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Differences in DNA Methylation and Functional Expression in Lactase Persistent and Non-persistent Individuals. Sci Rep 2018; 8:5649. [PMID: 29618745 PMCID: PMC5884863 DOI: 10.1038/s41598-018-23957-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 03/21/2018] [Indexed: 02/07/2023] Open
Abstract
In humans the expression of lactase changes during post-natal development, leading to phenotypes known as lactase persistence and non-persistence. Polymorphisms within the lactase gene (LCT) enhancer, in particular the −13910C > T, but also others, are linked to these phenotypes. We were interested in identifying dynamic mediators of LCT regulation, beyond the genotype at −13910C > T. To this end, we investigated two levels of lactase regulation in human intestinal samples obtained from New England children and adolescents of mixed European ancestry: differential expression of transcriptional regulators of LCT, and variations in DNA methylation, and their relation to phenotype. Variations in expression of CDX2, POU2F1, GATA4, GATA6, and HNF1α did not correlate with phenotype. However, an epigenome-wide approach using the Illumina Infinium HM450 bead chip identified a differentially methylated position in the LCT promoter where methylation levels are associated with the genotype at −13910C > T, the persistence/non-persistence phenotype and lactase enzymatic activity. DNA methylation levels at this promoter site and CpGs in the LCT enhancer are associated with genotype. Indeed, taken together they have a higher power to predict lactase phenotypes than the genotype alone.
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52
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Decato BE, Lopez-Tello J, Sferruzzi-Perri AN, Smith AD, Dean MD. DNA Methylation Divergence and Tissue Specialization in the Developing Mouse Placenta. Mol Biol Evol 2017; 34:1702-1712. [PMID: 28379409 DOI: 10.1093/molbev/msx112] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The placental epigenome plays a vital role in regulating mammalian growth and development. Aberrations in placental DNA methylation are linked to several disease states, including intrauterine growth restriction and preeclampsia. Studying the evolution and development of the placental epigenome is critical to understanding the origin and progression of such diseases. Although high-resolution studies have found substantial variation between placental methylomes of different species, the nature of methylome variation has yet to be characterized within any individual species. We conducted a study of placental DNA methylation at high resolution in multiple strains and closely related species of house mice (Mus musculus musculus, Mus m. domesticus, and M. spretus), across developmental timepoints (embryonic days 15-18), and between two distinct layers (labyrinthine transport and junctional endocrine). We observed substantial genome-wide methylation heterogeneity in mouse placenta compared with other differentiated tissues. Species-specific methylation profiles were concentrated in retrotransposon subfamilies, specifically RLTR10 and RLTR20 subfamilies. Regulatory regions such as gene promoters and CpG islands displayed cross-species conservation, but showed strong differences between layers and developmental timepoints. Partially methylated domains exist in the mouse placenta and widen during development. Taken together, our results characterize the mouse placental methylome as a highly heterogeneous and deregulated landscape globally, intermixed with actively regulated promoter and retrotransposon sequences.
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Affiliation(s)
- Benjamin E Decato
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA
| | - Jorge Lopez-Tello
- Department of Physiology, Development, and Neuroscience, Centre for Trophoblast Research, University of Cambridge, Cambridge, United Kingdom
| | - Amanda N Sferruzzi-Perri
- Department of Physiology, Development, and Neuroscience, Centre for Trophoblast Research, University of Cambridge, Cambridge, United Kingdom
| | - Andrew D Smith
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA
| | - Matthew D Dean
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA
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53
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Varga J, Greten FR. Cell plasticity in epithelial homeostasis and tumorigenesis. Nat Cell Biol 2017; 19:1133-1141. [PMID: 28945230 DOI: 10.1038/ncb3611] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 08/11/2017] [Indexed: 02/06/2023]
Abstract
The adult organism is characterized by remarkable plasticity, which enables efficient regeneration and restoration of homeostasis after damage. When aberrantly activated, this plasticity contributes to tumour initiation and progression. Here we review recent advances in this field with a focus on cell fate changes and the epithelial-mesenchymal transition-two distinct, yet closely related, forms of plasticity with fundamental roles in homeostasis and cancer.
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Affiliation(s)
- Julia Varga
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Paul-Ehrlich-Str. 42-44, 60596 Frankfurt/Main, Germany
| | - Florian R Greten
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Paul-Ehrlich-Str. 42-44, 60596 Frankfurt/Main, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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54
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Kazakevych J, Sayols S, Messner B, Krienke C, Soshnikova N. Dynamic changes in chromatin states during specification and differentiation of adult intestinal stem cells. Nucleic Acids Res 2017; 45:5770-5784. [PMID: 28334816 PMCID: PMC5449638 DOI: 10.1093/nar/gkx167] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 03/02/2017] [Indexed: 02/07/2023] Open
Abstract
Epigenetic mechanisms, including chromatin structure, chromatin dynamics and histone modifications play an important role for maintenance and differentiation of pluripotent embryonic stem cells. However, little is known about the molecular mechanisms of adult stem cell specification and differentiation. Here, we used intestinal stem cells (ISCs) as a model system to reveal the epigenetic changes coordinating gene expression programs during these processes. We found that two distinct epigenetic mechanisms participate in establishing the transcriptional program promoting ISC specification from embryonic progenitors. A large number of adult ISC signature genes are targets of repressive DNA methylation in embryonic intestinal epithelial progenitors. On the other hand, genes essential for embryonic development acquire H3K27me3 and are silenced during ISC specification. We also show that the repression of ISC signature genes as well as the activation of enterocyte specific genes is accompanied by a global loss of H2A.Z during ISCs differentiation. Our results reveal that, already during ISC specification, an extensive remodeling of chromatin both at promoters and distal regulatory elements organizes transcriptional landscapes operating in differentiated enterocytes, thus explaining similar chromatin modification patterns in the adult gut epithelium.
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Affiliation(s)
| | - Sergi Sayols
- Institute of Molecular Biology, D-55128 Mainz, Germany
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55
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Smith RJ, Rao-Bhatia A, Kim TH. Signaling and epigenetic mechanisms of intestinal stem cells and progenitors: insight into crypt homeostasis, plasticity, and niches. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2017. [PMID: 28644919 DOI: 10.1002/wdev.281] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The rapid turnover of intestinal epithelial cells is maintained by a small number of stem cells located in pocket-like gland structures called crypts. While our understanding of the identity and function of intestinal stem cells (ISCs) has rapidly progressed, epigenetic and transcriptional regulation in crypt stem cell and progenitor pools remains an active field of investigation. Surrounded by various types of cells in the stroma, crypt progenitors display high levels of plasticity, harboring the ability to interconvert in the face of epithelial damage. Recent studies analyzing epigenetic patterns of intestinal epithelial cells have provided evidence that plasticity is maintained by a broadly permissive epigenomic state, wherein cell-lineage specification is directed through activation of signaling pathways and transcription factor (TF) expression. New studies also have shown that the ISC niche, which is comprised of surrounding epithelial and mesenchymal tissues, plays a crucial role in supporting the maintenance and differentiation of stem cells by providing contextual information in the form of signaling cascades, such as Wnt, Notch, and Hippo. These cascades ultimately govern TF expression to promote early cell-lineage decisions in both crypt stem cells and progenitors. Highlighting recent studies investigating signaling, transcriptional, and epigenetic mechanisms of intestinal epithelial cells, we will discuss the mechanisms underlying crypt homeostasis, plasticity, and niches. WIREs Dev Biol 2017, 6:e281. doi: 10.1002/wdev.281 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Ryan J Smith
- Program of Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Abilasha Rao-Bhatia
- Program of Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Tae-Hee Kim
- Program of Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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56
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Huang CZ, Xu JH, Zhong W, Xia ZS, Wang SY, Cheng D, Li JY, Wu TF, Chen QK, Yu T. Sox9 transcriptionally regulates Wnt signaling in intestinal epithelial stem cells in hypomethylated crypts in the diabetic state. Stem Cell Res Ther 2017; 8:60. [PMID: 28279198 PMCID: PMC5345140 DOI: 10.1186/s13287-017-0507-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Revised: 01/19/2017] [Accepted: 02/11/2017] [Indexed: 12/16/2022] Open
Abstract
Background Distinctive structures called crypts harbor intestinal epithelial stem cells (IESCs) which generate progenitor and terminally differentiated cells in the intestinal epithelium. Mammalian IESCs and their daughter cells require the participation of DNA methylation and the transcription factor Sox9 for proliferation and differentiation. However, the association between Sox9 and DNA methylation in this process remains elusive. Methods The DNA methylation of small intestinal epithelial crypts in db/db mice was detected via combining methylated DNA immunoprecipitation with microarray hybridization. DNA methylation of Sox9 promoter in crypts and IESCs was validated using bisulfite sequence analysis. The target sequence of the transcription factor Sox9 in IESCs was investigated via chromatin immunoprecipitation (ChIP) combined with deep sequencing (ChIP-seq). Results Increased Sox9 expression is accompanied by the loss of methylation in its promoter in IESCs. Sox9 targets the enhancers of the Wnt signaling pathway-related genes. Sox9 predominantly acts as a transcriptional activator at proximal enhancers of Wnt4, Tab2, Sox4, and Fzd8, but also functions as a potential transcriptional inhibitor at a distant enhancer of Cdk1. Lack of Sox9 transcriptional activation in specific repressors of the Wnt signaling pathway leads to the loss of intrinsic inhibitory action and ultimately produces overactivation of this pathway in db/db mice. Conclusions Our study sheds light on the connections among DNA methylation, transcription factor modulation, and Wnt signaling in IESCs in the diabetic state. Hypomethylation in the Sox9 promoter is correlated to increased Sox9 expression in db/db IESCs. Although there is increased expression of Sox9 in db/db IESCs, the loss of Sox9 transcriptional activation in specific repressors of the Wnt signaling pathway might result in abnormalities in this pathway. Electronic supplementary material The online version of this article (doi:10.1186/s13287-017-0507-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Can-Ze Huang
- Department of Gastroenterology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 107 Yan Jiang Xi Road, Guangzhou, Guangdong, 510120, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 107 Yan Jiang Xi Road, Guangzhou, Guangdong, 510120, China
| | - Ji-Hao Xu
- Department of Gastroenterology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 107 Yan Jiang Xi Road, Guangzhou, Guangdong, 510120, China
| | - Wa Zhong
- Department of Gastroenterology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 107 Yan Jiang Xi Road, Guangzhou, Guangdong, 510120, China
| | - Zhong-Sheng Xia
- Department of Gastroenterology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 107 Yan Jiang Xi Road, Guangzhou, Guangdong, 510120, China
| | - Si-Yi Wang
- Department of Gastroenterology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 107 Yan Jiang Xi Road, Guangzhou, Guangdong, 510120, China
| | - Di Cheng
- Department of Gastroenterology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 107 Yan Jiang Xi Road, Guangzhou, Guangdong, 510120, China
| | - Jie-Yao Li
- Department of Gastroenterology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 107 Yan Jiang Xi Road, Guangzhou, Guangdong, 510120, China
| | - Ting-Feng Wu
- Department of Gastroenterology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 107 Yan Jiang Xi Road, Guangzhou, Guangdong, 510120, China
| | - Qi-Kui Chen
- Department of Gastroenterology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 107 Yan Jiang Xi Road, Guangzhou, Guangdong, 510120, China.
| | - Tao Yu
- Department of Gastroenterology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 107 Yan Jiang Xi Road, Guangzhou, Guangdong, 510120, China. .,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 107 Yan Jiang Xi Road, Guangzhou, Guangdong, 510120, China.
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57
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Meireles-Filho AC, Deplancke B. Gene regulatory mechanisms underlying the intestinal innate immune response. Curr Opin Genet Dev 2016; 43:46-52. [PMID: 28011293 DOI: 10.1016/j.gde.2016.11.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 11/17/2016] [Accepted: 11/21/2016] [Indexed: 12/24/2022]
Abstract
In the mammalian gastrointestinal tract, distinct types of cells, including epithelial cells and macrophages, collaborate to eliminate ingested pathogens while striving to preserve the commensal microbiota. The underlying innate immune response is driven by significant gene expression changes in each cell, and recent work has provided novel insights into the gene regulatory mechanisms that mediate such transcriptional changes. These mechanisms differ from those underlying the canonical cellular differentiation model in which a sequential deposition of DNA methylation and histone modification marks progressively restricts the chromatin landscape. Instead, inflammatory macrophages and intestinal epithelial cells appear to largely rely on transcription factors that explore an accessible chromatin landscape to generate dynamic stimulus-specific and spatial-specific physiological responses.
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Affiliation(s)
- Antonio Ca Meireles-Filho
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - Bart Deplancke
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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58
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Kim R, Sheaffer KL, Choi I, Won KJ, Kaestner KH. Epigenetic regulation of intestinal stem cells by Tet1-mediated DNA hydroxymethylation. Genes Dev 2016; 30:2433-2442. [PMID: 27856615 PMCID: PMC5131782 DOI: 10.1101/gad.288035.116] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 10/21/2016] [Indexed: 12/02/2022]
Abstract
Here, Kim et al. provide novel insights into the epigenomic changes that occur during intestinal stem cell development and differentiation. They demonstrate that Tet1-mediated DNA hydroxymethylation plays a critical role in the epigenetic regulation of the Wnt pathway in intestinal stem and progenitor cells and consequently in the self-renewal of the intestinal epithelium. Methylated cytosines are associated with gene silencing. The ten-eleven translocation (TET) hydroxylases, which oxidize methylated cytosines to 5-hydroxymethylcytosine (5hmC), are essential for cytosine demethylation. Gene silencing and activation are critical for intestinal stem cell (ISC) maintenance and differentiation, but the potential role of TET hydroxylases in these processes has not yet been examined. Here, we generated genome-wide maps of the 5hmC mark in ISCs and their differentiated progeny. Genes with high levels of hydroxymethylation in ISCs are strongly associated with Wnt signaling and developmental processes. We found Tet1 to be the most abundantly expressed Tet gene in ISCs; therefore, we analyzed intestinal development in Tet1-deficient mice and determined that these mice are growth-retarded, exhibit partial postnatal lethality, and have significantly reduced numbers of proliferative cells in the intestinal epithelium. In addition, the Tet1-deficient intestine displays reduced organoid-forming capacity. In the Tet1-deficient crypt, decreased expression of Wnt target genes such as Axin2 and Lgr5 correlates with lower 5hmC levels at their promoters. These data demonstrate that Tet1-mediated DNA hydroxymethylation plays a critical role in the epigenetic regulation of the Wnt pathway in intestinal stem and progenitor cells and consequently in the self-renewal of the intestinal epithelium.
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Affiliation(s)
- Rinho Kim
- Department of Genetics, Center for Molecular Studies in Digestive and Liver Diseases, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Karyn L Sheaffer
- Department of Genetics, Center for Molecular Studies in Digestive and Liver Diseases, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Inchan Choi
- Department of Genetics, Center for Molecular Studies in Digestive and Liver Diseases, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Kyoung-Jae Won
- Department of Genetics, Center for Molecular Studies in Digestive and Liver Diseases, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Klaus H Kaestner
- Department of Genetics, Center for Molecular Studies in Digestive and Liver Diseases, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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59
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Extensive Epigenetic Changes Accompany Terminal Differentiation of Mouse Hepatocytes After Birth. G3-GENES GENOMES GENETICS 2016; 6:3701-3709. [PMID: 27652892 PMCID: PMC5100869 DOI: 10.1534/g3.116.034785] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
DNA methylation is traditionally thought to be established during early development and to remain mostly unchanged thereafter in healthy tissues, although recent studies have shown that this epigenetic mark can be more dynamic. Epigenetic changes occur in the liver after birth, but the timing and underlying biological processes leading to DNA methylation changes are not well understood. We hypothesized that this epigenetic reprogramming was the result of terminal differentiation of hepatocyte precursors. Using genomic approaches, we characterized the DNA methylation patterns in mouse liver from E18.5 until adulthood to determine if the timing of the DNA methylation change overlaps with hepatocyte terminal differentiation, and to examine the genomic context of these changes and identify the regulatory elements involved. Out of 271,325 CpGs analyzed throughout the genome, 214,709 CpGs changed DNA methylation by more than 5% (e.g., from 5 to 10% methylation) between E18.5 and 9 wk of age, and 18,863 CpGs changed DNA methylation by more than 30%. Genome-scale data from six time points between E18.5 and P20 show that DNA methylation changes coincided with the terminal differentiation of hepatoblasts into hepatocytes. We also showed that epigenetic reprogramming occurred primarily in intergenic enhancer regions while gene promoters were less affected. Our data suggest that normal postnatal hepatic development and maturation involves extensive epigenetic remodeling of the genome, and that enhancers play a key role in controlling the transition from hepatoblasts to fully differentiated hepatocytes. Our study provides a solid foundation to support future research aimed at further revealing the role of epigenetics in stem cell biology.
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60
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Jones JC, Dempsey PJ. Enterocyte progenitors can dedifferentiate to replace lost Lgr5 + intestinal stem cells revealing that many different progenitor populations can regain stemness. Stem Cell Investig 2016; 3:61. [PMID: 27868043 DOI: 10.21037/sci.2016.09.15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 09/21/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Jennifer C Jones
- Cell Biology, Stem Cell and Development Graduate Program, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Peter J Dempsey
- Cell Biology, Stem Cell and Development Graduate Program, University of Colorado School of Medicine, Aurora, CO 80045, USA; Division of Gastroenterology, Hepatology and Nutrition, Dept. of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA
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61
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Fessler E, Medema JP. Colorectal Cancer Subtypes: Developmental Origin and Microenvironmental Regulation. Trends Cancer 2016; 2:505-518. [DOI: 10.1016/j.trecan.2016.07.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 07/28/2016] [Accepted: 07/29/2016] [Indexed: 12/21/2022]
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Parent-of-origin effects of A1CF and AGO2 on testicular germ-cell tumors, testicular abnormalities, and fertilization bias. Proc Natl Acad Sci U S A 2016; 113:E5425-33. [PMID: 27582469 DOI: 10.1073/pnas.1604773113] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Testicular tumors, the most common cancer in young men, arise from abnormalities in germ cells during fetal development. Unconventional inheritance for testicular germ cell tumor (TGCT) risk both in humans and mice implicates epigenetic mechanisms. Apolipoprotein B mRNA-editing enzyme complex 1 (APOBEC1) cytidine deaminase and Deadend-1, which are involved in C-to-U RNA editing and microRNA-dependent mRNA silencing, respectively, are potent epigenetic modifiers of TGCT susceptibility in the genetically predisposed 129/Sv inbred mouse strain. Here, we show that partial loss of either APOBEC1 complementation factor (A1CF), the RNA-binding cofactor of APOBEC1 in RNA editing, or Argonaute 2 (AGO2), a key factor in the biogenesis of certain noncoding RNAs, modulates risk for TGCTs and testicular abnormalities in both parent-of-origin and conventional genetic manners. In addition, non-Mendelian inheritance was found among progeny of A1cf and Ago2 mutant intercrosses but not in backcrosses and without fetal loss. Together these findings suggest nonrandom union of gametes rather than meiotic drive or preferential lethality. Finally, this survey also suggested that A1CF contributes to long-term reproductive performance. These results directly implicate the RNA-binding proteins A1CF and AGO2 in the epigenetic control of germ-cell fate, urogenital development, and gamete functions.
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63
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Abstract
Mammalian embryonic development is a tightly regulated process that, from a single zygote, produces a large number of cell types with hugely divergent functions. Distinct cellular differentiation programmes are facilitated by tight transcriptional and epigenetic regulation. However, the contribution of epigenetic regulation to tissue homeostasis after the completion of development is less well understood. In this Review, we explore the effects of epigenetic dysregulation on adult stem cell function. We conclude that, depending on the tissue type and the epigenetic regulator affected, the consequences range from negligible to stem cell malfunction and disruption of tissue homeostasis, which may predispose to diseases such as cancer.
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64
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Kaaij LJT, Mokry M, Zhou M, Musheev M, Geeven G, Melquiond ASJ, de Jesus Domingues AM, de Laat W, Niehrs C, Smith AD, Ketting RF. Enhancers reside in a unique epigenetic environment during early zebrafish development. Genome Biol 2016; 17:146. [PMID: 27381023 PMCID: PMC4934011 DOI: 10.1186/s13059-016-1013-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 06/20/2016] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Enhancers, not promoters, are the most dynamic in their DNA methylation status throughout development and differentiation. Generally speaking, enhancers that are primed to or actually drive gene expression are characterized by relatively low levels of DNA methylation (hypo-methylation), while inactive enhancers display hyper-methylation of the underlying DNA. The direct functional significance of the DNA methylation state of enhancers is, however, unclear for most loci. RESULTS In contrast to conventional epigenetic interactions at enhancers, we find that DNA methylation status and enhancer activity during early zebrafish development display very unusual correlation characteristics: hypo-methylation is a unique feature of primed enhancers whereas active enhancers are generally hyper-methylated. The hypo-methylated enhancers that we identify (hypo-enhancers) are enriched close to important transcription factors that act later in development. Interestingly, hypo-enhancers are de-methylated shortly before the midblastula transition and reside in a unique epigenetic environment. Finally, we demonstrate that hypo-enhancers do become active at later developmental stages and that they are physically associated with the transcriptional start site of target genes, irrespective of target gene activity. CONCLUSIONS We demonstrate that early development in zebrafish embodies a time window characterized by non-canonical DNA methylation-enhancer relationships, including global DNA hypo-methylation of inactive enhancers and DNA hyper-methylation of active enhancers.
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Affiliation(s)
- Lucas J T Kaaij
- Institute of Molecular Biology (IMB), Ackermannweg 4, D-55128, Mainz, Germany
| | - Michal Mokry
- Department of Pediatric Gastroenterology, Wilhelmina Children's Hospital, University Medical Centre Utrecht, 3508 AB, Utrecht, The Netherlands
| | - Meng Zhou
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Michael Musheev
- Institute of Molecular Biology (IMB), Ackermannweg 4, D-55128, Mainz, Germany
| | - Geert Geeven
- Hubrecht Institute-KNAW & University Medical Centre Utrecht, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Adrien S J Melquiond
- Hubrecht Institute-KNAW & University Medical Centre Utrecht, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | | | - Wouter de Laat
- Hubrecht Institute-KNAW & University Medical Centre Utrecht, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Christof Niehrs
- Institute of Molecular Biology (IMB), Ackermannweg 4, D-55128, Mainz, Germany.,Division of Molecular Embryology, DKFZ-ZMBH Alliance, D-69120, Heidelberg, Germany
| | - Andrew D Smith
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA, 90089, USA
| | - René F Ketting
- Institute of Molecular Biology (IMB), Ackermannweg 4, D-55128, Mainz, Germany.
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65
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Suelves M, Carrió E, Núñez-Álvarez Y, Peinado MA. DNA methylation dynamics in cellular commitment and differentiation. Brief Funct Genomics 2016; 15:443-453. [PMID: 27416614 DOI: 10.1093/bfgp/elw017] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
DNA methylation is an essential epigenetic modification for mammalian development and is crucial for the establishment and maintenance of cellular identity. Traditionally, DNA methylation has been considered as a permanent repressive epigenetic mark. However, the application of genome-wide approaches has allowed the analysis of DNA methylation in different genomic contexts, revealing a more dynamic regulation than originally thought, as active DNA methylation and demethylation occur during cell fate commitment and terminal differentiation. Recent data provide insights into the contribution of different epigenetic factors, and DNA methylation in particular, to the establishment of cellular memory during embryonic development and the modulation of cell type-specific gene regulation programs to ensure proper differentiation. This review summarizes published data regarding DNA methylation changes along lineage specification and differentiation programs. We also discuss the current knowledge about DNA methylation alterations occurring in physiological and pathological conditions such as aging and cancer.
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66
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Labrie V, Buske OJ, Oh E, Jeremian R, Ptak C, Gasiūnas G, Maleckas A, Petereit R, Žvirbliene A, Adamonis K, Kriukienė E, Koncevičius K, Gordevičius J, Nair A, Zhang A, Ebrahimi S, Oh G, Šikšnys V, Kupčinskas L, Brudno M, Petronis A. Lactase nonpersistence is directed by DNA-variation-dependent epigenetic aging. Nat Struct Mol Biol 2016; 23:566-73. [PMID: 27159559 PMCID: PMC4899171 DOI: 10.1038/nsmb.3227] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 04/14/2016] [Indexed: 02/06/2023]
Abstract
Inability to digest lactose due to lactase non-persistence is a common trait in adult mammals, with the exception of certain human populations that exhibit lactase persistence. It is not clear how the lactase gene can be dramatically downregulated with age in most individuals, but remains active in some. We performed a comprehensive epigenetic study of the human and mouse intestine using chromosome-wide DNA modification profiling and targeted bisulfite sequencing. Epigenetically-controlled regulatory elements were found to account for the differences in lactase mRNA levels between individuals, intestinal cell types and species. The importance of these regulatory elements in modulating lactase mRNA levels was confirmed by CRISPR-Cas9-induced deletions. Genetic factors contribute to epigenetic changes occurring with age at the regulatory elements, as lactase persistence- and non-persistence-DNA haplotypes demonstrated markedly different epigenetic aging. Thus, genetic factors facilitate a gradual accumulation of epigenetic changes with age to affect phenotypic outcome.
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Affiliation(s)
- Viviane Labrie
- Krembil Family Epigenetics Laboratory, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada.,Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada.,Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, Michigan, USA
| | - Orion J Buske
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.,Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Edward Oh
- Krembil Family Epigenetics Laboratory, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Richie Jeremian
- Krembil Family Epigenetics Laboratory, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Carolyn Ptak
- Krembil Family Epigenetics Laboratory, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Giedrius Gasiūnas
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Almantas Maleckas
- Department of Surgery, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Rūta Petereit
- Department of Gastroenterology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Aida Žvirbliene
- Department of Gastroenterology, Lithuanian University of Health Sciences, Kaunas, Lithuania.,Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Kęstutis Adamonis
- Department of Gastroenterology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Edita Kriukienė
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Karolis Koncevičius
- Institute of Mathematics and Informatics, Vilnius University, Vilnius, Lithuania
| | - Juozas Gordevičius
- Institute of Mathematics and Informatics, Vilnius University, Vilnius, Lithuania
| | - Akhil Nair
- Krembil Family Epigenetics Laboratory, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Aiping Zhang
- Krembil Family Epigenetics Laboratory, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Sasha Ebrahimi
- Krembil Family Epigenetics Laboratory, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Gabriel Oh
- Krembil Family Epigenetics Laboratory, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Virginijus Šikšnys
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Limas Kupčinskas
- Department of Gastroenterology, Lithuanian University of Health Sciences, Kaunas, Lithuania.,Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Michael Brudno
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.,Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Arturas Petronis
- Krembil Family Epigenetics Laboratory, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada.,Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
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67
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Abstract
Epithelia cover the surfaces and line the cavities of the body. Recent studies have highlighted the existence of multiple stem cell compartments within individual epithelia that exhibit striking plasticity in response to tissue damage, transplantation, or tumor development. New knowledge about the composition of the epithelial niche and the transcription factor networks that maintain cell identity has provided new insights into the extrinsic and intrinsic regulation of stem cell behavior. In addition new in vitro tissue substitutes allow better integration of data from human and mouse models.
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68
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Tetteh PW, Basak O, Farin HF, Wiebrands K, Kretzschmar K, Begthel H, van den Born M, Korving J, de Sauvage F, van Es JH, van Oudenaarden A, Clevers H. Replacement of Lost Lgr5-Positive Stem Cells through Plasticity of Their Enterocyte-Lineage Daughters. Cell Stem Cell 2016; 18:203-13. [PMID: 26831517 DOI: 10.1016/j.stem.2016.01.001] [Citation(s) in RCA: 391] [Impact Index Per Article: 48.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 11/03/2015] [Accepted: 01/04/2016] [Indexed: 01/30/2023]
Abstract
Intestinal crypts display robust regeneration upon injury. The relatively rare secretory precursors can replace lost stem cells, but it is unknown if the abundant enterocyte progenitors that express the Alkaline phosphate intestinal (Alpi) gene also have this capacity. We created an Alpi-IRES-CreERT2 (Alpi(CreER)) knockin allele for lineage tracing. Marked clones consist entirely of enterocytes and are all lost from villus tips within days. Genetic fate-mapping of Alpi(+) cells before or during targeted ablation of Lgr5-expressing stem cells generated numerous long-lived crypt-villus "ribbons," indicative of dedifferentiation of enterocyte precursors into Lgr5(+) stems. By single-cell analysis of dedifferentiating enterocytes, we observed the generation of Paneth-like cells and proliferative stem cells. We conclude that the highly proliferative, short-lived enterocyte precursors serve as a large reservoir of potential stem cells during crypt regeneration.
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Affiliation(s)
- Paul W Tetteh
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Onur Basak
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Henner F Farin
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Kay Wiebrands
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Kai Kretzschmar
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Harry Begthel
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Maaike van den Born
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Jeroen Korving
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Frederic de Sauvage
- Molecular Oncology Department, Genentech, South San Francisco, CA 94080, USA
| | - Johan H van Es
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Alexander van Oudenaarden
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
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69
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Johnson DC, Weinhold N, Mitchell JS, Chen B, Kaiser M, Begum DB, Hillengass J, Bertsch U, Gregory WA, Cairns D, Jackson GH, Försti A, Nickel J, Hoffmann P, Nöethen MM, Stephens OW, Barlogie B, Davis FE, Hemminki K, Goldschmidt H, Houlston RS, Morgan GJ. Genome-wide association study identifies variation at 6q25.1 associated with survival in multiple myeloma. Nat Commun 2016; 7:10290. [PMID: 26743840 PMCID: PMC4729868 DOI: 10.1038/ncomms10290] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 11/25/2015] [Indexed: 01/08/2023] Open
Abstract
Survival following a diagnosis of multiple myeloma (MM) varies between patients and some of these differences may be a consequence of inherited genetic variation. In this study, to identify genetic markers associated with MM overall survival (MM-OS), we conduct a meta-analysis of four patient series of European ancestry, totalling 3,256 patients with 1,200 MM-associated deaths. Each series is genotyped for ∼600,000 single nucleotide polymorphisms across the genome; genotypes for six million common variants are imputed using 1000 Genomes Project and UK10K as the reference. The association between genotype and OS is assessed by Cox proportional hazards model adjusting for age, sex, International staging system and treatment. We identify a locus at 6q25.1 marked by rs12374648 associated with MM-OS (hazard ratio=1.34, 95% confidence interval=1.22-1.48, P=4.69 × 10(-9)). Our findings have potential clinical implications since they demonstrate that inherited genotypes can provide prognostic information in addition to conventional tumor acquired prognostic factors.
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Affiliation(s)
- David C. Johnson
- Division of Molecular Pathology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Niels Weinhold
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
- Department of Internal Medicine V, University of Heidelberg, 69120 Heidelberg, Germany
| | - Jonathan S. Mitchell
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Bowang Chen
- German Cancer Research Center, 69121 Heidelberg, Germany
| | - Martin Kaiser
- Division of Molecular Pathology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Dil B. Begum
- Division of Molecular Pathology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Jens Hillengass
- Department of Internal Medicine V, University of Heidelberg, 69120 Heidelberg, Germany
| | - Uta Bertsch
- Department of Internal Medicine V, University of Heidelberg, 69120 Heidelberg, Germany
| | - Walter A. Gregory
- Leeds Institute of Molecular Medicine, Section of Clinical Trials Research, University of Leeds, Leeds LS2 9PH, UK
| | - David Cairns
- Leeds Institute of Molecular Medicine, Section of Clinical Trials Research, University of Leeds, Leeds LS2 9PH, UK
| | - Graham H. Jackson
- Department of Haematology, Newcastle University, Newcastle-upon-Tyne NE1 7RU, UK
| | - Asta Försti
- German Cancer Research Center, 69121 Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, 221 00 Malmö, Sweden
| | - Jolanta Nickel
- Department of Internal Medicine V, University of Heidelberg, 69120 Heidelberg, Germany
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, D-53127 Bonn, Germany
- Division of Medical Genetics, Department of Biomedicine, University of Basel, 4031 Basel, Switzerland
| | - Markus M. Nöethen
- Institute of Human Genetics, University of Bonn, D-53127 Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, D-53127 Bonn, Germany
| | - Owen W. Stephens
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
| | - Bart Barlogie
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
| | - Faith E. Davis
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
| | - Kari Hemminki
- German Cancer Research Center, 69121 Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, 221 00 Malmö, Sweden
| | - Hartmut Goldschmidt
- Department of Internal Medicine V, University of Heidelberg, 69120 Heidelberg, Germany
- National Center of Tumor Diseases, 69120 Heidelberg, Germany
| | - Richard S. Houlston
- Division of Molecular Pathology, The Institute of Cancer Research, London SW7 3RP, UK
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Gareth J. Morgan
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
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70
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TET-catalyzed 5-hydroxymethylcytosine regulates gene expression in differentiating colonocytes and colon cancer. Sci Rep 2015; 5:17568. [PMID: 26631571 PMCID: PMC4668370 DOI: 10.1038/srep17568] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 11/02/2015] [Indexed: 12/24/2022] Open
Abstract
The formation of differentiated cell types from pluripotent progenitors involves epigenetic regulation of gene expression. DNA hydroxymethylation results from the enzymatic oxidation of 5-methylcytosine (5-mC) to 5-hydroxymethylcytosine (5-hmC) by the ten-eleven translocation (TET) 5-mC dioxygenase enzymes. Previous work has mapped changes in 5-mC during differentiation of intestinal stem cells. However, whether or not 5-hmC regulates colonocyte differentiation is unknown. Here we show that 5-hmC regulates gene expression during colonocyte differentiation and controls gene expression in human colon cancers. Genome-wide profiling of 5-hmC during in vitro colonic differentiation demonstrated that 5-hmC is gained at highly expressed and induced genes and is associated with intestinal transcription factor binding sites, including those for HNF4A and CDX2. TET1 induction occurred during differentiation, and TET1 knockdown altered gene expression and inhibited barrier formation of colonocytes. We find that the 5-hmC distribution in primary human colonocytes parallels the distribution found in differentiated cells in vitro, and that gene-specific 5-hmC changes in human colon cancers are directly correlated with changes in gene expression. Our results support a model in which 5-hmC regulates differentiation of adult human intestine and 5-hmC alterations contribute to the disrupted gene expression in colon cancer.
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71
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Elliott EN, Kaestner KH. Epigenetic regulation of the intestinal epithelium. Cell Mol Life Sci 2015; 72:4139-56. [PMID: 26220502 PMCID: PMC4607638 DOI: 10.1007/s00018-015-1997-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 07/09/2015] [Accepted: 07/17/2015] [Indexed: 12/12/2022]
Abstract
The intestinal epithelium is an ideal model system for the study of normal and pathological differentiation processes. The mammalian intestinal epithelium is a single cell layer comprising proliferative crypts and differentiated villi. The crypts contain both proliferating and quiescent stem cell populations that self-renew and produce all the differentiated cell types, which are replaced every 3-5 days. The genetics of intestinal development, homeostasis, and disease are well defined, but less is known about the contribution of epigenetics in modulating these processes. Epigenetics refers to heritable phenotypic traits, including gene expression, which are independent of mutations in the DNA sequence. We have known for several decades that human colorectal cancers contain hypomethylated DNA, but the causes and consequences of this phenomenon are not fully understood. In contrast, tumor suppressor gene promoters are often hypermethylated in colorectal cancer, resulting in decreased expression of the associated gene. In this review, we describe the role that epigenetics plays in intestinal homeostasis and disease, with an emphasis on results from mouse models. We highlight the importance of producing and analyzing next-generation sequencing data detailing the epigenome from intestinal stem cell to differentiated intestinal villus cell.
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Affiliation(s)
- Ellen N Elliott
- Department of Genetics and Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, 12-126 Translational Research Center, 3400 Civic Center Boulevard, Philadelphia, PA, 19104, USA
| | - Klaus H Kaestner
- Department of Genetics and Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, 12-126 Translational Research Center, 3400 Civic Center Boulevard, Philadelphia, PA, 19104, USA.
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72
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Huang CZ, Yu T, Chen QK. DNA Methylation Dynamics During Differentiation, Proliferation, and Tumorigenesis in the Intestinal Tract. Stem Cells Dev 2015; 24:2733-9. [PMID: 26413818 DOI: 10.1089/scd.2015.0235] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
DNA methylation, an epigenetic control mechanism in mammals, is widely present in the intestinal tract during the differentiation and proliferation of epithelial cells. Cells in stem cell pools or villi have different patterns of DNA methylation. The process of DNA methylation is dynamic and occurs at many relevant regulatory elements during the rapid transition of stem cells into fully mature, differentiated epithelial cells. Changes in DNA methylation patterns most often take place in enhancer and promoter regions and are associated with transcription factor binding. During differentiation, enhancer regions associated with genes important to enterocyte differentiation are demethylated, activating gene expression. Abnormal patterns of DNA methylation during differentiation and proliferation in the intestinal tract can lead to the formation of aberrant crypt foci and destroy the barrier and absorptive functions of the intestinal epithelium. Accumulation of these epigenetic changes may even result in tumorigenesis. In the current review, we discuss recent findings on the association between DNA methylation and cell differentiation and proliferation in the small intestine and highlight the possible links between dysregulation of this process and tumorigenesis.
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Affiliation(s)
- Can-Ze Huang
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University , Guangzhou, Guangdong, People's Republic of China
| | - Tao Yu
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University , Guangzhou, Guangdong, People's Republic of China
| | - Qi-Kui Chen
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University , Guangzhou, Guangdong, People's Republic of China
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73
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Sobiak B, Graczyk‐Jarzynka A, Leśniak W. Comparison of DNA Methylation and Expression Pattern of S100 and Other Epidermal Differentiation Complex Genes in Differentiating Keratinocytes. J Cell Biochem 2015; 117:1092-8. [DOI: 10.1002/jcb.25392] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 10/05/2015] [Indexed: 02/05/2023]
Affiliation(s)
- Barbara Sobiak
- Department of Molecular and Cellular NeurobiologyNencki Institute of Experimental Biology, 3 Pasteur StreetWarsaw02‐093Poland
| | - Agnieszka Graczyk‐Jarzynka
- Department of Molecular and Cellular NeurobiologyNencki Institute of Experimental Biology, 3 Pasteur StreetWarsaw02‐093Poland
| | - Wiesława Leśniak
- Department of Molecular and Cellular NeurobiologyNencki Institute of Experimental Biology, 3 Pasteur StreetWarsaw02‐093Poland
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74
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Postnatal epigenetic regulation of intestinal stem cells requires DNA methylation and is guided by the microbiome. Genome Biol 2015; 16:211. [PMID: 26420038 PMCID: PMC4589031 DOI: 10.1186/s13059-015-0763-5] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 08/28/2015] [Indexed: 01/09/2023] Open
Abstract
Background DNA methylation is an epigenetic mechanism central to development and maintenance of complex mammalian tissues, but our understanding of its role in intestinal development is limited. Results We use whole genome bisulfite sequencing, and find that differentiation of mouse colonic intestinal stem cells to intestinal epithelium is not associated with major changes in DNA methylation. However, we detect extensive dynamic epigenetic changes in intestinal stem cells and their progeny during the suckling period, suggesting postnatal epigenetic development in this stem cell population. We find that postnatal DNA methylation increases at 3′ CpG islands (CGIs) correlate with transcriptional activation of glycosylation genes responsible for intestinal maturation. To directly test whether 3′ CGI methylation regulates transcription, we conditionally disrupted two major DNA methyltransferases, Dnmt1 or Dnmt3a, in fetal and adult intestine. Deficiency of Dnmt1 causes severe intestinal abnormalities in neonates and disrupts crypt homeostasis in adults, whereas Dnmt3a loss was compatible with intestinal development. These studies reveal that 3′ CGI methylation is functionally involved in the regulation of transcriptional activation in vivo, and that Dnmt1 is a critical regulator of postnatal epigenetic changes in intestinal stem cells. Finally, we show that postnatal 3′ CGI methylation and associated gene activation in intestinal epithelial cells are significantly altered by germ-free conditions. Conclusions Our results demonstrate that the suckling period is critical for epigenetic development of intestinal stem cells, with potential important implications for lifelong gut health, and that the gut microbiome guides and/or facilitates these postnatal epigenetic processes. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0763-5) contains supplementary material, which is available to authorized users.
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75
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Lamprecht S, Fich A. The cancer cells-of-origin in the gastrointestinal tract: progenitors revisited. Carcinogenesis 2015; 36:811-6. [PMID: 26116624 DOI: 10.1093/carcin/bgv095] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 06/20/2015] [Indexed: 01/01/2023] Open
Abstract
A prominent model of tumor progression posits that normal self-renewing and multipotent stem cells(SCs) are the initial target of transformation. This view has been robustly challenged by the recurring observation that transit-amplifying cells and differentiated progenitors can initiate neoplasia outside the SC zone thus qualifying as cancer cells-of-origin. The emerging concept is that a cancer SC and a cancer cell-of-origin are not necessarily the same cell. Importantly, progenitor cells were shown to possess remarkable plasticity and to revert, on demand, to a SC-like state. The present review revisits our early hypothesis that colonic progenitors acquiring a mutant adenomatous polyposis coli gene after exiting the stem zone may serve as genuine cancer cells-of-origin. New findings consonant with this view are examined, and tenable molecular and cellular mechanisms underpinning the plasticity of progenitor cells in the gastrointestinal tract and in other tissues are discussed. The translational impact of cell plasticity is addressed, and recommendations for future research are advanced.
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Affiliation(s)
- Sergio Lamprecht
- Department of Clinical Biochemistry and Pharmacology and Institute of Gastroenterology and Hepatology, Faculty of Health Sciences, Ben Gurion University of the Negev, Soroka University Medical Center, Beersheva, Israel
| | - Alexander Fich
- Institute of Gastroenterology and Hepatology, Faculty of Health Sciences, Ben Gurion University of the Negev, Soroka University Medical Center, Beersheva, Israel
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76
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Abstract
Stem cell decline is an important cellular driver of aging-associated pathophysiology in multiple tissues. Epigenetic regulation is central to establishing and maintaining stem cell function, and emerging evidence indicates that epigenetic dysregulation contributes to the altered potential of stem cells during aging. Unlike terminally differentiated cells, the impact of epigenetic dysregulation in stem cells is propagated beyond self; alterations can be heritably transmitted to differentiated progeny, in addition to being perpetuated and amplified within the stem cell pool through self-renewal divisions. This Review focuses on recent studies examining epigenetic regulation of tissue-specific stem cells in homeostasis, aging, and aging-related disease.
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Affiliation(s)
- Isabel Beerman
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02116, USA
| | - Derrick J Rossi
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02116, USA.
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77
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Forn M, Díez-Villanueva A, Merlos-Suárez A, Muñoz M, Lois S, Carriò E, Jordà M, Bigas A, Batlle E, Peinado MA. Overlapping DNA methylation dynamics in mouse intestinal cell differentiation and early stages of malignant progression. PLoS One 2015; 10:e0123263. [PMID: 25933092 PMCID: PMC4416816 DOI: 10.1371/journal.pone.0123263] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 02/17/2015] [Indexed: 12/20/2022] Open
Abstract
Mouse models of intestinal crypt cell differentiation and tumorigenesis have been used to characterize the molecular mechanisms underlying both processes. DNA methylation is a key epigenetic mark and plays an important role in cell identity and differentiation programs and cancer. To get insights into the dynamics of cell differentiation and malignant transformation we have compared the DNA methylation profiles along the mouse small intestine crypt and early stages of tumorigenesis. Genome-scale analysis of DNA methylation together with microarray gene expression have been applied to compare intestinal crypt stem cells (EphB2high), differentiated cells (EphB2negative), ApcMin/+ adenomas and the corresponding non-tumor adjacent tissue, together with small and large intestine samples and the colon cancer cell line CT26. Compared with late stages, small intestine crypt differentiation and early stages of tumorigenesis display few and relatively small changes in DNA methylation. Hypermethylated loci are largely shared by the two processes and affect the proximities of promoter and enhancer regions, with enrichment in genes associated with the intestinal stem cell signature and the PRC2 complex. The hypermethylation is progressive, with minute levels in differentiated cells, as compared with intestinal stem cells, and reaching full methylation in advanced stages. Hypomethylation shows different signatures in differentiation and cancer and is already present in the non-tumor tissue adjacent to the adenomas in ApcMin/+ mice, but at lower levels than advanced cancers. This study provides a reference framework to decipher the mechanisms driving mouse intestinal tumorigenesis and also the human counterpart.
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Affiliation(s)
- Marta Forn
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) 08916 Badalona, Barcelona, Spain
| | - Anna Díez-Villanueva
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) 08916 Badalona, Barcelona, Spain
| | - Anna Merlos-Suárez
- Institute for Research in Biomedicine (IRB Barcelona) 08028 Barcelona, Spain
| | - Mar Muñoz
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) 08916 Badalona, Barcelona, Spain
| | - Sergi Lois
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) 08916 Badalona, Barcelona, Spain
| | - Elvira Carriò
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) 08916 Badalona, Barcelona, Spain
| | - Mireia Jordà
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) 08916 Badalona, Barcelona, Spain
| | - Anna Bigas
- Institut Hospital del Mar d’Investigació Mèdica (IMIM) 08003 Barcelona, Spain
| | - Eduard Batlle
- Institute for Research in Biomedicine (IRB Barcelona) 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Miguel A. Peinado
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) 08916 Badalona, Barcelona, Spain
- * E-mail:
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78
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Cheng Y, Xie N, Jin P, Wang T. DNA methylation and hydroxymethylation in stem cells. Cell Biochem Funct 2015; 33:161-73. [PMID: 25776144 DOI: 10.1002/cbf.3101] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Revised: 02/17/2015] [Accepted: 02/24/2015] [Indexed: 12/18/2022]
Abstract
In mammals, DNA methylation and hydroxymethylation are specific epigenetic mechanisms that can contribute to the regulation of gene expression and cellular functions. DNA methylation is important for the function of embryonic stem cells and adult stem cells (such as haematopoietic stem cells, neural stem cells and germline stem cells), and changes in DNA methylation patterns are essential for successful nuclear reprogramming. In the past several years, the rediscovery of hydroxymethylation and the TET enzymes expanded our insights tremendously and uncovered more dynamic aspects of cytosine methylation regulation. Here, we review the current knowledge and highlight the most recent advances in DNA methylation and hydroxymethylation in embryonic stem cells, induced pluripotent stem cells and several well-studied adult stems cells. Our current understanding of stem cell epigenetics and new advances in the field will undoubtedly stimulate further clinical applications of regenerative medicine in the future.
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Affiliation(s)
- Ying Cheng
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - Nina Xie
- Department of Human Genetics, Emory University, Atlanta, GA, USA.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Peng Jin
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - Tao Wang
- Cardiovascular Research Institute and Department of Physiology, University of California, San Francisco, CA, USA
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79
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Ucar O, Rattay K. Promiscuous Gene Expression in the Thymus: A Matter of Epigenetics, miRNA, and More? Front Immunol 2015; 6:93. [PMID: 25784915 PMCID: PMC4347492 DOI: 10.3389/fimmu.2015.00093] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 02/17/2015] [Indexed: 12/17/2022] Open
Abstract
The induction of central tolerance in the course of T cell development crucially depends on promiscuous gene expression (pGE) in medullary thymic epithelial cells (mTECs). mTECs express a genome-wide variety of tissue-restricted antigens (TRAs), preventing the escape of autoreactive T cells to the periphery, and the development of severe autoimmunity. Most of our knowledge of how pGE is controlled comes from studies on the autoimmune regulator (Aire). Aire activates the expression of a large subset of TRAs by interacting with the general transcriptional machinery and promoting transcript elongation. However, further factors regulating Aire-independent TRAs must be at play. Recent studies demonstrated that pGE in general and the function of Aire in particular are controlled by epigenetic and post-transcriptional mechanisms. This mini-review summarizes current knowledge of the regulation of pGE by miRNA and epigenetic regulatory mechanisms such as DNA methylation, histone modifications, and chromosomal topology.
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Affiliation(s)
- Olga Ucar
- Division of Developmental Immunology, German Cancer Research Center , Heidelberg , Germany
| | - Kristin Rattay
- Division of Developmental Immunology, German Cancer Research Center , Heidelberg , Germany
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80
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Tetteh PW, Farin HF, Clevers H. Plasticity within stem cell hierarchies in mammalian epithelia. Trends Cell Biol 2015; 25:100-8. [DOI: 10.1016/j.tcb.2014.09.003] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 09/08/2014] [Accepted: 09/12/2014] [Indexed: 12/20/2022]
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81
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Vincent A, Kazmierczak C, Duchêne B, Jonckheere N, Leteurtre E, Van Seuningen I. Cryosectioning the intestinal crypt-villus axis: an ex vivo method to study the dynamics of epigenetic modifications from stem cells to differentiated cells. Stem Cell Res 2014; 14:105-13. [PMID: 25590428 DOI: 10.1016/j.scr.2014.12.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 11/26/2014] [Accepted: 12/12/2014] [Indexed: 11/16/2022] Open
Abstract
The intestinal epithelium is a particularly attractive biological adult model to study epigenetic mechanisms driving adult stem cell renewal and cell differentiation. Since epigenetic modifications are dynamic, we have developed an original ex vivo approach to study the expression and epigenetic profiles of key genes associated with either intestinal cell pluripotency or differentiation by isolating cryosections of the intestinal crypt-villus axis. Gene expression, DNA methylation and histone modifications were studied by qRT-PCR, methylation-specific PCR and micro-chromatin immunoprecipitation, respectively. Using this approach, it was possible to identify segment-specific methylation and chromatin profiles. We show that (i) expression of intestinal stem cell markers (Lgr5, Ascl2) exclusively in the crypt is associated with active histone marks, (ii) promoters of all pluripotency genes studied and transcription factors involved in intestinal cell fate (Cdx2) harbour a bivalent chromatin pattern in the crypts and (iii) expression of differentiation markers (Muc2, Sox9) along the crypt-villus axis is associated with DNA methylation. Hence, using an original model of cryosectioning along the crypt-villus axis that allows in situ detection of dynamic epigenetic modifications, we demonstrate that regulation of pluripotency and differentiation markers in healthy intestinal mucosa involves different and specific epigenetic mechanisms.
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Affiliation(s)
- Audrey Vincent
- Inserm, UMR837, Jean Pierre Aubert Research Center (JPARC), Team 5 "Mucins, Epithelial Differentiation and Carcinogenesis," rue Polonovski, Lille, France; Université Lille 2 Droit et Santé, Lille, France; Centre Hospitalier Régional et Universitaire de Lille, Lille, France.
| | - Catherine Kazmierczak
- Inserm, UMR837, Jean Pierre Aubert Research Center (JPARC), Team 5 "Mucins, Epithelial Differentiation and Carcinogenesis," rue Polonovski, Lille, France; Université Lille 2 Droit et Santé, Lille, France; Centre Hospitalier Régional et Universitaire de Lille, Lille, France; Centre de Biologie Pathologie, CHRU Lille, Lille, France
| | - Belinda Duchêne
- Inserm, UMR837, Jean Pierre Aubert Research Center (JPARC), Team 5 "Mucins, Epithelial Differentiation and Carcinogenesis," rue Polonovski, Lille, France; Université Lille 2 Droit et Santé, Lille, France; Centre Hospitalier Régional et Universitaire de Lille, Lille, France
| | - Nicolas Jonckheere
- Inserm, UMR837, Jean Pierre Aubert Research Center (JPARC), Team 5 "Mucins, Epithelial Differentiation and Carcinogenesis," rue Polonovski, Lille, France; Université Lille 2 Droit et Santé, Lille, France; Centre Hospitalier Régional et Universitaire de Lille, Lille, France
| | - Emmanuelle Leteurtre
- Inserm, UMR837, Jean Pierre Aubert Research Center (JPARC), Team 5 "Mucins, Epithelial Differentiation and Carcinogenesis," rue Polonovski, Lille, France; Université Lille 2 Droit et Santé, Lille, France; Centre Hospitalier Régional et Universitaire de Lille, Lille, France; Centre de Biologie Pathologie, CHRU Lille, Lille, France
| | - Isabelle Van Seuningen
- Inserm, UMR837, Jean Pierre Aubert Research Center (JPARC), Team 5 "Mucins, Epithelial Differentiation and Carcinogenesis," rue Polonovski, Lille, France; Université Lille 2 Droit et Santé, Lille, France; Centre Hospitalier Régional et Universitaire de Lille, Lille, France
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82
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Rinaldi L, Benitah SA. Epigenetic regulation of adult stem cell function. FEBS J 2014; 282:1589-604. [PMID: 25060320 DOI: 10.1111/febs.12946] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 07/17/2014] [Accepted: 07/22/2014] [Indexed: 01/09/2023]
Abstract
Understanding the cellular and molecular mechanisms that specify cell lineages throughout development, and that maintain tissue homeostasis during adulthood, is paramount towards our understanding of why we age or develop pathologies such as cancer. Epigenetic mechanisms ensure that genetically identical cells acquire different fates during embryonic development and are therefore essential for the proper progression of development. How they do so is still a matter of intense investigation, but there is sufficient evidence indicating that they act in a concerted manner with inductive signals and tissue-specific transcription factors to promote and stabilize fate changes along the three germ layers during development. In consequence, it is generally hypothesized that epigenetic mechanisms are also required for the continuous maintenance of cell fate during adulthood. However, in vivo models in which different epigenetic factors have been depleted in different tissues do not show overt changes in cell lineage, thus not strongly supporting this view. Instead, the function of some of these factors appears to be primarily associated with tissue functionality, and a strong causal relationship has been established between their misregulation and a diseased state. In this review, we summarize our current knowledge of the role of epigenetic factors in adult stem cell function and tissue homeostasis.
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Affiliation(s)
- Lorenzo Rinaldi
- Centre for Genomic Regulation, Barcelona, Spain; Universitat Pompeu Fabra, Barcelona, Spain; Institute for Research in Biomedicine, Barcelona, Spain
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83
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Molaro A, Falciatori I, Hodges E, Aravin AA, Marran K, Rafii S, McCombie WR, Smith AD, Hannon GJ. Two waves of de novo methylation during mouse germ cell development. Genes Dev 2014; 28:1544-9. [PMID: 25030694 PMCID: PMC4102761 DOI: 10.1101/gad.244350.114] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 06/16/2014] [Indexed: 11/24/2022]
Abstract
During development, mammalian germ cells reprogram their epigenomes via a genome-wide erasure and de novo rewriting of DNA methylation marks. We know little of how methylation patterns are specifically determined. The piRNA pathway is thought to target the bulk of retrotransposon methylation. Here we show that most retrotransposon sequences are modified by default de novo methylation. However, potentially active retrotransposon copies evade this initial wave, likely mimicking features of protein-coding genes. These elements remain transcriptionally active and become targets of piRNA-mediated methylation. Thus, we posit that these two waves play essential roles in resetting germ cell epigenomes at each generation.
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Affiliation(s)
- Antoine Molaro
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Ilaria Falciatori
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Emily Hodges
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Alexei A. Aravin
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
| | - Krista Marran
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Shahin Rafii
- Ansary Stem Cell Institute, Department of Genetic Medicine, Weill Cornell Medical College, New York, New York 10065, USA
| | - W. Richard McCombie
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Andrew D. Smith
- Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA
| | - Gregory J. Hannon
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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84
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Abstract
Intestinal stem cells (ISCs) and colorectal cancer (CRC) biology are tightly linked in many aspects. It is generally thought that ISCs are the cells of origin for a large proportion of CRCs and crucial ISC-associated signalling pathways are often affected in CRCs. Moreover, CRCs are thought to retain a cellular hierarchy that is reminiscent of the intestinal epithelium. Recent studies offer quantitative insights into the dynamics of ISC behaviour that govern homeostasis and thereby provide the necessary baseline parameters to begin to apply these analyses during the various stages of tumour development.
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Affiliation(s)
- Louis Vermeulen
- 1] Laboratory for Experimental Oncology and Radiobiology, Center for Experimental Molecular Medicine, Academic Medical Center, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands. [2] Cancer Research UK - Cambridge Institute, University of Cambridge, Robinson Way, CB2 0RE, Cambridge, UK
| | - Hugo J Snippert
- Molecular Cancer Research and Cancer Genomics Netherlands, Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands
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85
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van Wolfswinkel JC. Piwi and Potency: PIWI Proteins in Animal Stem Cells and Regeneration. Integr Comp Biol 2014; 54:700-13. [DOI: 10.1093/icb/icu084] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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86
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Sheaffer KL, Kim R, Aoki R, Elliott EN, Schug J, Burger L, Schübeler D, Kaestner KH. DNA methylation is required for the control of stem cell differentiation in the small intestine. Genes Dev 2014; 28:652-64. [PMID: 24637118 PMCID: PMC3967052 DOI: 10.1101/gad.230318.113] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
There is a tight correlation between the epigenetic status of genes and expression changes during differentiation. Sheaffer et al. used acute deletion of Dnmt1 to reduce DNA methylation maintenance in the intestinal epithelium. This caused crypt expansion and decreased differentiation. DNA methylation was dynamic at enhancers during the rapid transition from stem to differentiated epithelial cells. These findings reveal that the loss of DNA methylation at intestinal stem cell gene enhancers causes inappropriate gene expression and delayed differentiation. The mammalian intestinal epithelium has a unique organization in which crypts harboring stem cells produce progenitors and finally clonal populations of differentiated cells. Remarkably, the epithelium is replaced every 3–5 d throughout adult life. Disrupted maintenance of the intricate balance of proliferation and differentiation leads to loss of epithelial integrity or barrier function or to cancer. There is a tight correlation between the epigenetic status of genes and expression changes during differentiation; however, the mechanism of how changes in DNA methylation direct gene expression and the progression from stem cells to their differentiated descendants is unclear. Using conditional gene ablation of the maintenance methyltransferase Dnmt1, we demonstrate that reducing DNA methylation causes intestinal crypt expansion in vivo. Determination of the base-resolution DNA methylome in intestinal stem cells and their differentiated descendants shows that DNA methylation is dynamic at enhancers, which are often associated with genes important for both stem cell maintenance and differentiation. We establish that the loss of DNA methylation at intestinal stem cell gene enhancers causes inappropriate gene expression and delayed differentiation.
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Affiliation(s)
- Karyn L Sheaffer
- Department of Genetics, Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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87
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Beckerman P, Ko YA, Susztak K. Epigenetics: a new way to look at kidney diseases. Nephrol Dial Transplant 2014; 29:1821-7. [PMID: 24675284 DOI: 10.1093/ndt/gfu026] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Only a few percent of the 3 billion pairs of chemical letters in the human genome is responsible for protein-coding sequences. Recent advances in the field of epigenomics have helped us to understand how most of the remaining sequences are responsible for gene regulation at baseline and in disease conditions. Here we discuss recent advances in the area of epigenetics--specifically in cytosine modifications--and its application in the field of nephrology.
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Affiliation(s)
- Pazit Beckerman
- Renal Electrolyte and Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yi-An Ko
- Renal Electrolyte and Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Katalin Susztak
- Renal Electrolyte and Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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88
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Ikemura K, Iwamoto T, Okuda M. MicroRNAs as regulators of drug transporters, drug-metabolizing enzymes, and tight junctions: implication for intestinal barrier function. Pharmacol Ther 2014; 143:217-24. [PMID: 24631272 DOI: 10.1016/j.pharmthera.2014.03.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 02/28/2014] [Indexed: 12/16/2022]
Abstract
Drug transporters, drug-metabolizing enzymes, and tight junctions in the small intestine function as an absorption barrier and sometimes as a facilitator of orally administered drugs. The expression of these proteins often fluctuates and thereby causes individual pharmacokinetic variability. MicroRNAs (miRNAs), which are small non-coding RNAs, have recently emerged as a new class of gene regulator. MiRNAs post-transcriptionally regulate gene expression by binding to target mRNA to suppress its translation or regulate its degradation. They have been shown to be key regulators of proteins associated with pharmacokinetics. Moreover, the role of miRNAs on the expression of some proteins expressed in the small intestine has recently been clarified. In this review, we summarize current knowledge regarding the role of miRNAs in the regulation of drug transporters, drug-metabolizing enzymes, and tight junctions as well as its implication for intestinal barrier function. MiRNAs play vital roles in the differentiation, architecture, and barrier function of intestinal epithelial cells, and directly and/or indirectly regulate the expression and function of proteins associated with drug absorption in intestinal epithelial cells. Moreover, the variation of miRNA expression caused by pathological and physiological conditions as well as genetic factors should affect the expression of these proteins. Therefore, miRNAs could be significant factors affecting inter- and intra-individual variations in the pharmacokinetics and intestinal absorption of drugs. Overall, miRNAs could be promising targets for personalized pharmacotherapy or other attractive therapies through intestinal absorption of drugs.
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Affiliation(s)
- Kenji Ikemura
- Department of Pharmacy, Mie University Hospital, Tsu, Mie 514-8507, Japan
| | - Takuya Iwamoto
- Department of Pharmacy, Mie University Hospital, Tsu, Mie 514-8507, Japan; Department of Clinical Pharmacy and Biopharmaceutics, Mie University Graduate School of Medicine, Tsu, Mie 514-8507, Japan
| | - Masahiro Okuda
- Department of Pharmacy, Mie University Hospital, Tsu, Mie 514-8507, Japan; Department of Clinical Pharmacy and Biopharmaceutics, Mie University Graduate School of Medicine, Tsu, Mie 514-8507, Japan.
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89
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Abstract
Extracellular cues play critical roles in the establishment of the epigenome during development and may also contribute to epigenetic perturbations found in disease states. The direct role of the local tissue environment on the post-development human epigenome, however, remains unclear due to limitations in studies of human subjects. Here, we use an isogenic human ileal neobladder surgical model and compare global DNA methylation levels of intestinal epithelial cells pre- and post-neobladder construction using the Infinium HumanMethylation450 BeadChip. Our study is the first to quantify the effect of environmental cues on the human epigenome and show that the local tissue environment directly modulates DNA methylation patterns in normal differentiated cells in vivo. In the neobladder, the intestinal epithelial cells lose their tissue-specific epigenetic landscape in a time-dependent manner following the tissue’s exposure to a bladder environment. We find that de novo methylation of many intestine-specific enhancers occurs at the rate of 0.41% per month (P < 0.01, Pearson = 0.71), while demethylation of primarily non-intestine-specific transcribed regions occurs at the rate of −0.37% per month (P < 0.01, Pearson = −0.57). The dynamic resetting of the DNA methylome in the neobladder not only implicates local environmental cues in the shaping and maintenance of the epigenome but also illustrates an unexpected cross-talk between the epigenome and the cellular environment.
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90
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Broadly permissive intestinal chromatin underlies lateral inhibition and cell plasticity. Nature 2014; 506:511-5. [PMID: 24413398 PMCID: PMC4151315 DOI: 10.1038/nature12903] [Citation(s) in RCA: 178] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 11/19/2013] [Indexed: 12/22/2022]
Abstract
Cells differentiate when transcription factors bind accessible cis-regulatory elements to establish specific gene expression programs. In differentiating embryonic stem cells, chromatin at lineage-restricted genes becomes sequentially accessible, probably by means of 'pioneer' transcription factor activity, but tissues may use other strategies in vivo. Lateral inhibition is a pervasive process in which one cell forces a different identity on its neighbours, and it is unclear how chromatin in equipotent progenitors undergoing lateral inhibition quickly enables distinct, transiently reversible cell fates. Here we report the chromatin and transcriptional underpinnings of differentiation in mouse small intestine crypts, where notch signalling mediates lateral inhibition to assign progenitor cells into absorptive or secretory lineages. Transcript profiles in isolated LGR5(+) intestinal stem cells and secretory and absorptive progenitors indicated that each cell population was distinct and the progenitors specified. Nevertheless, secretory and absorptive progenitors showed comparable levels of H3K4me2 and H3K27ac histone marks and DNase I hypersensitivity--signifying accessible, permissive chromatin-at most of the same cis-elements. Enhancers acting uniquely in progenitors were well demarcated in LGR5(+) intestinal stem cells, revealing early priming of chromatin for divergent transcriptional programs, and retained active marks well after lineages were specified. On this chromatin background, ATOH1, a secretory-specific transcription factor, controls lateral inhibition through delta-like notch ligand genes and also drives the expression of numerous secretory lineage genes. Depletion of ATOH1 from specified secretory cells converted them into functional enterocytes, indicating prolonged responsiveness of marked enhancers to the presence or absence of a key transcription factor. Thus, lateral inhibition and intestinal crypt lineage plasticity involve interaction of a lineage-restricted transcription factor with broadly permissive chromatin established in multipotent stem cells.
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91
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Adult intestinal stem cells: critical drivers of epithelial homeostasis and regeneration. Nat Rev Mol Cell Biol 2013; 15:19-33. [PMID: 24326621 DOI: 10.1038/nrm3721] [Citation(s) in RCA: 828] [Impact Index Per Article: 75.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Small populations of adult stem cells are responsible for the remarkable ability of the epithelial lining of the intestine to be efficiently renewed and repaired throughout life. The recent discovery of specific markers for these stem cells, together with the development of new technologies to track endogenous stem cell activity in vivo and to exploit their ability to generate new epithelia ex vivo, has greatly improved our understanding of stem cell-driven homeostasis, regeneration and cancer in the intestine. These exciting new insights into the biology of intestinal stem cells have the potential to accelerate the development of stem cell-based therapies and ameliorate cancer treatments.
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92
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Song Q, Decato B, Hong EE, Zhou M, Fang F, Qu J, Garvin T, Kessler M, Zhou J, Smith AD. A reference methylome database and analysis pipeline to facilitate integrative and comparative epigenomics. PLoS One 2013; 8:e81148. [PMID: 24324667 PMCID: PMC3855694 DOI: 10.1371/journal.pone.0081148] [Citation(s) in RCA: 246] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 10/18/2013] [Indexed: 12/11/2022] Open
Abstract
DNA methylation is implicated in a surprising diversity of regulatory, evolutionary processes and diseases in eukaryotes. The introduction of whole-genome bisulfite sequencing has enabled the study of DNA methylation at a single-base resolution, revealing many new aspects of DNA methylation and highlighting the usefulness of methylome data in understanding a variety of genomic phenomena. As the number of publicly available whole-genome bisulfite sequencing studies reaches into the hundreds, reliable and convenient tools for comparing and analyzing methylomes become increasingly important. We present MethPipe, a pipeline for both low and high-level methylome analysis, and MethBase, an accompanying database of annotated methylomes from the public domain. Together these resources enable researchers to extract interesting features from methylomes and compare them with those identified in public methylomes in our database.
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Affiliation(s)
- Qiang Song
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Benjamin Decato
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Elizabeth E. Hong
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Meng Zhou
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Fang Fang
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Jianghan Qu
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Tyler Garvin
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Michael Kessler
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Jun Zhou
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Andrew D. Smith
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
- * E-mail:
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93
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Cullen SM, Goodell MA. Rising from the crypt: decreasing DNA methylation during differentiation of the small intestine. Genome Biol 2013; 14:116. [PMID: 23714004 PMCID: PMC4053750 DOI: 10.1186/gb-2013-14-5-116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The differentiation of intestinal stem cells involves few DNA methylation changes, assayed by bisulfite sequencing, in contrast to other adult somatic stem cell hierarchies. Please see related Research article: http://genomebiology.com/2013/14/5/R50
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