Article
Multidisciplinary Sciences
Sam Buckberry, Xiaodong Liu, Daniel Poppe, Jia Ping Tan, Guizhi Sun, Joseph Chen, Trung Viet Nguyen, Alex de Mendoza, Jahnvi Pflueger, Thomas Frazer, Dulce B. Vargas-Landin, Jacob M. Paynter, Nathan Smits, Ning Liu, John F. Ouyang, Fernando J. Rossello, Hun S. Chy, Owen J. L. Rackham, Andrew L. Laslett, James Breen, Geoffrey J. Faulkner, Christian M. Nefzger, Jose M. Polo, Ryan Lister
Summary: Cells undergo a significant epigenome reconfiguration during reprogramming to hiPS cells. The differences in epigenomes between hiPS cells and hES cells affect the function of hiPS cells. Researchers characterized the emergence and persistence of these epigenetic differences and developed a TNT reprogramming strategy that corrects epigenetic memory and aberrations, making hiPS cells more similar to hES cells at a molecular and functional level.
Letter
Cell Biology
Jakob V. Kanne, Masaki Ishikawa, Simon Bressendorff, Jeppe Ansbol, Mitsuyasu Hasebe, Eleazar Rodriguez, Morten Petersen
Summary: Animal and plant somatic cells have the ability to switch states or reprogram into stem cells to adapt to stress and injury, a process that requires macroautophagy/autophagy. Overexpression of ATG8/LC3 in the moss Physcomitrium patens enhances the ability of somatic cells to reprogram into stem cells when subjected to severe wounding, indicating that autophagy not only facilitates cell dedifferentiation but also increases their competence to do so.
Article
Multidisciplinary Sciences
Glenn J. Markov, Thach Mai, Surag Nair, Anna Shcherbina, Yu Xin Wang, David M. Burns, Anshul Kundaje, Helen M. Blau
Summary: The AP-1 transcription factor c-Jun plays a critical role in human somatic cell reprogramming by enhancing enhancer accessibility in fibroblasts and repressing OCT4 expression. Through epigenome remodeling, successful reprogramming of human fibroblasts to induced pluripotent stem cells was achieved.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Cell Biology
Jerry Hung-Hao Lo, Miguel Edwards, Justin Langerman, Rupa Sridharan, Kathrin Plath, Stephen T. Smale
Summary: By examining dynamic ranges of gene expression, the authors found that Oct4 and Sox2 binding is enriched near genes with large dynamic ranges of expression. Their results suggest that Oct4 and Sox2 directly establish both active and silent transcriptional states in pluripotent cells at a large number of genes subject to dynamic regulation.
GENES & DEVELOPMENT
(2022)
Article
Cell Biology
Jingsheng Li, Chunhong Dai, Wenyan Xie, Heyao Zhang, Xin Huang, Constantinos Chronis, Ying Ye, Wensheng Zhang
Summary: This study developed a one-step strategy to efficiently target and suppress endogenous pluripotent genes in mouse ESCs and replace their expression with AID-fused transgenes.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Review
Developmental Biology
Velinda Vidaurre, Xin Chen
Summary: The article mainly discusses the regulatory role of epigenetic mechanisms between germ cells and somatic cells on the identity and activity of germline stem cells, introducing the cellular differentiation mechanisms during gametogenesis.
DEVELOPMENTAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Daniel F. Kaemena, Masahito Yoshihara, Meryam Beniazza, James Ashmore, Suling Zhao, Marten Bertenstam, Victor Olariu, Shintaro Katayama, Keisuke Okita, Simon R. Tomlinson, Kosuke Yusa, Keisuke Kaji
Summary: CRISPR/Cas9-mediated genome-wide knockout screening identified 24 reprogramming roadblock genes, among which depletion of the predicted KRAB zinc finger protein Zfp266 consistently enhanced murine iPSC generation in various reprogramming settings. ZFP266 was found to bind to Short Interspersed Nuclear Elements (SINEs) near the binding sites of OCT4, SOX2, and KLF4, inhibiting chromatin opening. Replacement of the KRAB co-suppressor with co-activator domains transformed ZFP266 from an inhibitor to a potent facilitator of iPSC reprogramming. The interaction between SINE and KRAB-ZFP is proposed to be a critical regulator of chromatin accessibility for efficient cellular identity changes.
NATURE COMMUNICATIONS
(2023)
Review
Cell Biology
Ying Ye, Xi Chen, Wensheng Zhang
Summary: Embryonic stem cells have a unique ability to maintain and regulate the balance between self-renewal and multi-lineage cellular differentiation, largely dependent on gene expression regulations. Chromatin remodeling complexes play a crucial role in promoting chromatin structural changes that ultimately affect ESC fate choices.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Henry A. Ertl, Mark S. Hill, Patricia J. Wittkopp
Summary: This study reveals the role of chromatin remodeling factors and their relationship with gene expression and chromatin structure in gene regulatory mechanisms. The findings suggest that variations in chromatin accessibility and Grainy head binding contribute to the evolution of gene expression, shedding light on the complex interactions among molecular layers in gene regulation.
Article
Biology
David C. Klein, Santana M. Lardo, Kurtis N. McCannell, Sarah J. Hainer
Summary: The FACT complex maintains cellular pluripotency by regulating nucleosome positioning and transcription activity. FACT interacts with genes such as OCT4, SOX2, and NANOG, binding to both promoter and enhancer elements, and regulates their transcription and expression, thereby influencing cell fate decisions.
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
Tore Bleckwehl, Giuliano Crispatzu, Kaitlin Schaaf, Patricia Respuela, Michaela Bartusel, Laura Benson, Stephen J. Clark, Kristel M. Dorighi, Antonio Barral, Magdalena Laugsch, Wilfred F. J. van Ijcken, Miguel Manzanares, Joanna Wysocka, Wolf Reikf, Alvaro Rada-Iglesias
Summary: The study reveals that partial retention of histone H3K4 monomethylation within relevant enhancers is crucial for germline competence and specification in in vitro differentiated primordial germ cells.Loss of this histone modification reduces the germline competence of EpiLC and decreases PGCLC differentiation efficiency, suggesting a key role in facilitating enhancer activation during specific developmental transitions.
NATURE COMMUNICATIONS
(2021)
Editorial Material
Cell Biology
Ellen V. Rothenberg
Summary: Transcription factors bind to DNA in a sequence-specific manner and selectively impact gene expression, but their binding sites do not accurately predict the genes they directly control. A new study demonstrates that the same transcription factor binding sites have a greater impact on gene regulation during developmental change.
GENES & DEVELOPMENT
(2022)
Article
Biochemistry & Molecular Biology
Sachin Pundhir, Jinyu Su, Marta Tapia, Anne Meldgaard Hansen, James Seymour Haile, Klaus Hansen, Bo Torben Porse
Summary: SWI/SNF and NuRD protein complexes antagonistically regulate DNA accessibility, but inhibiting their activities often leads to unexpected changes in target gene expression (paradoxical). This study reveals that SWI/SNF and NuRD engage in a tug-of-war to regulate PRC2 occupancy at lowly expressed and bivalent genes in mouse embryonic stem cells (mESCs). Furthermore, they antagonistically modulate RNA polymerase II (Pol II) release kinetics at promoters of average or highly expressed genes, resulting in paradoxical changes in gene expression due to alterations in H3.3 and H2A.Z levels at promoter-flanking nucleosomes. The relative activities of these remodelers potentiate gene promoters towards Pol II-dependent open or PRC2-dependent closed chromatin states, with RNA Pol II occupancy playing a key role in determining the direction of gene expression changes in response to SWI/SNF and NuRD inactivation at gene promoters in mESCs.
Article
Biochemistry & Molecular Biology
Eun Kyoung Do, Hye Ji Moon, Kyung Taek Kang, Jung Won Yoon, Ye Seul Kim, Jeong Kon Seo, Jae Ho Kim
Summary: The study revealed that Kap1 regulates the pluripotency of ESCs and somatic cell reprogramming by inhibiting Itch-mediated ubiquitination of Oct4, increasing Oct4 stability. This finding may offer new insights for the treatment of stem cell and cell reprogramming-related diseases.
CELL DEATH AND DIFFERENTIATION
(2021)