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Xiao S, Lu J, Sridhar B, Cao X, Yu P, Zhao T, Chen CC, McDee D, Sloofman L, Wang Y, Rivas-Astroza M, Telugu BPVL, Levasseur D, Zhang K, Liang H, Zhao JC, Tanaka TS, Stormo G, Zhong S. SMARCAD1 Contributes to the Regulation of Naive Pluripotency by Interacting with Histone Citrullination. Cell Rep 2017; 18:3117-3128. [PMID: 28355564 DOI: 10.1016/j.celrep.2017.02.070] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 02/08/2017] [Accepted: 02/23/2017] [Indexed: 10/19/2022] Open
Abstract
Histone citrullination regulates diverse cellular processes. Here, we report that SMARCAD1 preferentially associates with H3 arginine 26 citrullination (H3R26Cit) peptides present on arrays composed of 384 histone peptides harboring distinct post-transcriptional modifications. Among ten histone modifications assayed by ChIP-seq, H3R26Cit exhibited the most extensive genomewide co-localization with SMARCAD1 binding. Increased Smarcad1 expression correlated with naive pluripotency in pre-implantation embryos. In the presence of LIF, Smarcad1 knockdown (KD) embryonic stem cells lost naive state phenotypes but remained pluripotent, as suggested by morphology, gene expression, histone modifications, alkaline phosphatase activity, energy metabolism, embryoid bodies, teratoma, and chimeras. The majority of H3R26Cit ChIP-seq peaks occupied by SMARCAD1 were associated with increased levels of H3K9me3 in Smarcad1 KD cells. Inhibition of H3Cit induced H3K9me3 at the overlapping regions of H3R26Cit peaks and SMARCAD1 peaks. These data suggest a model in which SMARCAD1 regulates naive pluripotency by interacting with H3R26Cit and suppressing heterochromatin formation.
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Affiliation(s)
- Shu Xiao
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jia Lu
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Bharat Sridhar
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Xiaoyi Cao
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Pengfei Yu
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Tianyi Zhao
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Chieh-Chun Chen
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Darina McDee
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Laura Sloofman
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yang Wang
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Marcelo Rivas-Astroza
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | | | - Dana Levasseur
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Kang Zhang
- Department of Ophthalmology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jing Crystal Zhao
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Tetsuya S Tanaka
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Gary Stormo
- Department of Genetics, Washington University at St. Louis, St. Louis, MO 63108, USA
| | - Sheng Zhong
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
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Tanaka TS. Maintenance, Transgene Delivery, and Pluripotency Measurement of Mouse Embryonic Stem Cells. Methods Mol Biol 2015; 1341:295-319. [PMID: 25863786 DOI: 10.1007/7651_2015_228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
This chapter describes standard techniques to (1) maintain mouse embryonic stem cell culture, (2) deliver transgenes into mouse embryonic stem cells mediated by electroporation, nucleofection, lipofection, and retro/lentiviruses, and (3) assess the pluripotency of mouse embryonic stem cells. The last part of this chapter presents induction of random cell differentiation followed by the alkaline phosphatase and embryoid body formation assays, immunofluorescence microscopy, and the teratoma formation assay.
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Affiliation(s)
- Tetsuya S Tanaka
- Department of Biological Sciences, Chemical and Biomolecular Engineering, University of Notre Dame, 49 Galvin Life Sciences, Notre Dame, IN, 46556, USA.
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3
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Tsugeno Y, Sato F, Muragaki Y, Kato Y. Cell culture of human gingival fibroblasts, oral cancer cells and mesothelioma cells with serum-free media, STK1 and STK2. Biomed Rep 2014; 2:644-648. [PMID: 25054004 DOI: 10.3892/br.2014.306] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 06/25/2014] [Indexed: 12/20/2022] Open
Abstract
The majority of cells are cultured with Dulbecco's modified Eagle's medium (DMEM) or RPMI supplemented with fetal bovine serum (FBS), which contains numerous factors, including cytokines, nutrients and unknown growth factors. These factors may affect cell growth, apoptosis and differentiation. The serum-free medium, STK2, has been previously reported as suitable for the cell culture of human mesenchymal stem cells. However, how STK1 or STK2 affect the cell proliferation of normal and cancer cells remains unknown. The present study examined the growth of the human gingival fibroblast (HGF-1) cell-line and the HSC-3, CA9-22 and MSTO cancer cell-lines, cultured with STK1 and STK2. STK1 increased the cell proliferation of HGF-1 compared to DMEM by assessment with the 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)- 2H-tetrazolium (MTS) assay, whereas STK1 and STK2 markedly inhibited the cell proliferation of HSC-3 and MSTO. The cell proliferation rate of CA9-22 cultured with STK1 or STK2 for 96 h was ~2-fold higher than the rate for 24 h culture. The shape of the HSC-3 cells was also found to have changed to round when cultured with STK2. These results indicate that STK1 increased the cell proliferation of HGF-1 compared to DMEM, whereas the proliferation of HSC-3 and MSTO was inhibited by STK1 and STK2. Thus, STK1 and STK2 had different affects on the cell growth of HGF-1, CA9-22, HSC-3 and MSTO.
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Affiliation(s)
- Yuta Tsugeno
- Department of Pathology and Bioscience, Hirosaki University Graduate School of Medicine, Hirosaki, Aomori 036-8562, Japan
| | - Fuyuki Sato
- Department of Pathology and Bioscience, Hirosaki University Graduate School of Medicine, Hirosaki, Aomori 036-8562, Japan ; First Department of Pathology, Wakayama Medical University School of Medicine, Wakayama 641-0012, Japan
| | - Yasuteru Muragaki
- First Department of Pathology, Wakayama Medical University School of Medicine, Wakayama 641-0012, Japan
| | - Yukio Kato
- Department of Dental and Medical Biochemistry, Hiroshima University Graduate School of Biomedical Science, Hiroshima 734-8553, Japan
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4
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Poh YC, Chen J, Hong Y, Yi H, Zhang S, Chen J, Wu DC, Wang L, Jia Q, Singh R, Yao W, Tan Y, Tajik A, Tanaka TS, Wang N. Generation of organized germ layers from a single mouse embryonic stem cell. Nat Commun 2014; 5:4000. [PMID: 24873804 PMCID: PMC4050279 DOI: 10.1038/ncomms5000] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 04/29/2014] [Indexed: 12/15/2022] Open
Abstract
Mammalian inner cell mass cells undergo lineage-specific differentiation into germ
layers of endoderm, mesoderm and ectoderm during gastrulation. It has been a
long-standing challenge in developmental biology to replicate these organized germ
layer patterns in culture. Here we present a method of generating organized germ
layers from a single mouse embryonic stem cell cultured in a soft fibrin matrix.
Spatial organization of germ layers is regulated by cortical tension of the colony,
matrix dimensionality and softness, and cell–cell adhesion. Remarkably,
anchorage of the embryoid colony from the 3D matrix to collagen-1-coated 2D
substrates of ~1 kPa results in self-organization of all three
germ layers: ectoderm on the outside layer, mesoderm in the middle and endoderm at
the centre of the colony, reminiscent of generalized gastrulating chordate embryos.
These results suggest that mechanical forces via cell–matrix and
cell–cell interactions are crucial in spatial organization of germ layers
during mammalian gastrulation. This new in vitro method could be used to gain
insights on the mechanisms responsible for the regulation of germ layer
formation. The three germ layers are formed from the inner cell mass of the
mammalian embryo during gastrulation. Here, the authors present a method by which a
single mouse embryonic stem cell, derived from inner cell mass, differentiates into the
three germ layers in a self-organized manner when cultured in soft fibrin gel.
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Affiliation(s)
- Yeh-Chuin Poh
- 1] Laboratory for Cell Biomechanics and Regenerative Medicine, Department of Biomedical Engineering, School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China [2] Department of Mechanical Science and Engineering, College of Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Junwei Chen
- Laboratory for Cell Biomechanics and Regenerative Medicine, Department of Biomedical Engineering, School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Ying Hong
- Laboratory for Cell Biomechanics and Regenerative Medicine, Department of Biomedical Engineering, School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Haiying Yi
- Laboratory for Cell Biomechanics and Regenerative Medicine, Department of Biomedical Engineering, School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Shuang Zhang
- Laboratory for Cell Biomechanics and Regenerative Medicine, Department of Biomedical Engineering, School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Junjian Chen
- Laboratory for Cell Biomechanics and Regenerative Medicine, Department of Biomedical Engineering, School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Douglas C Wu
- Department of Mechanical Science and Engineering, College of Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Lili Wang
- Laboratory for Cell Biomechanics and Regenerative Medicine, Department of Biomedical Engineering, School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Qiong Jia
- Laboratory for Cell Biomechanics and Regenerative Medicine, Department of Biomedical Engineering, School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Rishi Singh
- Department of Mechanical Science and Engineering, College of Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Wenting Yao
- Laboratory for Cell Biomechanics and Regenerative Medicine, Department of Biomedical Engineering, School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Youhua Tan
- 1] Laboratory for Cell Biomechanics and Regenerative Medicine, Department of Biomedical Engineering, School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China [2] Department of Mechanical Science and Engineering, College of Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Arash Tajik
- Department of Mechanical Science and Engineering, College of Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Tetsuya S Tanaka
- 1] Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA [2] Department of Biological Science, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Ning Wang
- 1] Laboratory for Cell Biomechanics and Regenerative Medicine, Department of Biomedical Engineering, School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China [2] Department of Mechanical Science and Engineering, College of Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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5
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Kurz V, Tanaka T, Timp G. Single cell transfection with single molecule resolution using a synthetic nanopore. NANO LETTERS 2014; 14:604-11. [PMID: 24471806 DOI: 10.1021/nl403789z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
We report the development of a single cell gene delivery system based on electroporation using a synthetic nanopore, that is not only highly specific and very efficient but also transfects with single molecule resolution at low voltage (1 V) with minimal perturbation to the cell. Such a system can be used to control gene expression with unprecedented precision--no other method offers such capabilities.
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Affiliation(s)
- Volker Kurz
- Department of Electrical Engineering, University of Notre Dame , Notre Dame, Indiana 46556, United States
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Li Y, Drnevich J, Akraiko T, Band M, Li D, Wang F, Matoba R, Tanaka TS. Gene expression profiling reveals the heterogeneous transcriptional activity of Oct3/4 and its possible interaction with Gli2 in mouse embryonic stem cells. Genomics 2013; 102:456-67. [PMID: 24121003 DOI: 10.1016/j.ygeno.2013.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 09/27/2013] [Accepted: 09/30/2013] [Indexed: 01/19/2023]
Abstract
We examined the transcriptional activity of Oct3/4 (Pou5f1) in mouse embryonic stem cells (mESCs) maintained under standard culture conditions to gain a better understanding of self-renewal in mESCs. First, we built an expression vector in which the Oct3/4 promoter drives the monocistronic transcription of Venus and a puromycin-resistant gene via the foot-and-mouth disease virus self-cleaving peptide T2A. Then, a genetically-engineered mESC line with the stable integration of this vector was isolated and cultured in the presence or absence of puromycin. The cultures were subsequently subjected to Illumina expression microarray analysis. We identified approximately 4600 probes with statistically significant differential expression. The genes involved in nucleic acid synthesis were overrepresented in the probe set associated with mESCs maintained in the presence of puromycin. In contrast, the genes involved in cell differentiation were overrepresented in the probe set associated with mESCs maintained in the absence of puromycin. Therefore, it is suggested with these data that the transcriptional activity of Oct3/4 fluctuates in mESCs and that Oct3/4 plays an essential role in sustaining the basal transcriptional activities required for cell duplication in populations with equal differentiation potential. Heterogeneity in the transcriptional activity of Oct3/4 was dynamic. Interestingly, we found that genes involved in the hedgehog signaling pathway showed unique expression profiles in mESCs and validated this observation by RT-PCR analysis. The expression of Gli2, Ptch1 and Smo was consistently detected in other types of pluripotent stem cells examined in this study. Furthermore, the Gli2 protein was heterogeneously detected in mESC nuclei by immunofluorescence microscopy and this result correlated with the detection of the Oct3/4 protein. Finally, forced activation of Gli2 in mESCs increased their proliferation rate. Collectively, it is suggested with these results that Gli2 may play a novel role in the self-renewal of pluripotent stem cells.
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Affiliation(s)
- Yanzhen Li
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jenny Drnevich
- The W.M. Keck Center for Comparative and Functional Genomics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tatiana Akraiko
- The W.M. Keck Center for Comparative and Functional Genomics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Mark Band
- The W.M. Keck Center for Comparative and Functional Genomics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Dong Li
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Fei Wang
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ryo Matoba
- DNA Chip Research Inc., Yokohama, Kanagawa 230-0045, Japan
| | - Tetsuya S Tanaka
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA; Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA.
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7
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Kramer AS, Harvey AR, Plant GW, Hodgetts SI. Systematic Review of Induced Pluripotent Stem Cell Technology as a Potential Clinical Therapy for Spinal Cord Injury. Cell Transplant 2013; 22:571-617. [DOI: 10.3727/096368912x655208] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Transplantation therapies aimed at repairing neurodegenerative and neuropathological conditions of the central nervous system (CNS) have utilized and tested a variety of cell candidates, each with its own unique set of advantages and disadvantages. The use and popularity of each cell type is guided by a number of factors including the nature of the experimental model, neuroprotection capacity, the ability to promote plasticity and guided axonal growth, and the cells' myelination capability. The promise of stem cells, with their reported ability to give rise to neuronal lineages to replace lost endogenous cells and myelin, integrate into host tissue, restore functional connectivity, and provide trophic support to enhance and direct intrinsic regenerative ability, has been seen as a most encouraging step forward. The advent of the induced pluripotent stem cell (iPSC), which represents the ability to “reprogram” somatic cells into a pluripotent state, hails the arrival of a new cell transplantation candidate for potential clinical application in therapies designed to promote repair and/or regeneration of the CNS. Since the initial development of iPSC technology, these cells have been extensively characterized in vitro and in a number of pathological conditions and were originally reported to be equivalent to embryonic stem cells (ESCs). This review highlights emerging evidence that suggests iPSCs are not necessarily indistinguishable from ESCs and may occupy a different “state” of pluripotency with differences in gene expression, methylation patterns, and genomic aberrations, which may reflect incomplete reprogramming and may therefore impact on the regenerative potential of these donor cells in therapies. It also highlights the limitations of current technologies used to generate these cells. Moreover, we provide a systematic review of the state of play with regard to the use of iPSCs in the treatment of neurodegenerative and neuropathological conditions. The importance of balancing the promise of this transplantation candidate in the light of these emerging properties is crucial as the potential application in the clinical setting approaches. The first of three sections in this review discusses (A) the pathophysiology of spinal cord injury (SCI) and how stem cell therapies can positively alter the pathology in experimental SCI. Part B summarizes (i) the available technologies to deliver transgenes to generate iPSCs and (ii) recent data comparing iPSCs to ESCs in terms of characteristics and molecular composition. Lastly, in (C) we evaluate iPSC-based therapies as a candidate to treat SCI on the basis of their neurite induction capability compared to embryonic stem cells and provide a summary of available in vivo data of iPSCs used in SCI and other disease models.
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Affiliation(s)
- Anne S. Kramer
- Spinal Cord Repair Laboratory, School of Anatomy, Physiology and Human Biology, The University of Western Australia, Perth, Western Australia
| | - Alan R. Harvey
- Spinal Cord Repair Laboratory, School of Anatomy, Physiology and Human Biology, The University of Western Australia, Perth, Western Australia
| | - Giles W. Plant
- Stanford Partnership for Spinal Cord Injury and Repair, Stanford Institute for Neuro-Innovation and Translational Neurosciences, Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Stuart I. Hodgetts
- Spinal Cord Repair Laboratory, School of Anatomy, Physiology and Human Biology, The University of Western Australia, Perth, Western Australia
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Abstract
Spatial organization of different epigenomic marks was used to infer functions of the epigenome. It remains unclear what can be learned from the temporal changes of the epigenome. Here, we developed a probabilistic model to cluster genomic sequences based on the similarity of temporal changes of multiple epigenomic marks during a cellular differentiation process. We differentiated mouse embryonic stem (ES) cells into mesendoderm cells. At three time points during this differentiation process, we used high-throughput sequencing to measure seven histone modifications and variants—H3K4me1/2/3, H3K27ac, H3K27me3, H3K36me3, and H2A.Z; two DNA modifications—5-mC and 5-hmC; and transcribed mRNAs and noncoding RNAs (ncRNAs). Genomic sequences were clustered based on the spatiotemporal epigenomic information. These clusters not only clearly distinguished gene bodies, promoters, and enhancers, but also were predictive of bidirectional promoters, miRNA promoters, and piRNAs. This suggests specific epigenomic patterns exist on piRNA genes much earlier than germ cell development. Temporal changes of H3K4me2, unmethylated CpG, and H2A.Z were predictive of 5-hmC changes, suggesting unmethylated CpG and H3K4me2 as potential upstream signals guiding TETs to specific sequences. Several rules on combinatorial epigenomic changes and their effects on mRNA expression and ncRNA expression were derived, including a simple rule governing the relationship between 5-hmC and gene expression levels. A Sox17 enhancer containing a FOXA2 binding site and a Foxa2 enhancer containing a SOX17 binding site were identified, suggesting a positive feedback loop between the two mesendoderm transcription factors. These data illustrate the power of using epigenome dynamics to investigate regulatory functions.
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Puri MC, Nagy A. Concise Review: Embryonic Stem Cells Versus Induced Pluripotent Stem Cells: The Game Is On. Stem Cells 2011; 30:10-4. [PMID: 22102565 DOI: 10.1002/stem.788] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Mira C Puri
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
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