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Prediction model construction of mouse stem cell pluripotency using CpG and non-CpG DNA methylation markers

Soobok Joe, Hojung Nam
2020 BMC Bioinformatics  
In this study, we investigated CpG and non-CpG methylation in relation to mouse stem cell pluripotency and developed a model thereon that successfully predicts the pluripotency of mouse ESCs.  ...  Here, using paired scBS-seq and scRNA-seq data of mice, we constructed a machine learning model that predicts degrees of pluripotency for mouse ESCs.  ...  Availability of data and materials We used public datasets for this study.  ... 
doi:10.1186/s12859-020-3448-3 pmid:32366211 fatcat:hfnbzvadejhk5lam4jguqvklpu

Genomic Approaches to Deconstruct Pluripotency

Yuin-Han Loh, Lin Yang, Jimmy Chen Yang, Hu Li, James J. Collins, George Q. Daley
2011 Annual review of genomics and human genetics (Print)  
Both types of pluripotent stem cells provide great potential for fundamental studies of tissue differentiation, and hold promise for disease modeling, drug development, and regenerative medicine.  ...  of self-renewal and pluripotency.  ...  Differential methylation of tissue-and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts. Nat. Genet. 41:1350-53 26.  ... 
doi:10.1146/annurev-genom-082410-101506 pmid:21801025 pmcid:PMC3652340 fatcat:qtegzsvu4vguhmawaunevizfqm

Predictive modeling of single-cell DNA methylome data enhances integration with transcriptome data [article]

Yasin Uzun, Hao Wu, Kai Tan
2020 biorxiv/medrxiv   pre-print
Although such data is rather sparse, they are sufficient to train supervised models that capture the complex relationship between DNA methylation and gene expression and predict gene activities at single-cell  ...  The advent of multi-omics data enables measurement of both DNA methylation and gene expression for the same single cells.  ...  This work was supported by National Institutes of Health of United States of America grants CA226187, CA233285, and HL156090 (to K.T.), a grant from the Leona M. and Harry B.  ... 
doi:10.1101/2020.06.05.137000 fatcat:i3tu4k3xvffuxbvzeaga3xnplq

Identification of an epigenetic signature in human induced pluripotent stem cells using a linear machine learning model

Koichiro Nishino, Ken Takasawa, Kohji Okamura, Yoshikazu Arai, Asato Sekiya, Hidenori Akutsu, Akihiro Umezawa
2020 Human Cell  
The use of human induced pluripotent stem cells (iPSCs), used as an alternative to human embryonic stem cells (ESCs), is a potential solution to challenges, such as immune rejection, and does not involve  ...  Therefore, in this study, we established a linear classification-based learning model to distinguish among ESCs, iPSCs, embryonal carcinoma cells (ECCs), and somatic cells on the basis of their DNA methylation  ...  Yukie Toyonaga, and Ms. Kae Inoue for performing cell culture. This research was supported in part by AMED under Grant number JP18bm0704003 and 19bk0104092h0001 to K. N.  ... 
doi:10.1007/s13577-020-00446-3 pmid:33047283 pmcid:PMC7788050 fatcat:fk2eqitl7bevhaznpeakkjmxa4

Predictive modeling of single-cell DNA methylome data enhances integration with transcriptome data

Yasin Uzun, Hao Wu, Kai Tan
2020 Genome Research  
start site for predicting gene expression, and increased predictive power of methylation signals in promoters located outside CpG islands and shores.  ...  Although such data is rather sparse, they are sufficient to train supervised models that capture the complex relationship between DNA methylation and gene expression and predict gene activities at single-cell  ...  Acknowledgements We thank the Research Information Services at the Children's Hospital of Philadelphia for providing computing support. This work was supported by National Institutes of  ... 
doi:10.1101/gr.267047.120 pmid:33219054 pmcid:PMC7849382 fatcat:uzy3t7snivdjhbivrjkfpnujhu

Development of an inducible caspase-9 safety switch for pluripotent stem cell–based therapies

Chuanfeng Wu, So Gun Hong, Thomas Winkler, David M Spencer, Alexander Jares, Brian Ichwan, Alina Nicolae, Vicky Guo, Andre Larochelle, Cynthia E Dunbar
2014 Molecular Therapy: Methods & Clinical Development  
EF1α-iCasp9 expression was downregulated during in vitro and in vivo differentiation due to DNA methylation at CpG islands within the promoter, and methylation, and thus decreased expression, could be  ...  Induced pluripotent stem cell (iPSC) therapies offer a promising path for patient-specific regenerative medicine.  ...  We thank Jichun Chen and Marie Desierto from the Hematology Branch, and ZuXi Yu from the NHLBI pathology core facility for their assistance with teratoma assays, and Vivian Diaz from NIH Mouse Imaging  ... 
doi:10.1038/mtm.2014.53 pmid:26052521 pmcid:PMC4448736 fatcat:3vppqkrrvzgphh5jjuytbuzii4

X Chromosome Dosage Influences DNA Methylation Dynamics during Reprogramming to Mouse iPSCs

Vincent Pasque, Rahul Karnik, Constantinos Chronis, Paula Petrella, Justin Langerman, Giancarlo Bonora, Juan Song, Lotte Vanheer, Anupama Sadhu Dimashkie, Alexander Meissner, Kathrin Plath
2018 Stem Cell Reports  
We analyzed DNA methylation changes during reprogramming of male and female somatic cells and in resulting induced pluripotent stem cells (iPSCs).  ...  A dramatic difference in global DNA methylation between male and female cells characterizes mouse embryonic stem cells (ESCs), unlike somatic cells.  ...  ACKNOWLEDGMENTS We thank members of the Plath and Pasque labs for feedback on the manuscript, F. Codrea  ... 
doi:10.1016/j.stemcr.2018.03.019 pmid:29681539 pmcid:PMC5995367 fatcat:wunlgctwxfcxtggnfwapajj6j4

Transition to naïve human pluripotency mirrors pan-cancer DNA hypermethylation

Hemalvi Patani, Michael D. Rushton, Jonathan Higham, Saul A. Teijeiro, David Oxley, Pedro Cutillas, Duncan Sproul, Gabriella Ficz
2020 Nature Communications  
Here we show that resetting from primed to naïve human pluripotency results in acquisition of a DNA methylation landscape mirroring the cancer DNA methylome, with gradual hypermethylation of bivalent developmental  ...  Additionally, we observe that promoter CpG island hypermethylation is not restricted solely to emerging naïve cells, suggesting that it is a feature of a heterogeneous intermediate population during resetting  ...  Data for human naive resetting methods were obtained from GSE60945, GSE76970, GSE90168, data for mouse 2i and serum ESCs from GSE42923, and data for human and mouse in vivo development from GSE34864 and  ... 
doi:10.1038/s41467-020-17269-3 pmid:32699299 fatcat:av5x25ebw5fnlhc5szh6monhce

An interspecies analysis reveals a key role for unmethylated CpG dinucleotides in vertebrate Polycomb complex recruitment

Magnus D Lynch, Andrew J H Smith, Marco De Gobbi, Maria Flenley, Jim R Hughes, Douglas Vernimmen, Helena Ayyub, Jacqueline A Sharpe, Jacqueline A Sloane-Stanley, Linda Sutherland, Stephen Meek, Tom Burdon (+3 others)
2011 EMBO Journal  
This model is supported by analysis of DNA methyltransferase-deficient embryonic stem cells. The EMBO Journal VOL 31 | NO 2 | 2012 EMBO THE EMBO JOURNAL THE EMBO JOURNAL  ...  In this study, we compare orthologous chromosomal regions for which the human locus establishes prominent sites of Polycomb complex recruitment in pluripotent stem cells, whereas the corresponding mouse  ...  Acknowledgements We thank S Butler for assistance with tissue culture, the Computational Biology Research Group, Oxford University for bioinformatic support and T Milne for critical reading of the manuscript  ... 
doi:10.1038/emboj.2011.399 pmid:22056776 pmcid:PMC3261560 fatcat:f7yffl6lyzfe5ps6cppxobsllq

Epigenetics, stem cells and epithelial cell fate

Audrey Vincent, Isabelle Van Seuningen
2009 Differentiation  
This review will focus on epithelial cells of the digestive tract, intestinal stem cell niches being a model of choice to understand how epigenetic changes can drive nuclear programming and specific cell  ...  Establishment and maintenance of epigenetic profiles are essential steps of development during which stem cells, despite identical genetic information, will acquire different and selective gene expression  ...  Thus, models and techniques used to isolate the intestinal crypts at different heights along the crypt-villus axis (Suzuki et al., 2008) and the recent identification of intestinal stem cell markers  ... 
doi:10.1016/j.diff.2009.07.002 pmid:19632029 fatcat:dfvne5u5uzhprm45ad6jhykyde

Chromatin Methylation Abnormalities in Autosomal Dominant Polycystic Kidney Disease

Jing Xu, Cheng Xue, Xiaodong Wang, Lei Zhang, Changlin Mei, Zhiguo Mao
2022 Frontiers in Medicine  
Chromatin methylation is a very important category of PKD epigenetic changes and mostly involves DNA, histone, and RNA methylation.  ...  , can be used as diagnostic or prognostic biomarkers to predict PKD progression.  ...  The research idea and study design were devised by ZM and CM. LZ revised the manuscript. JX and CX were the primary authors of this manuscript. XW finished data collection and statistical analysis.  ... 
doi:10.3389/fmed.2022.921631 pmid:35865176 pmcid:PMC9294145 fatcat:ilnl7v4l2zakfjb22dbhqm4kma

Mediators and dynamics of DNA methylation

Robert Shoemaker, Wei Wang, Kun Zhang
2010 Wiley Interdisciplinary Reviews: Systems Biology and Medicine  
These DNA methylation patterns can be modified via DNA demethylation, which is important for induced pluripotent stem reprogramming and primordial germ cells.  ...  As an inherited epigenetic marker occurring mainly on cytosines at CpG dinucleotides, DNA methylation occurs across many higher eukaryotic organisms.  ...  However, examples of non-CpG methylation are found in plants and human embryonic stem cells.  ... 
doi:10.1002/wsbm.124 pmid:20878927 fatcat:axxajm2w45fdviow5br7nlf5se

Genome-scale DNA methylation maps of pluripotent and differentiated cells

Alexander Meissner, Tarjei S. Mikkelsen, Hongcang Gu, Marius Wernig, Jacob Hanna, Andrey Sivachenko, Xiaolan Zhang, Bradley E. Bernstein, Chad Nusbaum, David B. Jaffe, Andreas Gnirke, Rudolf Jaenisch (+1 others)
2008 Nature  
conserved non-coding elements, transposons and other genomic features, for mouse embryonic stem cells, embryonic-stem-cell-derived and primary neural cells, and eight other primary tissues.  ...  Using high-throughput reduced representation bisulphite sequencing 6 and single-molecule-based sequencing, we generated DNA methylation maps covering most CpG islands, and a representative sampling of  ...  This research was supported by funds from the National Human Genome Research Institute, the National Cancer Institute, and the Broad Institute of MIT and Harvard.  ... 
doi:10.1038/nature07107 pmid:18600261 pmcid:PMC2896277 fatcat:zt6h36jl2vajtinpnjhrjav4pq

Epigenetic targeting of the Nanog pathway and signaling networks during chemical carcinogenesis

Stella Tommasi, Albert Zheng, Jae-In Yoon, Ahmad Besaratinia
2014 Carcinogenesis  
Members of the Nanog pathway that establishes and maintains pluripotency in embryonic stem cells and possibly triggers uncontrolled proliferation of neoplastic cells are preferential targets of aberrant  ...  Here, we demonstrate characteristic CpG island gain/loss of methylation and demethylation of repetitive DNA elements in carcinogen-treated mice, dependent on tumor progression.  ...  We also thank the City of Hope Bioinformatics Core Facility for initial microarray data analysis and Dr Sharon Wilczynski, from the Department of Anatomic Pathology, for help with H&E analysis.  ... 
doi:10.1093/carcin/bgu026 pmid:24480805 fatcat:gamvyro7izdnthhxiu7l3csiwm

Ribosomal DNA harbors an evolutionarily conserved clock of biological aging

Meng Wang, Bernardo Lemos
2019 Genome Research  
The rDNA is also a significant target of DNA methylation that silences supernumerary rDNA units and regulates nucleolar activity.  ...  Here, we introduce an age clock built exclusively with CpG methylation within the rDNA.  ...  Acknowledgments We thank several members of the Lemos laboratory for their comments and feedback during development of this work and three anonymous reviewers for their comments on an early draft of the  ... 
doi:10.1101/gr.241745.118 pmid:30765617 pmcid:PMC6396418 fatcat:cszeqsk3c5bk7ma6bburznjjey
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