transcription factors, with NFIC functioning cooperatively with DTX2 to promote hTERT transcription. Further investigation demonstrated that DTX2 mediates K63-linked ubiquitination of NFIC, which enhances NFIC binding to the hTERT promoter and increases hTERT expression.
Article
Biochemistry & Molecular Biology
Dongyu Zhao, Min Zhang, Shaodong Huang, Qi Liu, Sen Zhu, Yanqiang Li, Weihua Jiang, Daniel L. Kiss, Qi Cao, Lili Zhang, Kaifu Chen
Summary: In this study, elevated expression of CHD6 in prostate cancer is found to be associated with poor prognosis. CHD6 regulates the oncogenicity of prostate cancer cells by evicting nucleosomes and activating prostate cancer pathways.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Allergy
Mindy Tsai, Peter Valent, Stephen J. Galli
Summary: The discovery of the cell surface receptor KIT and its ligand, stem cell factor (SCF), in 1987/1988 and 1990 has greatly contributed to our understanding of the development and function of various cell lineages. Mutations in KIT or SCF can have significant effects on the development and/or function of hematopoietic progenitors, melanocytes, germ cells, and mast cells. The biological importance of KIT in other cell types is still not well understood.
JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY
(2022)
Article
Multidisciplinary Sciences
Saikat Bhattacharya, Suman Wang, Divya Reddy, Siyuan Shen, Ying Zhang, Ning Zhang, Hua Li, Michael P. Washburn, Laurence Florens, Yunyu Shi, Jerry L. Workman, Fudong Li
Summary: The paper describes the interaction between hnRNP L and SETD2, revealing their binding mechanism. The study demonstrates that a leucine pair in SETD2 inserts their side chains in hydrophobic pockets formed by hnRNP L RRM2 for interaction to occur, highlighting the importance of this binding interaction. The similarity in the mode of SETD2-hnRNP L interaction with other related protein-protein interactions suggests a conserved design for splicing regulators to interact with one another.
NATURE COMMUNICATIONS
(2021)
Article
Cell Biology
Zibo Zhao, Lu Wang, Andrew G. Volk, Noah W. Birch, Kristen L. Stoltz, Elizabeth T. Bartom, Stacy A. Marshall, Emily J. Rendleman, Carson M. Nestler, Joseph Shilati, Gary E. Schiltz, John D. Crispino, Ali Shilatifard
GENES & DEVELOPMENT
(2019)
Article
Hematology
James Lally, Kristian Boasman, Lilia Brown, Vincenzo Martinelli, Ilaria Cappuccio, Vishaka Sovani, Christian Marinaccio, John D. Crispino, Ciaren Graham, Ciro Rinaldi
JOURNAL OF THROMBOSIS AND HAEMOSTASIS
(2019)
Article
Oncology
Naseema Gangat, Christian Marinaccio, Ronan Swords, Justin M. Watts, Sandeep Gurbuxani, Alfred Rademaker, Angela J. Fought, Olga Frankfurt, Jessica K. Altman, Qiang Jeremy Wen, Noushin Farnoud, Christopher A. Famulare, Akshar Patel, Roberto Tapia, Rangit R. Vallapureddy, Stephanie Barath, Amy Graf, Amy Handlogten, Darci Zblewski, Mrinal M. Patnaik, Aref Al-kali, Yvonne Trang Dinh, Kristen Englund Prahl, Shradha Patel, Juan Carlos Nobrega, Dalissa Tejera, Amber Thomassen, Juehua Gao, Peng Ji, Raajit K. Rampal, Francis J. Giles, Ayalew Tefferi, Brady Stein, John D. Crispino
CLINICAL CANCER RESEARCH
(2019)
Article
Oncology
Maurice Labuhn, Kelly Perkins, Soeren Matzk, Leila Varghese, Catherine Garnett, Elli Papaemmanuil, Marlen Metzner, Alison Kennedy, Vyacheslav Amstislayskiy, Thomas Risch, Raj Bhayadia, David Samulowski, David Cruz Hernandez, Bilyana Stoilova, Valentina Lotchkova, Udo Oppermann, Carina Scheer, Kenichi Yoshida, Adrian Schwarzer, Jeffrey Taub, John D. Crispino, Mitchell J. Weiss, Asuhide Hayashi, Takashi Taga, Etsuro Ito, Seishi Ogawa, Dirk Reinhardt, Marie-Laure Yaspo, Peter J. Campbell, Irene Roberts, Stefan Constantinescu, Paresh Vyas, Dirk Heckl, Jan-Henning Klusmann
Article
Oncology
Brittany Woods, Wei Chen, Sophia Chiu, Christian Marinaccio, Chunling Fu, Lilly Gu, Marinka Bulic, Qiong Yang, Anouar Zouak, Shengxian Jia, Praveen Kumar Suraneni, Kailin Xu, Ross L. Levine, John D. Crispino, Qiang Jeremy Wen
CLINICAL CANCER RESEARCH
(2019)
Article
Gastroenterology & Hepatology
Yutao Wang, Huan Wen, Jiajun Fu, Lin Cai, Peng-Long Li, Chang-Ling Zhao, Zhu-feng Dong, Jun-peng Ma, Xi Wang, Han Tian, Yan Zhang, Ye Liu, Jingjing Cai, Zhi-Gang She, Zan Huang, Wenhua Li, Hongliang Li
Article
Hematology
Te Ling, Yehudit Birger, Monika J. Stankiewicz, Nissim Ben-Haim, Tomer Kalisky, Avigail Rein, Eitan Kugler, Wei Chen, Chunling Fu, Kevin Zhang, Hiral Patel, Jacek W. Sikora, Young Ah Goo, Neil Kelleher, Lihua Zou, Shai Izraeli, John D. Crispino
Review
Oncology
Michael Schieber, John D. Crispino, Brady Stein
BLOOD CANCER JOURNAL
(2019)
Article
Medicine, Research & Experimental
Maureen McNulty, John D. Crispino
COLD SPRING HARBOR PERSPECTIVES IN MEDICINE
(2020)
Article
Biochemistry & Molecular Biology
Te Ling, John D. Crispino
Editorial Material
Biochemistry & Molecular Biology
John Strouboulis, John D. Crispino
Article
Cell Biology
Dan Liu, Peng Zhang, Junjie Zhou, Rufang Liao, Yan Che, Mao-Mao Gao, Jiaqi Sun, Jingjing Cai, Xu Cheng, Yongping Huang, Guopeng Chen, Hongyu Nie, Yan-Xiao Ji, Xiao-Jing Zhang, Zan Huang, Haibo Xu, Zhi-Gang She, Hongliang Li
Article
Cell Biology
Chongshu Jian, Jiajun Fu, Xu Cheng, Li-Jun Shen, Yan-Xiao Ji, Xiaoming Wang, Shan Pan, Han Tian, Song Tian, Rufang Liao, Kehan Song, Hai-Ping Wang, Xin Zhang, Yibin Wang, Zan Huang, Zhi-Gang She, Xiao-Jing Zhang, Lihua Zhu, Hongliang Li
Article
Biochemistry & Molecular Biology
Manman Wang, Tan Zhang, Xuechun Zhang, Zhou Jiang, Min Peng, Zan Huang
CELL AND BIOSCIENCE
(2020)
Article
Oncology
Qi Jin, Carlos A. Martinez, Kelly M. Arcipowski, Yixing Zhu, Blanca T. Gutierrez-Diaz, Kenneth K. Wang, Megan R. Johnson, Andrew G. Volk, Feng Wang, Jian Wu, Charles Grove, Hui Wang, Ivan Sokirniy, Paul M. Thomas, Young Ah Goo, Nebiyu A. Abshiru, Nobuko Hijiya, Sofie Peirs, Niels Vandamme, Geert Berx, Steven Goosens, Stacy A. Marshall, Emily J. Rendleman, Yoh-hei Takahashi, Lu Wang, Radhika Rawat, Elizabeth T. Bartom, Clayton K. Collings, Pieter Van Vlierberghe, Alexandros Strikoudis, Stephen Kelly, Beatrix Ueberheide, Christine Mantis, Irawati Kandela, Jean-Pierre Bourquin, Beat Bornhauser, Valentina Serafin, Silvia Bresolin, Maddalena Paganin, Benedetta Accordi, Giuseppe Basso, Neil L. Kelleher, Joseph Weinstock, Suresh Kumar, John D. Crispino, Ali Shilatifard, Panagiotis Ntziachristos
CLINICAL CANCER RESEARCH
(2019)