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| Open AccessCommon anti-cancer therapies induce somatic mutations in stem cells of healthy tissue
Specific anti-cancer therapies are highly mutagenic to cancer cells but the mutational impact on healthy tissues remains elusive. Here, the authors use organoids and whole-genome sequencing to characterise somatic mutations in healthy colon and liver adult stem cells after chemo- or radiotherapy.
- Ewart Kuijk
- , Onno Kranenburg
- & Arne Van Hoeck
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Article
| Open AccessModeling human telencephalic development and autism-associated SHANK3 deficiency using organoids generated from single neural rosettes
Our understanding of human brain development in health and disease is limited. The authors generated human brain organoids from stem cell-derived isolated single neural rosettes to study human cortico-striatal development and deficits caused by an autism-associated genetic abnormality in SHANK3.
- Yueqi Wang
- , Simone Chiola
- & Aleksandr Shcheglovitov
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Article
| Open AccessEndothelial cell cycle state determines propensity for arterial-venous fate
During blood vessel development, endothelial cells become specified toward arterial or venous fates. Chavkin et al find that distinct endothelial cell cycle states provide windows of opportunity for the molecular induction of arterial or venous fate.
- Nicholas W. Chavkin
- , Gael Genet
- & Karen K. Hirschi
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Article
| Open AccessVitamin C epigenetically controls osteogenesis and bone mineralization
For decades vitamin C’s primary function in bone has been attributed to its involvement in collagen synthesis. Here, the authors uncover that vitamin C’s central role in bone is to globally orchestrate osteogenesis via epigenetic mechanisms.
- Roman Thaler
- , Farzaneh Khani
- & Andre J. van Wijnen
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Article
| Open AccessExploration of nuclear body-enhanced sumoylation reveals that PML represses 2-cell features of embryonic stem cells
Here the authors identify novel PML-partners and demonstrate that PML NBs control their sumoylation and that PML-controlled sumoylation of transcriptional regulators maintains the embryonic stem cell transcriptome and transposable element silencing.
- Sarah Tessier
- , Omar Ferhi
- & Valérie Lallemand-Breitenbach
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Article
| Open AccessEvolutionary origin of vertebrate OCT4/POU5 functions in supporting pluripotency
By constructing an evolutionary trajectory of the cyclostome-gnathostome Pou5 gene family and comparing the structural and phenotypic protein variations, the authors uncover the origin of functional characteristics for the pluripotency factor Oct4.
- Woranop Sukparangsi
- , Elena Morganti
- & Joshua M. Brickman
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Article
| Open AccessA stem cell roadmap of ribosome heterogeneity reveals a function for RPL10A in mesoderm production
How ribosomes differ in composition and function to regulate gene expression is poorly understood. Here, the authors show that ribosome composition changes during stem cell differentiation and identify a ribosomal protein that regulates production of the mesoderm lineage.
- Naomi R. Genuth
- , Zhen Shi
- & Maria Barna
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Article
| Open AccessAngiocrine extracellular vesicles impose mesenchymal reprogramming upon proneural glioma stem cells
Glioma stem-like cells (GSCs) exhibit plasticity during proneural-to-mesenchymal transition. Here the authors show that extracellular vesicles from endothelial cells can promote this transition of GSCs through activation of MMPs and NFkB, and inactivation of NOTCH.
- Lata Adnani
- , Jordan Kassouf
- & Janusz Rak
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Article
| Open AccessImprinting fidelity in mouse iPSCs depends on sex of donor cell and medium formulation
Reprogramming somatic cells to induced pluripotent stem cells (iPSCs) is associated with epigenetic alterations. Here the authors assess DNA methylation in detail in multiple female and male mouse iPSC lines generated with different protocols and find that defects depend on the sex of donor cells and can be partially mitigated by Vitamin C.
- Maria Arez
- , Melanie Eckersley-Maslin
- & Simão Teixeira da Rocha
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Article
| Open AccessMurine fetal bone marrow does not support functional hematopoietic stem and progenitor cells until birth
Relatively little is known about the first hematopoietic stem and progenitor cells to arrive in the fetal bone marrow. Here they characterize the frequency, function, and molecular identity of fetal BM HSPCs and their bone marrow niche, and show that most BM HSPCs have little hematopoietic function until birth.
- Trent D. Hall
- , Hyunjin Kim
- & Shannon McKinney-Freeman
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Article
| Open AccessEffects of biological sex mismatch on neural progenitor cell transplantation for spinal cord injury in mice
In this study, Pitonak et al. report that transplantation of neural progenitor cells derived from male donors trigger an immune rejection response following transplantation into sites of spinal cord injury in female mice.
- Michael Pitonak
- , Miriam Aceves
- & Jennifer N. Dulin
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Article
| Open AccessGermline-somatic JAK2 interactions are associated with clonal expansion in myelofibrosis
Myelofibrosis is a risk factor for the development of Acute Myeloid Leukaemia. Here, the authors carry out an integrated genomic investigation of 933 myelofibrosis patients, and identified interactions between germline and somatic variation in patients who required haematopoietic cell transplantation.
- Derek W. Brown
- , Weiyin Zhou
- & Mitchell J. Machiela
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Article
| Open AccessdevCellPy is a machine learning-enabled pipeline for automated annotation of complex multilayered single-cell transcriptomic data
A major informatic challenge in single cell RNA-sequencing analysis is the precise annotation of datasets where cells exhibit complex multilayered identities or transitory states. Here the authors present devCellPy, a Python-based package that enables the automated prediction of cell types across complex cellular hierarchies, species, and experimental systems with high accuracy, particularly for developmental scRNA-seq datasets.
- Francisco X. Galdos
- , Sidra Xu
- & Sean M. Wu
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Article
| Open AccessMsx1+ stem cells recruited by bioactive tissue engineering graft for bone regeneration
Critical-sized bone defects still present clinical challenges. Here the authors show that transplantation of neurotrophic supplement-incorporated hydrogel grafts promote full-thickness regeneration of the calvarium and perform scRNA-seq to reveal contributing stem/progenitor cells, notably a resident Msx1+ skeletal stem cell population.
- Xianzhu Zhang
- , Wei Jiang
- & Hongwei Ouyang
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Article
| Open AccessTaz protects hematopoietic stem cells from an aging-dependent decrease in PU.1 activity
Immune system function declines with age, a consequence of defects in hematopoietic stem cells (HSCs). Here the authors show that TAZ buffers age-related loss of PU.1 activity to maintain HSC functionality and identify the surface protein Clca3a1 as a marker of “young-like” HSCs, even in old mice.
- Kyung Mok Kim
- , Anna Mura-Meszaros
- & Björn von Eyss
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Article
| Open AccessCellular taxonomy of Hic1+ mesenchymal progenitor derivatives in the limb: from embryo to adult
Mesenchymal progenitors (MPs) are fundamental to tissue development and regeneration, however, their embryonic origin is unclear. Single cell-omics coupled with lineage tracing reveal a unique somite-derived MP hierarchy in limb morphogenesis.
- Martin Arostegui
- , R. Wilder Scott
- & T. Michael Underhill
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Article
| Open AccessMultiscale light-sheet organoid imaging framework
Live imaging of organoid growth remains a challenge: it requires long-term imaging of several samples simultaneously and dedicated analysis pipelines. Here the authors report an experimental and image processing framework to turn long-term light-sheet imaging of intestinal organoids into digital organoids.
- Gustavo de Medeiros
- , Raphael Ortiz
- & Prisca Liberali
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Article
| Open AccessSpatiotemporal single-cell regulatory atlas reveals neural crest lineage diversification and cellular function during tooth morphogenesis
The mechanisms that govern cell fate decisions of postmigratory cranial neural crest cells remain largely unknown. Here the authors present a spatiotemporal single-cell regulatory atlas tracking these cells’ dental lineage diversification.
- Junjun Jing
- , Jifan Feng
- & Yang Chai
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Article
| Open AccessPrimary cilia and SHH signaling impairments in human and mouse models of Parkinson’s disease
Here, the authors reveal using single-cell RNA sequencing that Parkinson’s disease (PD) patient-derived neuronal cells show altered primary cilia morphology and signaling suggesting cilia dysfunction may underlie PD pathogenesis.
- Sebastian Schmidt
- , Malte D. Luecken
- & Wolfgang Wurst
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Article
| Open AccessUltra-deep sequencing validates safety of CRISPR/Cas9 genome editing in human hematopoietic stem and progenitor cells
As CRISPR-based therapies enter the clinic, evaluation of safety remains a critical and active area of study. Here the authors use next generation sequencing to achieve high sequencing depth and demonstrate that clinically relevant delivery of high-fidelity Cas9 to primary HSPCs and ex vivo culture up to 10 days does not introduce or enrich for tumorigenic variants.
- M. Kyle Cromer
- , Valentin V. Barsan
- & Matthew H. Porteus
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Article
| Open AccessThy1 marks a distinct population of slow-cycling stem cells in the mouse epidermis
Koren and Feldman et al. report a distinct population of Thy1-expressing stem cells in the basal layer of the mouse epidermis. These stem cells do not compete neutrally and contribute long-term to both epidermal replenishment and wound repair.
- Elle Koren
- , Alona Feldman
- & Yaron Fuchs
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Article
| Open AccessPCGF6 controls neuroectoderm specification of human pluripotent stem cells by activating SOX2 expression
Variant Polycomb complexes can have tissue-specific roles during development. Here they show that PCGF6 controls lineage-specification in human PSCs by promoting neuroectoderm differentiation and repressing mesendoderm differentiation via distinct downstream targets.
- Xianchun Lan
- , Song Ding
- & Wei Jiang
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Article
| Open AccessFate mapping of hematopoietic stem cells reveals two pathways of native thrombopoiesis
Hematopoietic stem cells produce diverse cell lineages. Here, the authors apply single-cell RNA-seq, computational integration of non-perturbative approaches for fate-mapping, and mitotic tracking to chart lineage decisions in native hematopoiesis and identify megakaryocyte progenitors that directly link HSCs to megakaryocytes.
- Mina N. F. Morcos
- , Congxin Li
- & Alexander Gerbaulet
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Article
| Open AccessRibosome impairment regulates intestinal stem cell identity via ZAKɑ activation
Intestinal stem cells are responsible for replenishing cells within the high-turnover intestinal epithelium. Here they show that ribosome dynamics affect intestinal stem cell identity through a mechanism that is triggered by changes in nutrient availability.
- Joana Silva
- , Ferhat Alkan
- & William James Faller
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Article
| Open AccessROR2 regulates self-renewal and maintenance of hair follicle stem cells
Wnt signaling functions in tissue homeostasis and tumorigenesis. Here the authors show that ROR2, a Wnt receptor, plays roles not only in transducing Wnt signaling, but also in regulation of DNA damage response critical for stem cell maintenance.
- Anthony Veltri
- , Christopher M. R. Lang
- & Wen-Hui Lien
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Article
| Open AccessCDK9 activity switch associated with AFF1 and HEXIM1 controls differentiation initiation from epidermal progenitors
Epidermal progenitors are poised for differentiation, which allows for continual balance of self-renewal and differentiation. Here they show that the Super Elongation Complex regulates this process through direct regulation of a set of rapid response genes that involves a CDK9 activity switch.
- Sarah M. Lloyd
- , Daniel B. Leon
- & Xiaomin Bao
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Article
| Open AccessA multimodal iPSC platform for cystic fibrosis drug testing
Hundreds of mutations in the gene CFTR lead to cystic fibrosis and represent a challenge to developing therapeutics. Here, authors demonstrate the ability of airway cells derived from human iPSCs to model genotype-specific CFTR function as well as pharmacologic rescue of disease causing mutations.
- Andrew Berical
- , Rhianna E. Lee
- & Finn J. Hawkins
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Article
| Open AccessTranscriptomic and proteomic retinal pigment epithelium signatures of age-related macular degeneration
Age-related macular degeneration (AMD) is a leading cause of vision loss, and there is no approved treatment for AMD with geographic atrophy. Here, the authors used transcriptomic and proteomic analyses of patient induced pluripotent stem cell-derived retinal pigment epithelium to better understand disease mechanisms.
- Anne Senabouth
- , Maciej Daniszewski
- & Alice Pébay
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Article
| Open AccessA brain precursor atlas reveals the acquisition of developmental-like states in adult cerebral tumours
The link between neural development and tumourigenesis in adult glioma remains unclear. Here, the authors monitor the developmental stages of Sox2 + /− stem cells from a mouse model using single-cell RNA sequencing and suggest the acquisition of embryonic-like states in the adult glioma development.
- Akram A. Hamed
- , Daniel J. Kunz
- & Peter B. Dirks
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Article
| Open AccessN6-methyladenosine modification-mediated mRNA metabolism is essential for human pancreatic lineage specification and islet organogenesis
Ma et al. profile the dynamic landscape of m6A during pancreatic differentiation, and identify ALKBH5 as an essential m6A regulator supporting pancreatic differentiation, indicating a role for m6A-mediated mRNA metabolism in cell-fate specification.
- Xiaojie Ma
- , Jie Cao
- & Saiyong Zhu
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Article
| Open AccessPeriosteal stem cells control growth plate stem cells during postnatal skeletal growth
Intramembranous and endochondral bone formation have been considered to be independent processes mediated by independent stem cells. Here the authors show that periosteal stem cells participate in both types of bone formation, supporting endochondral formation by producing Ihh.
- Masayuki Tsukasaki
- , Noriko Komatsu
- & Hiroshi Takayanagi
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Article
| Open AccessZnT8 loss-of-function accelerates functional maturation of hESC-derived β cells and resists metabolic stress in diabetes
Immature function and fragility hinder application of hESC-derived β cells (SC-β cell) for diabetes cell therapy. Here, the authors identify ZnT8 as a gene editing target to enhance the insulin secretion and cell survival under metabolic stress by abolishing zinc transport in SC-β cells.
- Qing Ma
- , Yini Xiao
- & Weida Li
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Article
| Open AccessSomatic cell fate maintenance in mouse fetal testes via autocrine/paracrine action of AMH and activin B
Fate determination and maintenance of foetal testes in most animals occurs cell autonomously. Here the authors show in mouse XY embryos that Sertoli cell derived AMH and activin B together maintain Sertoli cell identity, and lack of both AMH and activin B leads to transdifferentiation into female granulosa cells.
- Karina F. Rodriguez
- , Paula R. Brown
- & Humphrey Hung-Chang Yao
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Article
| Open AccessSpatially resolved proteomic map shows that extracellular matrix regulates epidermal growth
Ling Leng et al. construct a hierarchical skin proteome map and identify an extracellular matrix glycoprotein TGFBI, which is located in basement membrane and could enhance the growth and function of epidermal stem cells and promote wound healing.
- Jun Li
- , Jie Ma
- & Ling Leng
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Article
| Open AccessInterchromosomal interaction of homologous Stat92E alleles regulates transcriptional switch during stem-cell differentiation
Asymmetric inheritance of organelles, proteins and RNAs occurs during stem cell division. Here the authors show the strength of pairing of homologous Stat92E loci, a stem cell-specific gene, changes immediately after the asymmetric division due to asymmetric inheritance of new histones to one of the daughter cells and is important for turning off gene expression in this cell as it differentiates.
- Matthew Antel
- , Romir Raj
- & Mayu Inaba
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Article
| Open AccessA Nodal enhanced micropeptide NEMEP regulates glucose uptake during mesendoderm differentiation of embryonic stem cells
Fu et al. identify the highly conserved, transmembrane micropeptide, NEMEP, as a direct target of Nodal signaling, essential for mesendoderm differentiation. NEMEP interacts with the glucose transporters GLUT1/GLUT3 and promotes glucose uptake.
- Haipeng Fu
- , Tingyu Wang
- & Qiaoran Xi
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Article
| Open AccessAcetyl-CoA-Carboxylase 1-mediated de novo fatty acid synthesis sustains Lgr5+ intestinal stem cell function
Here the authors report that inhibition of de novo fatty acid synthesis by deleting the enzyme Acetyl-CoA-Carboxylase 1 in the intestinal epithelium results in the loss of crypt structures and a specific decline in Lgr5+ intestinal epithelial stem cells.
- Shuting Li
- , Chia-Wen Lu
- & Matthias Lochner
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Article
| Open AccessGLI3 regulates muscle stem cell entry into GAlert and self-renewal
Primary cilia regulate the processing of the GLI transcription factors and Hedgehog signaling. Here, the authors show that cilia-related GLI3 controls both the quiescence-to-activation transition and self-renewal in muscle stem cells.
- Caroline E. Brun
- , Marie-Claude Sincennes
- & Michael A. Rudnicki
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Article
| Open AccessTET1 dioxygenase is required for FOXA2-associated chromatin remodeling in pancreatic beta-cell differentiation
Here the authors show that TET1 is required for the generation of functional insulin-producing cells, FOXA2 physically interacts with TET1 and contributes to specific recruitment of TET1 to mediate chromatin opening at the regulatory elements of pancreatic lineage determinants.
- Jianfang Li
- , Xinwei Wu
- & Ruiyu Xie
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Article
| Open AccessDynamic enlargement and mobilization of lipid droplets in pluripotent cells coordinate morphogenesis during mouse peri-implantation development
Prior to its implantation into the uterus, the mammalian embryo stores substantial lipids. Here the authors unveil how lipid storage and morphogenesis of pluripotent stem cells are fundamentally connected during peri-implantation development.
- King Hang Tommy Mau
- , Donja Karimlou
- & Véronique Azuara
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Article
| Open AccessThe splicing factor RBM17 drives leukemic stem cell maintenance by evading nonsense-mediated decay of pro-leukemic factors
Leukemic stem cells (LSCs) drive chemoresistance and relapse in acute myeloid leukemia. Here, the authors show that the splicing factor RBM17 supports LSCs through avoiding nonsense-mediated decay of pro-leukaemic factors such as the translation initiation factor EIF4A2.
- Lina Liu
- , Ana Vujovic
- & Yu Lu
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Article
| Open AccessIntestine-enriched apolipoprotein b orthologs are required for stem cell progeny differentiation and regeneration in planarians
Lipid metabolism regulates stem cell states and differentiation. Here, the authors demonstrate a requirement in planarians for Apolipoprotein B-mediated neutral lipid transport from intestinal stores to stem cells and their progeny during differentiation and whole-body regeneration.
- Lily L. Wong
- , Christina G. Bruxvoort
- & David J. Forsthoefel
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Article
| Open AccessG1/S restriction point coordinates phasic gene expression and cell differentiation
Somatic cells display phasic gene expression with compartmentalized gene expression during the cell cycle, while pluripotent cells lack phasic expression. Here, the authors describe a pathway linking microRNA regulation of the G1/S restriction point with phasic gene expression and cell differentiation during mammalian development.
- Brian DeVeale
- , Leqian Liu
- & Robert Blelloch
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Article
| Open AccessWiskott-Aldrich syndrome protein forms nuclear condensates and regulates alternative splicing
Wiskott-Aldrich syndrome is caused by mutations in WASP, but the underlying mechanisms remain to be explored. Here the authors reveal that WASP deficiency results in aberrant RNA splicing, and that WASP regulates the transcription of splicing factor genes and co-transcriptional RNA splicing via a phase-separation process that involves splicing factors and nascent RNA.
- Baolei Yuan
- , Xuan Zhou
- & Mo Li
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Article
| Open AccessTranscription factor-driven coordination of cell cycle exit and lineage-specification in vivo during granulocytic differentiation
Here the authors show that differentiation of haematopoietic stem cells into mature blood cells is primed by cell type-specific transcription factors at the enhancer level during early differentiation, before they confere promoter-driven growth arrest, and activate post-mitotic terminal differentiation.
- Kim Theilgaard-Mönch
- , Sachin Pundhir
- & Bo T. Porse
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Article
| Open AccessNANOG initiates epiblast fate through the coordination of pluripotency genes expression
Pluripotent epiblast cells segregate from primitive endoderm in the blastocyst inner cell mass (ICM). Here the authors show that mosaic epiblast differentiation during mouse and human preimplantation development initiates stochastically in ICM progenitors, independently of the FGF pathway, and requires NANOG activity
- Nicolas Allègre
- , Sabine Chauveau
- & Claire Chazaud
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Article
| Open AccessSatellite repeat transcripts modulate heterochromatin condensates and safeguard chromosome stability in mouse embryonic stem cells
Here the authors show satellite transcripts in mouse embryonic stem cells drive HP1α into droplets in vitro and also control HP1α organisation and association with chromatin in vivo. Depleting the satellite transcripts converts heterochromatin into a less dynamic and more static state and leads to chromosome instability.
- Clara Lopes Novo
- , Emily V. Wong
- & Peter J. Rugg-Gunn
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Article
| Open AccessComparative parallel multi-omics analysis during the induction of pluripotent and trophectoderm states
Ectopic transcription factor expression can reprogram mouse fibroblasts to pluripotent or trophoblast stem cells. Here the authors apply multi-omics analyses to the induction of pluripotency and trophoblast stem cell state from fibroblasts, comparing these with the changes in transcriptome of early embryonic cells.
- Mohammad Jaber
- , Ahmed Radwan
- & Yosef Buganim
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Article
| Open AccessZFP281-BRCA2 prevents R-loop accumulation during DNA replication
R-loops are prevalent in mammalian genomes and involved in many fundamental cellular processes. Here, Wang et al. report that ZFP281 cooperates with BRCA2 in preventing R-loop accumulation to facilitate DNA replication in embryonic stem cells.
- Yan Wang
- , Binbin Ma
- & Zhuojuan Luo
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