1
|
Monteagudo-Sánchez A, Richard Albert J, Scarpa M, Noordermeer D, Greenberg MVC. The impact of the embryonic DNA methylation program on CTCF-mediated genome regulation. Nucleic Acids Res 2024:gkae724. [PMID: 39180406 DOI: 10.1093/nar/gkae724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 07/23/2024] [Accepted: 08/21/2024] [Indexed: 08/26/2024] Open
Abstract
During mammalian embryogenesis, both the 5-cytosine DNA methylation (5meC) landscape and three dimensional (3D) chromatin architecture are profoundly remodeled during a process known as 'epigenetic reprogramming.' An understudied aspect of epigenetic reprogramming is how the 5meC flux, per se, affects the 3D genome. This is pertinent given the 5meC-sensitivity of DNA binding for a key regulator of chromosome folding: CTCF. We profiled the CTCF binding landscape using a mouse embryonic stem cell (ESC) differentiation protocol that models embryonic 5meC dynamics. Mouse ESCs lacking DNA methylation machinery are able to exit naive pluripotency, thus allowing for dissection of subtle effects of CTCF on gene expression. We performed CTCF HiChIP in both wild-type and mutant conditions to assess gained CTCF-CTCF contacts in the absence of 5meC. We performed H3K27ac HiChIP to determine the impact that ectopic CTCF binding has on cis-regulatory contacts. Using 5meC epigenome editing, we demonstrated that the methyl-mark is able to impair CTCF binding at select loci. Finally, a detailed dissection of the imprinted Zdbf2 locus showed how 5meC-antagonism of CTCF allows for proper gene regulation during differentiation. This work provides a comprehensive overview of how 5meC impacts the 3D genome in a relevant model for early embryonic events.
Collapse
Affiliation(s)
| | | | - Margherita Scarpa
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Daan Noordermeer
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), F-91998 Gif-sur-Yvette, France
| | | |
Collapse
|
2
|
Scalia P, Williams SJ, Fujita-Yamaguchi Y. Human IGF2 Gene Epigenetic and Transcriptional Regulation: At the Core of Developmental Growth and Tumorigenic Behavior. Biomedicines 2023; 11:1655. [PMID: 37371750 DOI: 10.3390/biomedicines11061655] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/02/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Regulation of the human IGF2 gene displays multiple layers of control, which secures a genetically and epigenetically predetermined gene expression pattern throughout embryonal growth and postnatal life. These predominantly nuclear regulatory mechanisms converge on the function of the IGF2-H19 gene cluster on Chromosome 11 and ultimately affect IGF2 gene expression. Deregulation of such control checkpoints leads to the enhancement of IGF2 gene transcription and/or transcript stabilization, ultimately leading to IGF-II peptide overproduction. This type of anomaly is responsible for the effects observed in terms of both abnormal fetal growth and increased cell proliferation, typically observed in pediatric overgrowth syndromes and cancer. We performed a review of relevant experimental work on the mechanisms affecting the human IGF2 gene at the epigenetic, transcriptional and transcript regulatory levels. The result of our work, indeed, provides a wider and diversified scenario for IGF2 gene activation than previously envisioned by shedding new light on its extended regulation. Overall, we focused on the functional integration between the epigenetic and genetic machinery driving its overexpression in overgrowth syndromes and malignancy, independently of the underlying presence of loss of imprinting (LOI). The molecular landscape provided at last strengthens the role of IGF2 in cancer initiation, progression and malignant phenotype maintenance. Finally, this review suggests potential actionable targets for IGF2 gene- and regulatory protein target-degradation therapies.
Collapse
Key Words
- (IGF2/H19) IG-DMR, intergenic differentially methylated region
- BWS, Beckwith–Wiedemann syndrome
- CCD, centrally conserved domain
- CNV, copy number variation
- CTCF, CCCTC binding factor
- DMD, differentially methylated domain
- DMR, differentially methylated region
- GOM, gain of methylation
- ICR1, imprinting control region 1
- IGF-II, insulin-like growth factor-2 peptide
- IGF2, insulin-like growth factor 2 gene
- LOI, loss of imprinting
- LOM, loss of methylation
- MOI, maintenance of imprinting
- SRS, Silver Russel Syndrome
- TF: transcription factor
- UPD, uniparental disomy
- WT1, Wilms Tumor protein 1
- mRNA transcript
- p0–p4: IGF2 promoters 0–4
Collapse
Affiliation(s)
- Pierluigi Scalia
- ISOPROG-Somatolink EPFP Research Network, Philadelphia, PA 19102, USA, and 93100 Caltanissetta, Italy
- Sbarro Cancer Institute for Cancer Research and Molecular Medicine, CST, Biology Department, Temple University, Philadelphia, PA 19122, USA
| | - Stephen J Williams
- ISOPROG-Somatolink EPFP Research Network, Philadelphia, PA 19102, USA, and 93100 Caltanissetta, Italy
- Sbarro Cancer Institute for Cancer Research and Molecular Medicine, CST, Biology Department, Temple University, Philadelphia, PA 19122, USA
| | - Yoko Fujita-Yamaguchi
- Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| |
Collapse
|
3
|
Lemma RB, Fleischer T, Martinsen E, Ledsaak M, Kristensen V, Eskeland R, Gabrielsen OS, Mathelier A. Pioneer transcription factors are associated with the modulation of DNA methylation patterns across cancers. Epigenetics Chromatin 2022; 15:13. [PMID: 35440061 PMCID: PMC9016969 DOI: 10.1186/s13072-022-00444-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/14/2022] [Indexed: 12/15/2022] Open
Abstract
Methylation of cytosines on DNA is a prominent modification associated with gene expression regulation. Aberrant DNA methylation patterns have recurrently been linked to dysregulation of the regulatory program in cancer cells. To shed light on the underlying molecular mechanism driving this process, we hypothesised that aberrant methylation patterns could be controlled by the binding of specific transcription factors (TFs) across cancer types. By combining DNA methylation arrays and gene expression data with TF binding sites (TFBSs), we explored the interplay between TF binding and DNA methylation in 19 cancer types. We performed emQTL (expression-methylation quantitative trait loci) analyses independently in each cancer type and identified 13 TFs whose expression levels are correlated with local DNA methylation patterns around their binding sites in at least 2 cancer types. The 13 TFs are mainly associated with local demethylation and are enriched for pioneer function, suggesting a specific role for these TFs in modulating chromatin structure and transcription in cancer patients. Furthermore, we confirmed that de novo methylation is precluded across cancers at CpGs lying in genomic regions enriched for TF binding signatures associated with SP1, CTCF, NRF1, GABPA, KLF9, and/or YY1. The modulation of DNA methylation associated with TF binding was observed at cis-regulatory regions controlling immune- and cancer-associated pathways, corroborating that the emQTL signals were derived from both cancer and tumor-infiltrating cells. As a case example, we experimentally confirmed that FOXA1 knock-down is associated with higher methylation in regions bound by FOXA1 in breast cancer MCF-7 cells. Finally, we reported physical interactions between FOXA1 with TET1 and TET2 both in an in vitro setup and in vivo at physiological levels in MCF-7 cells, adding further support for FOXA1 attracting TET1 and TET2 to induce local demethylation in cancer cells.
Collapse
Affiliation(s)
- Roza Berhanu Lemma
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway
| | - Thomas Fleischer
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Emily Martinsen
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway
- Institute of Basic Medical Sciences, Department of Molecular Medicine, and Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Marit Ledsaak
- Institute of Basic Medical Sciences, Department of Molecular Medicine, and Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Vessela Kristensen
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Ragnhild Eskeland
- Institute of Basic Medical Sciences, Department of Molecular Medicine, and Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | | | - Anthony Mathelier
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway.
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.
| |
Collapse
|
4
|
Chachoua I, Tzelepis I, Dai H, Lim JP, Lewandowska-Ronnegren A, Casagrande FB, Wu S, Vestlund J, Mallet de Lima CD, Bhartiya D, Scholz BA, Martino M, Mehmood R, Göndör A. Canonical WNT signaling-dependent gating of MYC requires a noncanonical CTCF function at a distal binding site. Nat Commun 2022; 13:204. [PMID: 35017527 PMCID: PMC8752836 DOI: 10.1038/s41467-021-27868-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 12/19/2021] [Indexed: 01/21/2023] Open
Abstract
Abnormal WNT signaling increases MYC expression in colon cancer cells in part via oncogenic super-enhancer-(OSE)-mediated gating of the active MYC to the nuclear pore in a poorly understood process. We show here that the principal tenet of the WNT-regulated MYC gating, facilitating nuclear export of the MYC mRNA, is regulated by a CTCF binding site (CTCFBS) within the OSE to confer growth advantage in HCT-116 cells. To achieve this, the CTCFBS directs the WNT-dependent trafficking of the OSE to the nuclear pore from intra-nucleoplasmic positions in a stepwise manner. Once the OSE reaches a peripheral position, which is triggered by a CTCFBS-mediated CCAT1 eRNA activation, its final stretch (≤0.7 μm) to the nuclear pore requires the recruitment of AHCTF1, a key nucleoporin, to the CTCFBS. Thus, a WNT/ß-catenin-AHCTF1-CTCF-eRNA circuit enables the OSE to promote pathological cell growth by coordinating the trafficking of the active MYC gene within the 3D nuclear architecture. Gene-gating of a MYC oncogenic super-enhancer (OSE) increases its expression in colon cancer cells in a poorly understood process. Here the authors show that MYC gating requires a CTCF binding site (CTCFBS) within the OSE that directs the stepwise trafficking of the OSE to the nuclear pore to facilitate increased nuclear export of MYC mRNA, which results in a growth advantage.
Collapse
Affiliation(s)
- Ilyas Chachoua
- Department of Oncology and Pathology, Bioclinicum, Karolinska University Hospital, U2, Akademiska Stråket 1, Karolinska Institutet, Stockholm, Sweden
| | - Ilias Tzelepis
- Department of Oncology and Pathology, Bioclinicum, Karolinska University Hospital, U2, Akademiska Stråket 1, Karolinska Institutet, Stockholm, Sweden
| | - Hao Dai
- Department of Oncology and Pathology, Bioclinicum, Karolinska University Hospital, U2, Akademiska Stråket 1, Karolinska Institutet, Stockholm, Sweden.,Department of Breast Disease, Henan Breast Cancer Center, The affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Jia Pei Lim
- Department of Oncology and Pathology, Bioclinicum, Karolinska University Hospital, U2, Akademiska Stråket 1, Karolinska Institutet, Stockholm, Sweden
| | - Anna Lewandowska-Ronnegren
- Department of Oncology and Pathology, Bioclinicum, Karolinska University Hospital, U2, Akademiska Stråket 1, Karolinska Institutet, Stockholm, Sweden
| | - Felipe Beccaria Casagrande
- Department of Oncology and Pathology, Bioclinicum, Karolinska University Hospital, U2, Akademiska Stråket 1, Karolinska Institutet, Stockholm, Sweden
| | - Shuangyang Wu
- Department of Oncology and Pathology, Bioclinicum, Karolinska University Hospital, U2, Akademiska Stråket 1, Karolinska Institutet, Stockholm, Sweden
| | - Johanna Vestlund
- Department of Oncology and Pathology, Bioclinicum, Karolinska University Hospital, U2, Akademiska Stråket 1, Karolinska Institutet, Stockholm, Sweden
| | - Carolina Diettrich Mallet de Lima
- Department of Oncology and Pathology, Bioclinicum, Karolinska University Hospital, U2, Akademiska Stråket 1, Karolinska Institutet, Stockholm, Sweden
| | - Deeksha Bhartiya
- Department of Oncology and Pathology, Bioclinicum, Karolinska University Hospital, U2, Akademiska Stråket 1, Karolinska Institutet, Stockholm, Sweden
| | - Barbara A Scholz
- Department of Oncology and Pathology, Bioclinicum, Karolinska University Hospital, U2, Akademiska Stråket 1, Karolinska Institutet, Stockholm, Sweden
| | - Mirco Martino
- Department of Oncology and Pathology, Bioclinicum, Karolinska University Hospital, U2, Akademiska Stråket 1, Karolinska Institutet, Stockholm, Sweden
| | - Rashid Mehmood
- Department of Oncology and Pathology, Bioclinicum, Karolinska University Hospital, U2, Akademiska Stråket 1, Karolinska Institutet, Stockholm, Sweden
| | - Anita Göndör
- Department of Oncology and Pathology, Bioclinicum, Karolinska University Hospital, U2, Akademiska Stråket 1, Karolinska Institutet, Stockholm, Sweden.
| |
Collapse
|
5
|
Wang B, Suen CW, Ma H, Wang Y, Kong L, Qin D, Lee YWW, Li G. The Roles of H19 in Regulating Inflammation and Aging. Front Immunol 2020; 11:579687. [PMID: 33193379 PMCID: PMC7653221 DOI: 10.3389/fimmu.2020.579687] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 10/05/2020] [Indexed: 12/17/2022] Open
Abstract
Accumulating evidence suggests that long non-coding RNA H19 correlates with several aging processes. However, the role of H19 in aging remains unclear. Many studies have elucidated a close connection between H19 and inflammatory genes. Chronic systemic inflammation is an established factor associated with various diseases during aging. Thus, H19 might participate in the development of age-related diseases by interplay with inflammation and therefore provide a protective function against age-related diseases. We investigated the inflammatory gene network of H19 to understand its regulatory mechanisms. H19 usually controls gene expression by acting as a microRNA sponge, or through mir-675, or by leading various protein complexes to genes at the chromosome level. The regulatory gene network has been intensively studied, whereas the biogenesis of H19 remains largely unknown. This literature review found that the epithelial-mesenchymal transition (EMT) and an imprinting gene network (IGN) might link H19 with inflammation. Evidence indicates that EMT and IGN are also tightly controlled by environmental stress. We propose that H19 is a stress-induced long non-coding RNA. Because environmental stress is a recognized age-related factor, inflammation and H19 might serve as a therapeutic axis to fight against age-related diseases.
Collapse
Affiliation(s)
- Bin Wang
- The Chinese University of Hong Kong (CUHK)-Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GDL), Advanced Institute for Regenerative MedicineBioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China.,Innovation Center for Translational Medicine, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Chun Wai Suen
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Haibin Ma
- The Chinese University of Hong Kong (CUHK)-Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GDL), Advanced Institute for Regenerative MedicineBioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Yan Wang
- Innovation Center for Translational Medicine, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ling Kong
- The Chinese University of Hong Kong (CUHK)-Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GDL), Advanced Institute for Regenerative MedicineBioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Dajiang Qin
- The Chinese University of Hong Kong (CUHK)-Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GDL), Advanced Institute for Regenerative MedicineBioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China.,Innovation Center for Translational Medicine, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yuk Wai Wayne Lee
- Department of Orthopaedics & Traumatology, Stem Cells and Regenerative Medicine Laboratory, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, China
| | - Gang Li
- The Chinese University of Hong Kong (CUHK)-Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GDL), Advanced Institute for Regenerative MedicineBioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China.,Department of Orthopaedics & Traumatology, Stem Cells and Regenerative Medicine Laboratory, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, China.,Ministry of Education Key Laboratory for Regenerative Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Innovation Center for Translational Medicine, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| |
Collapse
|
6
|
Tong D, Zhang J, Wang X, Li Q, Liu L, Lu A, Guo B, Yang J, Ni L, Qin H, Zhao L, Huang C. MiR-22, regulated by MeCP2, suppresses gastric cancer cell proliferation by inducing a deficiency in endogenous S-adenosylmethionine. Oncogenesis 2020; 9:99. [PMID: 33168819 PMCID: PMC7652948 DOI: 10.1038/s41389-020-00281-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 10/01/2020] [Accepted: 10/08/2020] [Indexed: 02/08/2023] Open
Abstract
This study investigated the effect of methyl-CpG-binding protein 2 (MeCP2) on miRNA transcription. Our results of miRNA chip assay and ChIP-seq showed that MeCP2 inhibited the expressions of numerous miRNAs by binding to their upstream elements, including not only the promoter but also the distal enhancer. Among the affected miRNAs, miR-22 was identified to remarkably suppress gastric cancer (GC) cell proliferation, arrest G1-S cell cycle transition, and induce cell apoptosis by targeting MeCP2, MTHFD2, and MTHFR. Understanding GC metabolism characteristics is the key to developing novel therapies that target GC metabolic pathways. Our study revealed that the metabolic profiles in GC tissues were altered. SAM (S-adenosylmethionine), a universal methyl donor for histone and DNA methylation, which is specifically involved in the epigenetic maintenance of cancer cells, was found increased. The production of SAM is promoted by the folate cycle. Knockdown of MTHFD2 and MTHFR, two key enzymes in folate metabolism and methyl donor SAM production, significantly suppressed GC cell proliferation. MiR-22 overexpression reduced the level of endogenous SAM by suppressing MTHFD2 and MTHFR, inducing P16, PTEN, and RASSF1A hypomethylation. In conclusion, our study suggests that miR-22 was inhibited by MeCP2, resulting in deficiency of endogenous SAM, and ultimately leading to tumor suppressor dysregulation.
Collapse
Affiliation(s)
- Dongdong Tong
- Department of Cell Biology and Genetics/Key Laboratory of Environment and Genes Related to Diseases, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
- Institute of Genetics and Developmental Biology, Translational Medicine Institute, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
| | - Jing Zhang
- Department of Clinical Medicine, Medical College of Yan'an University, Yan'an, 716000, Shanxi, China
| | - Xiaofei Wang
- Department of Cell Biology and Genetics/Key Laboratory of Environment and Genes Related to Diseases, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
| | - Qian Li
- Department of Cell Biology and Genetics/Key Laboratory of Environment and Genes Related to Diseases, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
- Institute of Genetics and Developmental Biology, Translational Medicine Institute, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
| | - Liying Liu
- Department of Cell Biology and Genetics/Key Laboratory of Environment and Genes Related to Diseases, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
| | - Axin Lu
- Instrument Analysis Center, Xi'an Jiaotong University, 710049, Shaanxi Province, China
| | - Bo Guo
- Department of Cell Biology and Genetics/Key Laboratory of Environment and Genes Related to Diseases, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
- Institute of Genetics and Developmental Biology, Translational Medicine Institute, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
| | - Juan Yang
- Department of Cell Biology and Genetics/Key Laboratory of Environment and Genes Related to Diseases, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
- Institute of Genetics and Developmental Biology, Translational Medicine Institute, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
| | - Lei Ni
- Department of Cell Biology and Genetics/Key Laboratory of Environment and Genes Related to Diseases, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
| | - Hao Qin
- Department of peripheral vascular disease, 1st Affiliated Hospital of Xi'an Jiaotong University, 710061, Shaanxi Province, China
| | - Lingyu Zhao
- Department of Cell Biology and Genetics/Key Laboratory of Environment and Genes Related to Diseases, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China.
- Institute of Genetics and Developmental Biology, Translational Medicine Institute, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China.
| | - Chen Huang
- Department of Cell Biology and Genetics/Key Laboratory of Environment and Genes Related to Diseases, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China.
- Institute of Genetics and Developmental Biology, Translational Medicine Institute, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China.
| |
Collapse
|
7
|
Moon Y, Kim I, Chang S, Park B, Lee S, Yoo S, Chae S, Hwang D, Park H. Hypoxia regulates allele-specific histone modification of the imprinted H19 gene. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194643. [DOI: 10.1016/j.bbagrm.2020.194643] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 07/29/2020] [Accepted: 10/02/2020] [Indexed: 01/20/2023]
|
8
|
Alharbi AB, Schmitz U, Marshall AD, Vanichkina D, Nagarajah R, Vellozzi M, Wong JJ, Bailey CG, Rasko JE. Ctcf haploinsufficiency mediates intron retention in a tissue-specific manner. RNA Biol 2020; 18:93-103. [PMID: 32816606 PMCID: PMC7834090 DOI: 10.1080/15476286.2020.1796052] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
CTCF is a master regulator of gene transcription and chromatin organisation with occupancy at thousands of DNA target sites genome-wide. While CTCF is essential for cell survival, CTCF haploinsufficiency is associated with tumour development and hypermethylation. Increasing evidence demonstrates CTCF as a key player in several mechanisms regulating alternative splicing (AS), however, the genome-wide impact of Ctcf dosage on AS has not been investigated. We examined the effect of Ctcf haploinsufficiency on gene expression and AS in five tissues from Ctcf hemizygous (Ctcf+/-) mice. Reduced Ctcf levels caused distinct tissue-specific differences in gene expression and AS in all tissues. An increase in intron retention (IR) was observed in Ctcf+/- liver and kidney. In liver, this specifically impacted genes associated with cytoskeletal organisation, splicing and metabolism. Strikingly, most differentially retained introns were short, with a high GC content and enriched in Ctcf binding sites in their proximal upstream genomic region. This study provides new insights into the effects of CTCF haploinsufficiency on organ transcriptomes and the role of CTCF in AS regulation.
Collapse
Affiliation(s)
- Adel B Alharbi
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney , Camperdown, Australia.,Computational BioMedicine Laboratory Centenary Institute, The University of Sydney , Camperdown, Australia.,Faculty of Medicine and Health, The University of Sydney , Camperdown, Australia.,Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Umm Al-Qura University , Makkah, Saudi Arabia
| | - Ulf Schmitz
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney , Camperdown, Australia.,Computational BioMedicine Laboratory Centenary Institute, The University of Sydney , Camperdown, Australia.,Faculty of Medicine and Health, The University of Sydney , Camperdown, Australia
| | - Amy D Marshall
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney , Camperdown, Australia
| | - Darya Vanichkina
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney , Camperdown, Australia.,Faculty of Medicine and Health, The University of Sydney , Camperdown, Australia.,Sydney Informatics Hub, University of Sydney , Darlington, Australia
| | - Rajini Nagarajah
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney , Camperdown, Australia
| | - Melissa Vellozzi
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney , Camperdown, Australia.,Computational BioMedicine Laboratory Centenary Institute, The University of Sydney , Camperdown, Australia
| | - Justin Jl Wong
- Faculty of Medicine and Health, The University of Sydney , Camperdown, Australia.,Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney , Camperdown, Australia
| | - Charles G Bailey
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney , Camperdown, Australia.,Faculty of Medicine and Health, The University of Sydney , Camperdown, Australia
| | - John Ej Rasko
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney , Camperdown, Australia.,Faculty of Medicine and Health, The University of Sydney , Camperdown, Australia.,Cell & Molecular Therapies, Royal Prince Alfred Hospital , Camperdown, Australia
| |
Collapse
|
9
|
Patel M, Patel D, Datta S, Singh U. CGGBP1-regulated cytosine methylation at CTCF-binding motifs resists stochasticity. BMC Genet 2020; 21:84. [PMID: 32727353 PMCID: PMC7392725 DOI: 10.1186/s12863-020-00894-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 07/23/2020] [Indexed: 12/03/2022] Open
Abstract
Background The human CGGBP1 binds to GC-rich regions and interspersed repeats, maintains homeostasis of stochastic cytosine methylation and determines DNA-binding of CTCF. Interdependence between regulation of cytosine methylation and CTCF occupancy by CGGBP1 remains unknown. Results By analyzing methylated DNA-sequencing data obtained from CGGBP1-depleted cells, we report that some transcription factor-binding sites, including CTCF, resist stochastic changes in cytosine methylation. By analysing CTCF-binding sites we show that cytosine methylation changes at CTCF motifs caused by CGGBP1 depletion resist stochastic changes. These CTCF-binding sites are positioned at locations where the spread of cytosine methylation in cis depends on the levels of CGGBP1. Conclusion Our findings suggest that CTCF occupancy and functions are determined by CGGBP1-regulated cytosine methylation patterns.
Collapse
Affiliation(s)
- Manthan Patel
- HoMeCell Lab, Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, 382355, Gujarat, India
| | - Divyesh Patel
- HoMeCell Lab, Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, 382355, Gujarat, India
| | - Subhamoy Datta
- HoMeCell Lab, Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, 382355, Gujarat, India
| | - Umashankar Singh
- HoMeCell Lab, Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, 382355, Gujarat, India.
| |
Collapse
|
10
|
Hori N, Kubo S, Sakasegawa T, Sakurai C, Hatsuzawa K. OCT3/4-binding sequence-dependent maintenance of the unmethylated state of CTCF-binding sequences with DNA demethylation and suppression of de novo DNA methylation in the H19 imprinted control region. Gene 2020; 743:144606. [DOI: 10.1016/j.gene.2020.144606] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 03/16/2020] [Accepted: 03/18/2020] [Indexed: 11/25/2022]
|
11
|
Wang AJ, Han Y, Jia N, Chen P, Minden MD. NPM1c impedes CTCF functions through cytoplasmic mislocalization in acute myeloid leukemia. Leukemia 2019; 34:1278-1290. [PMID: 31831844 DOI: 10.1038/s41375-019-0681-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 11/10/2019] [Accepted: 12/05/2019] [Indexed: 11/09/2022]
Abstract
Normal cytogenetic acute myeloid leukemia (AML) frequently harbor a TCTG insertion in exon 12 of Nucleophosmin 1 (NPM1); the resulting frameshift creates a nuclear export signal (NES) and cytoplasmic localization of NPM1c. However, how NPM1c causes AML is not completely understood. NPM1 participates in multiple protein-protein interactions one of which involves the CCCTC-binding factor (CTCF). Through binding of CTCF binding sites (CBS), CTCF mediates nuclear functions including DNA looping, regulation of gene expression, and RNA splicing. We hypothesized that mislocalization of CTCF into the cytoplasm by NPM1c reduces the functional level of nuclear CTCF and so alters gene expression. We verified the interaction of CTCF with NPM1 and showed that CTCF interacts with NPM1c, with redistribution of CTCF into the cytoplasm. The interaction of CTCF and NPM1c involves the amino terminus of CTCF and the last 50 amino acids of NPM1. By interfering with the interaction of CTCF and NPM1c, CTCF becomes relocalized into the nucleus.
Collapse
Affiliation(s)
- Atom J Wang
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Center, University Health Network, Toronto, Canada.,Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Youqi Han
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Center, University Health Network, Toronto, Canada
| | - Nanyang Jia
- Department of Computer Science, Faculty of Arts and Science, University of Toronto, Toronto, Canada
| | - Peikun Chen
- Department of Computer Science, Faculty of Arts and Science, University of Toronto, Toronto, Canada
| | - Mark D Minden
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Center, University Health Network, Toronto, Canada. .,Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Canada.
| |
Collapse
|
12
|
Scholz BA, Sumida N, de Lima CDM, Chachoua I, Martino M, Tzelepis I, Nikoshkov A, Zhao H, Mehmood R, Sifakis EG, Bhartiya D, Göndör A, Ohlsson R. WNT signaling and AHCTF1 promote oncogenic MYC expression through super-enhancer-mediated gene gating. Nat Genet 2019; 51:1723-1731. [DOI: 10.1038/s41588-019-0535-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 10/23/2019] [Indexed: 01/10/2023]
|
13
|
|
14
|
Freschi A, Hur SK, Valente FM, Ideraabdullah FY, Sparago A, Gentile MT, Oneglia A, Di Nucci D, Colucci-D'Amato L, Thorvaldsen JL, Bartolomei MS, Riccio A, Cerrato F. Tissue-specific and mosaic imprinting defects underlie opposite congenital growth disorders in mice. PLoS Genet 2018; 14:e1007243. [PMID: 29470501 PMCID: PMC5839592 DOI: 10.1371/journal.pgen.1007243] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 03/06/2018] [Accepted: 02/05/2018] [Indexed: 11/18/2022] Open
Abstract
Differential DNA methylation defects of H19/IGF2 are associated with congenital growth disorders characterized by opposite clinical pictures. Due to structural differences between human and mouse, the mechanisms by which mutations of the H19/IGF2 Imprinting Control region (IC1) result in these diseases are undefined. To address this issue, we previously generated a mouse line carrying a humanized IC1 (hIC1) and now replaced the wildtype with a mutant IC1 identified in the overgrowth-associated Beckwith-Wiedemann syndrome. The new humanized mouse line shows pre/post-natal overgrowth on maternal transmission and pre/post-natal undergrowth on paternal transmission of the mutation. The mutant hIC1 acquires abnormal methylation during development causing opposite H19/Igf2 imprinting defects on maternal and paternal chromosomes. Differential and possibly mosaic Igf2 expression and imprinting is associated with asymmetric growth of bilateral organs. Furthermore, tissue-specific imprinting defects result in deficient liver- and placenta-derived Igf2 on paternal transmission and excessive Igf2 in peripheral tissues on maternal transmission, providing a possible molecular explanation for imprinting-associated and phenotypically contrasting growth disorders.
Collapse
Affiliation(s)
- Andrea Freschi
- Department of Environmental Technologies, Biological and Pharmaceutical Sciences, University of Campania, "Luigi Vanvitelli", Naples, Italy
| | - Stella K Hur
- Epigenetics Institute, Department of Cell & Developmental Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Federica Maria Valente
- Department of Environmental Technologies, Biological and Pharmaceutical Sciences, University of Campania, "Luigi Vanvitelli", Naples, Italy
| | - Folami Y Ideraabdullah
- Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America.,Department of Nutrition, Gillings School of Public Health, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Angela Sparago
- Department of Environmental Technologies, Biological and Pharmaceutical Sciences, University of Campania, "Luigi Vanvitelli", Naples, Italy
| | - Maria Teresa Gentile
- Department of Environmental Technologies, Biological and Pharmaceutical Sciences, University of Campania, "Luigi Vanvitelli", Naples, Italy
| | - Andrea Oneglia
- Department of Environmental Technologies, Biological and Pharmaceutical Sciences, University of Campania, "Luigi Vanvitelli", Naples, Italy.,Institute of Genetics and Biophysics, "Adriano Buzzati Traverso" - CNR, Naples, Italy
| | - Diego Di Nucci
- Department of Experimental Medicine, University of Campania, "Luigi Vanvitelli", Naples, Italy
| | - Luca Colucci-D'Amato
- Department of Environmental Technologies, Biological and Pharmaceutical Sciences, University of Campania, "Luigi Vanvitelli", Naples, Italy
| | - Joanne L Thorvaldsen
- Epigenetics Institute, Department of Cell & Developmental Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Marisa S Bartolomei
- Epigenetics Institute, Department of Cell & Developmental Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Andrea Riccio
- Department of Environmental Technologies, Biological and Pharmaceutical Sciences, University of Campania, "Luigi Vanvitelli", Naples, Italy.,Institute of Genetics and Biophysics, "Adriano Buzzati Traverso" - CNR, Naples, Italy
| | - Flavia Cerrato
- Department of Environmental Technologies, Biological and Pharmaceutical Sciences, University of Campania, "Luigi Vanvitelli", Naples, Italy
| |
Collapse
|
15
|
Damaschke NA, Yang B, Bhusari S, Avilla M, Zhong W, Blute ML, Huang W, Jarrard DF. Loss of Igf2 Gene Imprinting in Murine Prostate Promotes Widespread Neoplastic Growth. Cancer Res 2017; 77:5236-5247. [PMID: 28775169 PMCID: PMC9741865 DOI: 10.1158/0008-5472.can-16-3089] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 05/12/2017] [Accepted: 07/28/2017] [Indexed: 02/07/2023]
Abstract
Loss of imprinting (LOI) is an epigenetic event that relaxes an allele-specific restriction on gene expression. One gene that experiences LOI is the paracrine insulin-like growth factor IGF2, which occurs commonly in human prostate tissues during aging and tumorigenesis. However, the relationship between IGF2 LOI and prostate tumorigenesis has not been established functionally. In this study, we created a mouse model with CTCF-binding site mutations at the Igf2-H19 imprint control region that abolishes CTCF insulator activity, resulting in biallelic Igf2 expression that mimics increased levels seen with aging-induced LOI. We found that Igf2 LOI increased the prevalence and severity of prostatic intraepithelial neoplasia (PIN), a premalignant lesion. Engineering Nkx3.1 deficiency into our model increased the frequency of PIN lesions in an additive fashion. Prostates harboring LOI displayed increased MAPK signaling and epithelial proliferation. In human prostate tissue arrays, we documented a positive correlation in benign tissues of IGF2 levels with phospho-ERK and phospho-AKT levels. Overall, our results establish that Igf2 LOI is sufficient on its own to increase rates of neoplastic development in the prostate by upregulating critical cancer-associated signaling pathways. Cancer Res; 77(19); 5236-47. ©2017 AACR.
Collapse
Affiliation(s)
- Nathan A. Damaschke
- Department of Urology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Bing Yang
- Department of Urology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Sachin Bhusari
- Department of Urology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Mele Avilla
- Department of Urology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Weixiong Zhong
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI, USA
| | - Michael L. Blute
- Department of Urology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Wei Huang
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI, USA
| | - David F. Jarrard
- Department of Urology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA, Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA, University of Wisconsin Carbone Comprehensive Cancer Center, Madison, WI, USA, Environmental and Molecular Toxicology, University of Wisconsin, Madison, WI, USA Madison, WI, USA,Corresponding author: D.F. Jarrard, M.D, 7037 Wisconsin Institute for Medical Research, 1111 Highland Avenue, Madison, WI 53792. Phone 608-252-0937, Fax (608)265-0614,
| |
Collapse
|
16
|
Monte E, Rosa-Garrido M, Karbassi E, Chen H, Lopez R, Rau CD, Wang J, Nelson SF, Wu Y, Stefani E, Lusis AJ, Wang Y, Kurdistani SK, Franklin S, Vondriska TM. Reciprocal Regulation of the Cardiac Epigenome by Chromatin Structural Proteins Hmgb and Ctcf: IMPLICATIONS FOR TRANSCRIPTIONAL REGULATION. J Biol Chem 2016; 291:15428-46. [PMID: 27226577 DOI: 10.1074/jbc.m116.719633] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Indexed: 02/05/2023] Open
Abstract
Transcriptome remodeling in heart disease occurs through the coordinated actions of transcription factors, histone modifications, and other chromatin features at pathology-associated genes. The extent to which genome-wide chromatin reorganization also contributes to the resultant changes in gene expression remains unknown. We examined the roles of two chromatin structural proteins, Ctcf (CCCTC-binding factor) and Hmgb2 (high mobility group protein B2), in regulating pathologic transcription and chromatin remodeling. Our data demonstrate a reciprocal relationship between Hmgb2 and Ctcf in controlling aspects of chromatin structure and gene expression. Both proteins regulate each others' expression as well as transcription in cardiac myocytes; however, only Hmgb2 does so in a manner that involves global reprogramming of chromatin accessibility. We demonstrate that the actions of Hmgb2 on local chromatin accessibility are conserved across genomic loci, whereas the effects on transcription are loci-dependent and emerge in concert with histone modification and other chromatin features. Finally, although both proteins share gene targets, Hmgb2 and Ctcf, neither binds these genes simultaneously nor do they physically colocalize in myocyte nuclei. Our study uncovers a previously unknown relationship between these two ubiquitous chromatin proteins and provides a mechanistic explanation for how Hmgb2 regulates gene expression and cellular phenotype. Furthermore, we provide direct evidence for structural remodeling of chromatin on a genome-wide scale in the setting of cardiac disease.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Yong Wu
- From the Departments of Anesthesiology
| | | | - Aldons J Lusis
- Medicine, Human Genetics, Microbiology, Immunology and Molecular Genetics, and
| | - Yibin Wang
- From the Departments of Anesthesiology, Medicine, Physiology, David Geffen School of Medicine at UCLA, Los Angeles, California 90095 and
| | | | - Sarah Franklin
- the Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah 84112
| | - Thomas M Vondriska
- From the Departments of Anesthesiology, Medicine, Physiology, David Geffen School of Medicine at UCLA, Los Angeles, California 90095 and
| |
Collapse
|
17
|
Marcho C, Bevilacqua A, Tremblay KD, Mager J. Tissue-specific regulation of Igf2r/Airn imprinting during gastrulation. Epigenetics Chromatin 2015; 8:10. [PMID: 25918552 PMCID: PMC4410455 DOI: 10.1186/s13072-015-0003-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 02/13/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Appropriate epigenetic regulation of gene expression during lineage allocation and tissue differentiation is required for normal development. One example is genomic imprinting, which is defined as parent-of-origin mono-allelic gene expression. Imprinting is established largely due to epigenetic differences arriving in the zygote from sperm and egg haploid genomes. In the mouse, there are approximately 150 known imprinted genes, many of which occur in imprinted gene clusters that are regulated together. One imprinted cluster includes the maternally expressed Igf2r, Slc22a2, and Slc22a3 genes and the paternally expressed long non-coding RNA (lncRNA) Airn. Although it is known that Igf2r and Airn are reciprocally imprinted, the timing of imprinted expression and accompanying epigenetic changes have not been well characterized in vivo. RESULTS Here we show lineage- and temporal-specific regulation of DNA methylation and histone modifications at the Igf2r/Airn locus correlating with differential establishment of imprinted expression during gastrulation. Our results show that Igf2r is expressed from both alleles in the E6.5 epiblast. After gastrulation commences, the locus becomes imprinted in the embryonic lineage with the lncRNA Airn expressed from the paternal allele and Igf2r restricted to maternal allele expression. We document differentially enriched allele-specific histone modifications in extraembryonic and embryonic tissues. We also document for the first time allele-specific spreading of DNA methylation during gastrulation concurrent with establishment of imprinted expression of Igf2r. Importantly, we show that imprinted expression does not change in the extraembryonic lineage even though maternal DMR2 methylation spreading does occur, suggesting distinct mechanisms at play in embryonic and extraembryonic lineages. CONCLUSIONS These results indicate that similar to preimplantation, gastrulation represents a window of dynamic lineage-specific epigenetic regulation in vivo.
Collapse
Affiliation(s)
- Chelsea Marcho
- Department of Veterinary and Animal Sciences, University of Massachusetts at Amherst, ISB 427M, 661 N. Pleasant Street, Amherst, MA 01003 USA
| | - Ariana Bevilacqua
- Department of Veterinary and Animal Sciences, University of Massachusetts at Amherst, ISB 427M, 661 N. Pleasant Street, Amherst, MA 01003 USA
| | - Kimberly D Tremblay
- Department of Veterinary and Animal Sciences, University of Massachusetts at Amherst, ISB 427M, 661 N. Pleasant Street, Amherst, MA 01003 USA
| | - Jesse Mager
- Department of Veterinary and Animal Sciences, University of Massachusetts at Amherst, ISB 427M, 661 N. Pleasant Street, Amherst, MA 01003 USA
| |
Collapse
|
18
|
Schoborg T, Labrador M. Expanding the roles of chromatin insulators in nuclear architecture, chromatin organization and genome function. Cell Mol Life Sci 2014; 71:4089-113. [PMID: 25012699 PMCID: PMC11113341 DOI: 10.1007/s00018-014-1672-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 05/31/2014] [Accepted: 06/23/2014] [Indexed: 01/08/2023]
Abstract
Of the numerous classes of elements involved in modulating eukaryotic chromosome structure and function, chromatin insulators arguably remain the most poorly understood in their contribution to these processes in vivo. Indeed, our view of chromatin insulators has evolved dramatically since their chromatin boundary and enhancer blocking properties were elucidated roughly a quarter of a century ago as a result of recent genome-wide, high-throughput methods better suited to probing the role of these elements in their native genomic contexts. The overall theme that has emerged from these studies is that chromatin insulators function as general facilitators of higher-order chromatin loop structures that exert both physical and functional constraints on the genome. In this review, we summarize the result of recent work that supports this idea as well as a number of other studies linking these elements to a diverse array of nuclear processes, suggesting that chromatin insulators exert master control over genome organization and behavior.
Collapse
Affiliation(s)
- Todd Schoborg
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland Avenue, Knoxville, TN 37996 USA
- Present Address: Laboratory of Molecular Machines and Tissue Architecture, Cell Biology and Physiology Center, National Heart, Lung and Blood Institute, National Institutes of Health, 50 South Dr Rm 2122, Bethesda, MD 20892 USA
| | - Mariano Labrador
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland Avenue, Knoxville, TN 37996 USA
| |
Collapse
|
19
|
Ideraabdullah FY, Thorvaldsen JL, Myers JA, Bartolomei MS. Tissue-specific insulator function at H19/Igf2 revealed by deletions at the imprinting control region. Hum Mol Genet 2014; 23:6246-59. [PMID: 24990148 DOI: 10.1093/hmg/ddu344] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Parent-of-origin-specific expression at imprinted genes is regulated by allele-specific DNA methylation at imprinting control regions (ICRs). This mechanism of gene regulation, where one element controls allelic expression of multiple genes, is not fully understood. Furthermore, the mechanism of gene dysregulation through ICR epimutations, such as loss or gain of DNA methylation, remains a mystery. We have used genetic mouse models to dissect ICR-mediated genetic and epigenetic regulation of imprinted gene expression. The H19/insulin-like growth factor 2 (Igf2) ICR has a multifunctional role including insulation, activation and repression. Microdeletions at the human H19/IGF2 ICR (IC1) are proposed to be responsible for IC1 epimutations associated with imprinting disorders such as Beckwith-Wiedemann syndrome (BWS). Here, we have generated and characterized a mouse model that mimics BWS microdeletions to define the role of the deleted sequence in establishing and maintaining epigenetic marks and imprinted expression at the H19/IGF2 locus. These mice carry a 1.3 kb deletion at the H19/Igf2 ICR [Δ2,3] removing two of four CCCTC-binding factor (CTCF) sites and the intervening sequence, ∼75% of the ICR. Surprisingly, the Δ2,3 deletion does not perturb DNA methylation at the ICR; however, it does disrupt imprinted expression. While repressive functions of the ICR are compromised by the deletion regardless of tissue type, insulator function is only disrupted in tissues of mesodermal origin where a significant amount of CTCF is poly(ADP-ribosyl)ated. These findings suggest that insulator activity of the H19/Igf2 ICR varies by cell type and may depend on cell-specific enhancers as well as posttranslational modifications of the insulator protein CTCF.
Collapse
Affiliation(s)
- Folami Y Ideraabdullah
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, 9-123 SCTR, 3400 Civic Center Boulevard, Philadelphia PA 19104, USA and Department of Genetics, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA
| | - Joanne L Thorvaldsen
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, 9-123 SCTR, 3400 Civic Center Boulevard, Philadelphia PA 19104, USA and
| | - Jennifer A Myers
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, 9-123 SCTR, 3400 Civic Center Boulevard, Philadelphia PA 19104, USA and
| | - Marisa S Bartolomei
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, 9-123 SCTR, 3400 Civic Center Boulevard, Philadelphia PA 19104, USA and
| |
Collapse
|
20
|
Zhang H, Zhu L, He H, Zhu S, Zhang W, Liu X, Zhao X, Gao C, Mei M, Bao S, Zheng H. NF-kappa B mediated up-regulation of CCCTC-binding factor in pediatric acute lymphoblastic leukemia. Mol Cancer 2014; 13:5. [PMID: 24393203 PMCID: PMC3928924 DOI: 10.1186/1476-4598-13-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 01/03/2014] [Indexed: 11/25/2022] Open
Abstract
Background Acute lymphoblastic leukemia (ALL) is the most frequently occurring malignant neoplasm in children. Despite advances in treatment and outcomes for ALL patients, the pathogenesis of the disease remains unclear. Microarray analysis of samples from 100 Chinese children with ALL revealed the up-regulation of CTCF (CCCTC binding factor). CTCF is a highly conserved 11-zinc finger protein that is involved in many human cancers; however, the biological function of CTCF in pediatric ALL is unknown. Methods The expression patterns of CTCF were evaluated in matched newly diagnosed (ND), complete remission (CR), and relapsed (RE) bone marrow samples from 28 patients. The potential oncogenic mechanism of CTCF and related pathways in leukemogenesis were investigated in leukemia cell lines. Results We identified significant up-regulation of CTCF in the ND samples. Importantly, the expression of CTCF returned to normal levels after CR but rebounded in the RE samples. In the pre-B ALL cell line Nalm-6, siRNA-mediated silencing of CTCF expression promoted cell apoptosis and reduced cell proliferation; accordingly, over-expression of a cDNA encoding full-length CTCF protected cells from apoptosis and enhanced cell proliferation. Furthermore, inhibition or activation of the nuclear factor-kappa B (NF-κB) pathway resulted in marked variations in the levels of CTCF mRNA and protein in leukemic cells, indicating that CTCF may be involved downstream of the NF-κB pathway. Moreover, inhibition of the NF-κB pathway increased cell apoptosis, which was partially rescued by ectopic over-expression of CTCF, suggesting that CTCF may play a significant role in the anti-apoptotic pathway mediated by NF-κB. Conclusions Our results indicate that CTCF serves as both an anti-apoptotic factor and a proliferative factor in leukemic cells. It potentially contributes to leukemogenesis through the NF-κB pathway in pediatric ALL patients.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Shilai Bao
- Beijing Key Laboratory of Pediatric Hematology Oncology; National Key Discipline of Pediatrics, Ministry of Education; Key Laboratory of Major Diseases in Children, Ministry of Education; Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, 56 Nanlishi Road, Beijing, 100045, China.
| | | |
Collapse
|
21
|
Martínez JA, Milagro FI, Claycombe KJ, Schalinske KL. Epigenetics in adipose tissue, obesity, weight loss, and diabetes. Adv Nutr 2014; 5:71-81. [PMID: 24425725 PMCID: PMC3884103 DOI: 10.3945/an.113.004705] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Given the role that diet and other environmental factors play in the development of obesity and type 2 diabetes, the implication of different epigenetic processes is being investigated. Although it is well known that external factors can cause cell type-dependent epigenetic changes, including DNA methylation, histone tail modifications, and chromatin remodeling, the regulation of these processes, the magnitude of the changes and the cell types in which they occur, the individuals more predisposed, and the more crucial stages of life remain to be elucidated. There is evidence that obese and diabetic people have a pattern of epigenetic marks different from nonobese and nondiabetic individuals. The main long-term goals in this field are the identification and understanding of the role of epigenetic marks that could be used as early predictors of metabolic risk and the development of drugs or diet-related treatments able to delay these epigenetic changes and even reverse them. But weight gain and insulin resistance/diabetes are influenced not only by epigenetic factors; different epigenetic biomarkers have also been identified as early predictors of weight loss and the maintenance of body weight after weight loss. The characterization of all the factors that are able to modify the epigenetic signatures and the determination of their real importance are hindered by the following factors: the magnitude of change produced by dietary and environmental factors is small and cumulative; there are great differences among cell types; and there are many factors involved, including age, with multiple interactions between them.
Collapse
Affiliation(s)
- J. Alfredo Martínez
- Department of Nutrition, Food Science and Physiology, University of Navarra, Pamplona, Spain,CIBERobn, Physiopathology of Obesity and Nutrition, Institute of Health Carlos III, Madrid, Spain,To whom correspondence should be addressed. E-mail:
| | - Fermín I. Milagro
- Department of Nutrition, Food Science and Physiology, University of Navarra, Pamplona, Spain,CIBERobn, Physiopathology of Obesity and Nutrition, Institute of Health Carlos III, Madrid, Spain
| | - Kate J. Claycombe
- USDA-Agricultural Research Service, Grand Forks Human Nutrition Research Center, Grand Forks, ND; and
| | - Kevin L. Schalinske
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA
| |
Collapse
|
22
|
Higashimoto K, Jozaki K, Kosho T, Matsubara K, Fuke T, Yamada D, Yatsuki H, Maeda T, Ohtsuka Y, Nishioka K, Joh K, Koseki H, Ogata T, Soejima H. A novel de novo point mutation of the OCT-binding site in the IGF2/H19-imprinting control region in a Beckwith-Wiedemann syndrome patient. Clin Genet 2013; 86:539-44. [PMID: 24299031 DOI: 10.1111/cge.12318] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 10/21/2013] [Accepted: 11/06/2013] [Indexed: 11/29/2022]
Abstract
The IGF2/H19-imprinting control region (ICR1) functions as an insulator to methylation-sensitive binding of CTCF protein, and regulates imprinted expression of IGF2 and H19 in a parental origin-specific manner. ICR1 methylation defects cause abnormal expression of imprinted genes, leading to Beckwith-Wiedemann syndrome (BWS) or Silver-Russell syndrome (SRS). Not only ICR1 microdeletions involving the CTCF-binding site, but also point mutations and a small deletion of the OCT-binding site have been shown to trigger methylation defects in BWS. Here, mutational analysis of ICR1 in 11 BWS and 12 SRS patients with ICR1 methylation defects revealed a novel de novo point mutation of the OCT-binding site on the maternal allele in one BWS patient. In BWS, all reported mutations and the small deletion of the OCT-binding site, including our case, have occurred within repeat A2. These findings indicate that the OCT-binding site is important for maintaining an unmethylated status of maternal ICR1 in early embryogenesis.
Collapse
Affiliation(s)
- K Higashimoto
- Division of Molecular Genetics & Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, Japan
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Claycombe KJ, Uthus EO, Roemmich JN, Johnson LK, Johnson WT. Prenatal low-protein and postnatal high-fat diets induce rapid adipose tissue growth by inducing Igf2 expression in Sprague Dawley rat offspring. J Nutr 2013; 143:1533-9. [PMID: 23946348 DOI: 10.3945/jn.113.178038] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Maternal low-protein diets result in lower birth weight followed by accelerated catch-up growth that is accompanied by the development of obesity and glucose intolerance in later life. Whether postnatal high-fat (HF) diets further contribute to the development of obesity and insulin resistance in offspring by affecting adipose tissue metabolism and DNA methylation is currently unknown. Obese-prone Sprague-Dawley rats were fed 8% low protein (LP) or 20% normal protein diets for 3 wk prior to conception and throughout pregnancy and lactation to investigate whether prenatal LP and postnatal HF diets affect the rate of adipose tissue growth, insulin-like growth factor 2 (Igf2) expression, and DNA methylation in male offspring. At weaning, the offspring were fed 10% normal fat or 45% HF diets for 12 wk. The adipose tissue growth rate was increased (up to 26-fold) by the LP prenatal and HF postnatal diets. Adipose tissue Igf2 mRNAs and DNA methylation were increased by the LP prenatal and HF postnatal diets. The LP prenatal and HF postnatal diet increased the number of small adipocytes in adipose tissue and decreased insulin sensitivity. These findings suggest that prenatal LP and postnatal HF intake result in adipose tissue catch-up growth through alterations in the expression of the Igf2 gene and DNA methylation within adipocytes. These alterations in adiposity are accompanied by an increased risk of development of type 2 diabetes.
Collapse
Affiliation(s)
- Kate J Claycombe
- USDA Agricultural Research Service, Grand Forks Human Nutrition Research Center, Grand Forks, ND
| | | | | | | | | |
Collapse
|
24
|
Sakaguchi R, Okamura E, Matsuzaki H, Fukamizu A, Tanimoto K. Sox-Oct motifs contribute to maintenance of the unmethylated H19 ICR in YAC transgenic mice. Hum Mol Genet 2013; 22:4627-37. [DOI: 10.1093/hmg/ddt311] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
|
25
|
Regional DNA methylation differences between humans and chimpanzees are associated with genetic changes, transcriptional divergence and disease genes. J Hum Genet 2013; 58:446-54. [PMID: 23739127 DOI: 10.1038/jhg.2013.55] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 04/26/2013] [Accepted: 05/01/2013] [Indexed: 12/22/2022]
Abstract
Changes in gene expression have been proposed to have an important role in the evolutionary changes in phenotypes. Interspecific changes in gene expression can result not only from genetic changes in regulatory regions but also from epigenetic changes in such regions. Here we report the identification of genomic regions showing differences in DNA methylation between humans and chimpanzees (termed S-DMRs for species-specific differentially methylated regions) on chromosomes 21 and 22. These regional methylation differences are frequently associated with genes, including those relevant to a disease, such as Alzheimer's disease, diabetes mellitus or cancer. Methylation differences are often correlated with changes in promoter activity or alternative splicing. Comparative studies including other great ape species provide evidence for the contribution of genetic changes to some of these S-DMRs. Genetic changes responsible for the S-DMRs include gain or loss of CTCF-binding site and changes in CpG density in microsatellite repeats. Our results suggest that DNA methylation changes, often caused by small sequence changes, contribute to transcriptional and phenotypic diversification in hominid evolution.
Collapse
|
26
|
Wang H, Maurano MT, Qu H, Varley KE, Gertz J, Pauli F, Lee K, Canfield T, Weaver M, Sandstrom R, Thurman RE, Kaul R, Myers RM, Stamatoyannopoulos JA. Widespread plasticity in CTCF occupancy linked to DNA methylation. Genome Res 2013; 22:1680-8. [PMID: 22955980 PMCID: PMC3431485 DOI: 10.1101/gr.136101.111] [Citation(s) in RCA: 433] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
CTCF is a ubiquitously expressed regulator of fundamental genomic processes including transcription, intra- and interchromosomal interactions, and chromatin structure. Because of its critical role in genome function, CTCF binding patterns have long been assumed to be largely invariant across different cellular environments. Here we analyze genome-wide occupancy patterns of CTCF by ChIP-seq in 19 diverse human cell types, including normal primary cells and immortal lines. We observed highly reproducible yet surprisingly plastic genomic binding landscapes, indicative of strong cell-selective regulation of CTCF occupancy. Comparison with massively parallel bisulfite sequencing data indicates that 41% of variable CTCF binding is linked to differential DNA methylation, concentrated at two critical positions within the CTCF recognition sequence. Unexpectedly, CTCF binding patterns were markedly different in normal versus immortal cells, with the latter showing widespread disruption of CTCF binding associated with increased methylation. Strikingly, this disruption is accompanied by up-regulation of CTCF expression, with the result that both normal and immortal cells maintain the same average number of CTCF occupancy sites genome-wide. These results reveal a tight linkage between DNA methylation and the global occupancy patterns of a major sequence-specific regulatory factor.
Collapse
Affiliation(s)
- Hao Wang
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Beygo J, Citro V, Sparago A, De Crescenzo A, Cerrato F, Heitmann M, Rademacher K, Guala A, Enklaar T, Anichini C, Cirillo Silengo M, Graf N, Prawitt D, Cubellis MV, Horsthemke B, Buiting K, Riccio A. The molecular function and clinical phenotype of partial deletions of the IGF2/H19 imprinting control region depends on the spatial arrangement of the remaining CTCF-binding sites. Hum Mol Genet 2012; 22:544-57. [PMID: 23118352 PMCID: PMC3542864 DOI: 10.1093/hmg/dds465] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
At chromosome 11p15.5, the imprinting centre 1 (IC1) controls the parent of origin-specific expression of the IGF2 and H19 genes. The 5 kb IC1 region contains multiple target sites (CTS) for the zinc-finger protein CTCF, whose binding on the maternal chromosome prevents the activation of IGF2 and allows that of H19 by common enhancers. CTCF binding helps maintaining the maternal IC1 methylation-free, whereas on the paternal chromosome gamete-inherited DNA methylation inhibits CTCF interaction and enhancer-blocking activity resulting in IGF2 activation and H19 silencing. Maternally inherited 1.4–2.2 kb deletions are associated with methylation of the residual CTSs and Beckwith–Wiedemann syndrome, although with different penetrance and expressivity. We explored the relationship between IC1 microdeletions and phenotype by analysing a number of previously described and novel mutant alleles. We used a highly quantitative assay based on next generation sequencing to measure DNA methylation in affected families and analysed enhancer-blocking activity and CTCF binding in cultured cells. We demonstrate that the microdeletions mostly affect IC1 function and CTCF binding by changing CTS spacing. Thus, the extent of IC1 inactivation and the clinical phenotype are influenced by the arrangement of the residual CTSs. A CTS spacing similar to the wild-type allele results in moderate IC1 inactivation and is associated with stochastic DNA methylation of the maternal IC1 and incomplete penetrance. Microdeletions with different CTS spacing display severe IC1 inactivation and are associated with IC1 hypermethylation and complete penetrance. Careful characterization of the IC1 microdeletions is therefore needed to predict recurrence risks and phenotypical outcomes.
Collapse
Affiliation(s)
- Jasmin Beygo
- Institut für Humangenetik, Universitätsklinikum Essen, Essen, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Singh P, Lee DH, Szabó PE. More than insulator: multiple roles of CTCF at the H19-Igf2 imprinted domain. Front Genet 2012; 3:214. [PMID: 23087708 PMCID: PMC3471092 DOI: 10.3389/fgene.2012.00214] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Accepted: 09/27/2012] [Indexed: 12/28/2022] Open
Abstract
CTCF (CCCTC-binding factor)-mediated insulation at the H19-Insulin-like growth factor 2 (Igf2) imprinted domain is a classic example for imprinted gene regulation. DNA methylation difference in the imprinting control region (ICR) is inherited from the gametes and subsequently determines parental allele-specific enhancer blocking and imprinted expression in the soma. Recent genetic studies showed that proper monoallelic enhancer blocking at the H19-Igf2 ICR is critical for development. Strict biallelic insulation at this locus causes perinatal lethality, whereas leaky biallelic insulation results in smaller size but no lethality. Apart from enhancer blocking, CTCF is also the master organizer of chromatin composition in the maternal allele along this imprinted domain, affecting not only histone tail covalent modifications but also those in the histone core. Additionally, CTCF binding in the soma protects the maternal allele from de novo DNA methylation. CTCF binding is not involved in the establishment of the gametic marks at the ICR, but it slightly delays de novo methylation in the maternally inherited ICR allele in prospermatogonia. This review focuses on the developmental and epigenetic consequences of CTCF binding at the H19-Igf2 ICR.
Collapse
Affiliation(s)
- Purnima Singh
- Department of Molecular and Cellular Biology, Beckman Research Institute Duarte, CA, USA
| | | | | |
Collapse
|
29
|
Akhtar M, Holmgren C, Göndör A, Vesterlund M, Kanduri C, Larsson C, Ekström TJ. Cell type and context-specific function of PLAG1 for IGF2 P3 promoter activity. Int J Oncol 2012; 41:1959-66. [PMID: 23023303 PMCID: PMC3583874 DOI: 10.3892/ijo.2012.1641] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 08/14/2012] [Indexed: 12/23/2022] Open
Abstract
The fetal transcription factor PLAG1 is found to be overexpressed in cancers, and has been suggested to bind the insulin like growth factor 2 (IGF2) P3 promoter, and to activate the IGF2 gene. The expression of IGF2 has partly been linked to loss of CTCF-dependent chromatin insulator function at the H19 imprinting control region (ICR). We investigated the role of PLAG1 for IGF2 regulation in Hep3B and JEG-3 cell lines. Chromatin immunoprecipitation revealed cell type-specific binding of PLAG1 to the IGF2 P3 promoter, which was substantially insensitive to recombinant PLAG1 overexpression in the endogenous context. We hypothesized that the H19 chromatin insulator may be involved in the cell type-specific PLAG1 response. By using a GFP reporter gene/insulator assay plasmid construct with and without the H19 ICR and/or an SV40 enhancer, we confirm that the effect of the insulator is specifically associated with the activity of the IGF2 P3 promoter in the GFP reporter system, and furthermore, that the reporter insulator is functional in JEG-3 but not in Hep3B cells. FACS analysis was used to assess the function of PLAG1 in low endogenously expressing, but Zn-inducible stable PLAG1 expressing JEG-3 cell clones. Considerable increase in IGF2 expression upon PLAG1 induction with a partial insulator overriding activity was found using the reporter constructs. This is in contrast to the effect of the endogenous IGF2 gene which was insensitive to PLAG1 expression in JEG-3, while modestly induced the already highly expressed IGF2 gene in Hep3B cells. We suggest that the PLAG1 binding to the IGF2 P3 promoter and IGF2 expression is cell type-specific, and that the PLAG1 transcription factor acts as a transcriptional facilitator that partially overrides the insulation by the H19 ICR.
Collapse
Affiliation(s)
- Monira Akhtar
- Department of Clinical Neuroscience, Karolinska Institutet, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | | | | | | | | | | | | |
Collapse
|
30
|
Guibert S, Zhao Z, Sjölinder M, Göndör A, Fernandez A, Pant V, Ohlsson R. CTCF-binding sites within the H19 ICR differentially regulate local chromatin structures and cis-acting functions. Epigenetics 2012; 7:361-9. [PMID: 22415163 DOI: 10.4161/epi.19487] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
It is generally assumed that CTCF-binding sites are synonymous with the demarcation of expression domains by promoting the formation of chromatin loops. We have proposed earlier, however, that such features may be context-dependent. In support of this notion, we show here that chromatin loop structures, impinging on CTCF-binding sites 1/2 and 3/4 at the 5' and 3'-ends, respectively, within the maternal allele of the H19 imprinting control region (ICR), differ significantly. Although abrogation of CTCF binding to the maternal H19 ICR allele results in loss of chromatin loops in the 3'-region, there is a dramatic gain of long-range chromatin loops impinging on the 5'-region. As the degree of occupancy of its four CTCF-binding sites discriminates between the chromatin insulator and replication timing functions, we submit that the CTCF-binding sites within the H19 ICR are functionally diverse and organize context-dependent higher order chromatin conformations.
Collapse
Affiliation(s)
- Sylvain Guibert
- Department of Development and Genetics, Evolution Biology Centre, Uppsala University, Uppsala, Sweden.
| | | | | | | | | | | | | |
Collapse
|
31
|
ADP-ribose polymers localized on Ctcf-Parp1-Dnmt1 complex prevent methylation of Ctcf target sites. Biochem J 2012; 441:645-52. [PMID: 21985173 PMCID: PMC3258657 DOI: 10.1042/bj20111417] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
PARylation [poly(ADP-ribosyl)ation] is involved in the maintenance of genomic methylation patterns through its control of Dnmt1 [DNA (cytosine-5)-methyltransferase 1] activity. Our previous findings indicated that Ctcf (CCCTC-binding factor) may be an important player in key events whereby PARylation controls the unmethylated status of some CpG-rich regions. Ctcf is able to activate Parp1 [poly(ADP-ribose) polymerase 1], which ADP-ribosylates itself and, in turn, inhibits DNA methylation via non-covalent interaction between its ADP-ribose polymers and Dnmt1. By such a mechanism, Ctcf may preserve the epigenetic pattern at promoters of important housekeeping genes. The results of the present study showed Dnmt1 as a new protein partner of Ctcf. Moreover, we show that Ctcf forms a complex with Dnmt1 and PARylated Parp1 at specific Ctcf target sequences and that PARylation is responsible for the maintenance of the unmethylated status of some Ctcf-bound CpGs. We suggest a mechanism by which Parp1, tethered and activated at specific DNA target sites by Ctcf, preserves their methylation-free status.
Collapse
|
32
|
Genomic imprinting: recognition and marking of imprinted loci. Curr Opin Genet Dev 2011; 22:72-8. [PMID: 22195775 DOI: 10.1016/j.gde.2011.12.001] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Revised: 11/30/2011] [Accepted: 12/01/2011] [Indexed: 11/21/2022]
Abstract
Genomic imprinting is an epigenetic process resulting in the monoallelic parent-of-origin-specific expression of a subset of genes in the mammalian genome. The parental alleles are differentially marked by DNA methylation during gametogenesis when the genomes are in separate compartments. How methylation machinery recognizes and differentially modifies these imprinted regions in germ cells remains a key question in the field. While studies have focused on determining a sequence signature that alone could distinguish imprinted regions from the rest of the genome, recent reports do not support such a hypothesis. Rather, it is becoming clear that features such as transcription, histone modifications and higher order chromatin are employed either individually or in combination to set up parental imprints.
Collapse
|
33
|
Bhusari S, Yang B, Kueck J, Huang W, Jarrard DF. Insulin-like growth factor-2 (IGF2) loss of imprinting marks a field defect within human prostates containing cancer. Prostate 2011; 71:1621-30. [PMID: 21432864 PMCID: PMC3825178 DOI: 10.1002/pros.21379] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Accepted: 02/17/2011] [Indexed: 11/11/2022]
Abstract
BACKGROUND Loss of imprinting (LOI) is an epigenetic alteration involving loss of parental origin-specific expression at normally imprinted genes. A LOI for IGF2, a paracrine growth factor, has been implicated in the development of prostate and other cancers. In the current study, we define IGF2 LOI in histologically normal prostate tissues in relationship to tumor foci and gene expression. METHODS Microdissected tumor associated (TA) adjacent (2 mm) and distant (10 mm) tissues surrounding tumor foci were generated. IGF2 imprinting in informative prostate tissue sets was quantitated using a fluorescent primer extension assay and expression analyzed utilizing quantitative PCR. DNA methylation analyses were performed using quantitative pyrosequencing. RESULTS A marked IGF2 LOI was found in adjacent TA tissues (39 ± 3.1%) and did not significantly decrease in tissues distant (38 ± 5.3%) from tumor foci (45 ± 2.9%; P = 0.21). IGF2 imprinting correlated with IGF2 expression in TA tissues, but not within the tumor foci. Hypomethylation of the IGF2 DMR0 region correlated with decreased IGF2 expression in tumors (P < 0.01). The expression of IGF2 and its adjacent imprinted gene H19 were increased in adjacent and distant tissues compared to tumors (P < 0.05) indicating the importance of factors other than LOI in driving IGF2 expression. CONCLUSIONS LOI of IGF2 occurs not only adjacent to prostate tumor foci, but is widely prevalent even in distant areas within the peripheral zone. These data provide evidence for a widespread epigenetic field defect in histologically normal tissues that might be employed to identify prostate cancer in patients.
Collapse
Affiliation(s)
- Sachin Bhusari
- Department of Urology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Bing Yang
- Department of Urology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Jessica Kueck
- Department of Urology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Wei Huang
- University of Wisconsin Carbone Comprehensive Cancer Center, Madison, Wisconsin
- Pathology and Laboratory Medicine, University of Wisconsin, Madison, Wisconsin
| | - David F. Jarrard
- Department of Urology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
- University of Wisconsin Carbone Comprehensive Cancer Center, Madison, Wisconsin
- Environmental and Molecular Toxicology, University of Wisconsin, Madison, Wisconsin
- Correspondence to: David F. Jarrard, MD, 7037, Wisconsin Institutes of Medical Research, 1111 Highland Avenue, Madison, WI 53792.
| |
Collapse
|
34
|
Abstract
Genome instability is a hallmark of cancer cells and how it arises is still not completely understood. Correct chromosome segregation is a pre-requisite for preserving genome integrity. Cohesin helps to ensure faithful chromosome segregation during cell cycle, however, much evidence regarding its functions have come to light over the last few years and suggest that cohesin plays multiple roles in the maintenance of genome stability. Here we review our rapidly increasing knowledge on the involvement of cohesin pathway in genome stability and cancer.
Collapse
Affiliation(s)
- Linda Mannini
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Richerche, Pisa, Italy
| | | |
Collapse
|
35
|
Abstract
Chromatin insulators are DNA-protein complexes with broad functions in nuclear biology. Based on the ability of insulator proteins to interact with each other, it was originally found that insulators form loops that bring together distant regions of the genome. Data from genome-wide localization studies indicate that insulator proteins can be present in intergenic regions as well as at the 5', introns or 3' of genes, suggesting a variety of roles for insulator loops in chromosome biology. Recent results suggest that insulators mediate intra- and interchromosomal interactions to affect transcription, imprinting, and recombination. Cells have developed mechanisms to control insulator activity by recruiting specialized proteins or by covalent modification of core components. It is then possible that insulator-mediated interactions set up cell-specific blueprints of nuclear organization that may contribute to the establishment of different patterns of gene expression during cell differentiation and development. As a consequence, disruption of insulator activity could result in the development of cancer or other disease states.
Collapse
Affiliation(s)
- Jingping Yang
- Department of Biology, Emory University, Atlanta, GA, USA
| | | |
Collapse
|
36
|
Identification of genetic elements that autonomously determine DNA methylation states. Nat Genet 2011; 43:1091-7. [PMID: 21964573 DOI: 10.1038/ng.946] [Citation(s) in RCA: 314] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Accepted: 08/25/2011] [Indexed: 12/12/2022]
Abstract
Cytosine methylation is a repressive, epigenetically propagated DNA modification. Although patterns of DNA methylation seem tightly regulated in mammals, it is unclear how these are specified and to what extent this process entails genetic or epigenetic regulation. To dissect the role of the underlying DNA sequence, we sequentially inserted over 50 different DNA elements into the same genomic locus in mouse stem cells. Promoter sequences of approximately 1,000 bp autonomously recapitulated correct DNA methylation in pluripotent cells. Moreover, they supported proper de novo methylation during differentiation. Truncation analysis revealed that this regulatory potential is contained within small methylation-determining regions (MDRs). MDRs can mediate both hypomethylation and de novo methylation in cis, and their activity depends on developmental state, motifs for DNA-binding factors and a critical CpG density. These results demonstrate that proximal sequence elements are both necessary and sufficient for regulating DNA methylation and reveal basic constraints of this regulation.
Collapse
|
37
|
Ideraabdullah FY, Abramowitz LK, Thorvaldsen JL, Krapp C, Wen SC, Engel N, Bartolomei MS. Novel cis-regulatory function in ICR-mediated imprinted repression of H19. Dev Biol 2011; 355:349-57. [PMID: 21600199 DOI: 10.1016/j.ydbio.2011.04.036] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Revised: 04/25/2011] [Accepted: 04/30/2011] [Indexed: 11/27/2022]
Abstract
Expression of coregulated imprinted genes, H19 and Igf2, is monoallelic and parent-of-origin-dependent. Like most imprinted genes, H19 and Igf2 are regulated by a differentially methylated imprinting control region (ICR). CTCF binding sites and DNA methylation at the ICR have previously been identified as key cis-acting elements required for proper H19/Igf2 imprinting. Here, we use mouse models to elucidate further the mechanism of ICR-mediated gene regulation. We specifically address the question of whether sequences outside of CTCF sites at the ICR are required for paternal H19 repression. To this end, we generated two types of mutant ICRs in the mouse: (i) deletion of intervening sequence between CTCF sites (H19(ICR∆IVS)), which changes size and CpG content at the ICR; and (ii) CpG depletion outside of CTCF sites (H19(ICR-8nrCG)), which only changes CpG content at the ICR. Individually, both mutant alleles (H19(ICR∆IVS) and H19(ICR-8nrCG)) show loss of imprinted repression of paternal H19. Interestingly, this loss of repression does not coincide with a detectable change in methylation at the H19 ICR or promoter. Thus, neither intact CTCF sites nor hypermethylation at the ICR is sufficient for maintaining the fully repressed state of the paternal H19 allele. Our findings demonstrate, for the first time in vivo, that sequence outside of CTCF sites at the ICR is required in cis for ICR-mediated imprinted repression at the H19/Igf2 locus. In addition, these results strongly implicate a novel role of ICR size and CpG density in paternal H19 repression.
Collapse
Affiliation(s)
- Folami Y Ideraabdullah
- Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, 415 Curie Boulevard, Philadelphia, PA 19104, USA
| | | | | | | | | | | | | |
Collapse
|
38
|
Amouyal M. Gene insulation. Part II: natural strategies in vertebrates. Biochem Cell Biol 2011; 88:885-98. [PMID: 21102651 DOI: 10.1139/o10-111] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The way a gene is insulated from its genomic environment in vertebrates is not basically different from what is observed in yeast and Drosophila (preceding article in this issue). If the formation of a looped chromatin domain, whether generated by attachment to the nuclear matrix or not, has become a classic way to confine an enhancer to a specific genomic domain and to coordinate, sequentially or simultaneously, gene expression in a given program, its role has been extended to new networks of genes or regulators within the same gene. A wider definition of the bases of the chromatin loops (nonchromosomal nuclear structures or genomic interacting elements) is also available. However, whereas insulation in Drosophila is due to a variety of proteins, in vertebrates insulators are still practically limited to CTCF (the CCCTC-binding factor), which appears in all cases to be the linchpin of an architecture that structures the assembly of DNA-protein interactions for gene regulation. As in yeast and Drosophila, the economy of means is the rule and the same unexpected diversion of known transcription elements (active or poised RNA polymerases, TFIIIC elements out of tRNA genes, permanent histone replacement) is observed, with variants peculiar to CTCF. Thus, besides structuring DNA looping, CTCF is a barrier to DNA methylation or interferes with all sorts of transcription processes, such as that generating heterochromatin.
Collapse
|
39
|
Lee DH, Tran DA, Singh P, Oates N, Rivas GE, Larson GP, Pfeifer GP, Szabó PE. MIRA-SNuPE, a quantitative, multiplex method for measuring allele-specific DNA methylation. Epigenetics 2011; 6:212-23. [PMID: 20948294 DOI: 10.4161/epi.6.2.13699] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
5-methyl-C (5mC) and 5-hydroxymethyl-C (5hmC) are epigenetic marks with well known and putative roles in gene regulation, respectively. These two DNA covalent modifications cannot be distinguished by bisulfite sequencing or restriction digestion, the standard methods of 5mC detection. The methylated CpG island recovery assay (MIRA), however, specifically detects 5mC but not 5hmC. We further developed MIRA for the analysis of allele-specific CpG methylation at differentially methylated regions (DMRs) of imprinted genes. MIRA specifically distinguished between the parental alleles by capturing the paternally methylated H19/Igf2 DMR and maternally methylated KvDMR1 in mouse embryo fibroblasts (MEFs) carrying paternal and maternal duplication of mouse distal Chr7, respectively. MIRA in combination with multiplex single nucleotide primer extension (SNuPE) assays specifically captured the methylated parental allele from normal cells at a set of maternally and paternally methylated DMRs. The assay correctly recognized aberrant biallelic methylation in a case of loss-of imprinting. The MIRA-SNuPE assays revealed that placenta exhibited less DNA methylation bias at DMRs compared to yolk sac, amnion, brain, heart, kidney, liver and muscle. This method should be useful for the analysis of allele-specific methylation events related to genomic imprinting, X chromosome inactivation and for verifying and screening haplotype-associated methylation differences in the human population.
Collapse
Affiliation(s)
- Dong-Hoon Lee
- Department of Molecular and Cellular Biology, City of Hope National Medical Center, Duarte, CA, USA
| | | | | | | | | | | | | | | |
Collapse
|
40
|
Woodfine K, Huddleston JE, Murrell A. Quantitative analysis of DNA methylation at all human imprinted regions reveals preservation of epigenetic stability in adult somatic tissue. Epigenetics Chromatin 2011; 4:1. [PMID: 21281512 PMCID: PMC3038880 DOI: 10.1186/1756-8935-4-1] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Accepted: 01/31/2011] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Genes subject to genomic imprinting are mono-allelically expressed in a parent-of-origin dependent manner. Each imprinted locus has at least one differentially methylated region (DMR) which has allele specific DNA methylation and contributes to imprinted gene expression. Once DMRs are established, they are potentially able to withstand normal genome reprogramming events that occur during cell differentiation and germ-line DMRs are stably maintained throughout development. These DMRs, in addition to being either maternally or paternally methylated, have differences in whether methylation was acquired in the germ-line or post fertilization and are present in a variety of genomic locations with different Cytosine-phosphate guanine (CpG) densities and CTCF binding capacities. We therefore examined the stability of maintenance of DNA methylation imprints and determined the normal baseline DNA methylation levels in several adult tissues for all imprinted genes. In order to do this, we first developed and validated 50 highly specific, quantitative DNA methylation pyrosequencing assays for the known DMRs associated with human imprinted genes. RESULTS Remarkable stability of the DNA methylation imprint was observed in all germ-line DMRs and paternally methylated somatic DMRs (which maintained average methylation levels of between 35% - 65% in all somatic tissues, independent of gene expression). Maternally methylated somatic DMRs were found to have more variation with tissue specific methylation patterns. Most DMRs, however, showed some intra-individual variability for DNA methylation levels in peripheral blood, suggesting that more than one DMR needs to be examined in order to get an overall impression of the epigenetic stability in a tissue. The plasticity of DNA methylation at imprinted genes was examined in a panel of normal and cancer cell lines. All cell lines showed changes in DNA methylation, especially at the paternal germ-line and the somatic DMRs. CONCLUSIONS Our validated pyrosequencing methylation assays can be widely used as a tool to investigate DNA methylation levels of imprinted genes in clinical samples. This first comprehensive analysis of normal methylation levels in adult somatic tissues at human imprinted regions confirm that, despite intra-individual variability and tissue specific expression, imprinted genes faithfully maintain their DNA methylation in healthy adult tissue. DNA methylation levels of a selection of imprinted genes are, therefore, a valuable indicator for epigenetic stability.
Collapse
Affiliation(s)
- Kathryn Woodfine
- Department of Oncology, University of Cambridge, Cancer Research UK Cambridge Research Institute, Cambridge, UK
| | - Joanna E Huddleston
- Department of Oncology, University of Cambridge, Cancer Research UK Cambridge Research Institute, Cambridge, UK
| | - Adele Murrell
- Department of Oncology, University of Cambridge, Cancer Research UK Cambridge Research Institute, Cambridge, UK
| |
Collapse
|
41
|
Wilkins JF, Úbeda F. Diseases associated with genomic imprinting. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2011; 101:401-45. [PMID: 21507360 DOI: 10.1016/b978-0-12-387685-0.00013-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Genomic imprinting is the phenomenon where the expression of a locus differs between the maternally and paternally inherited alleles. Typically, this manifests as transcriptional silencing of one of the alleles, although many genes are imprinted in a tissue- or isoform-specific manner. Diseases associated with imprinted genes include various cancers, disorders of growth and metabolism, and disorders in neurodevelopment, cognition, and behavior, including certain major psychiatric disorders. In many cases, the disease phenotypes associated with dysfunction at particular imprinted loci can be understood in terms of the evolutionary processes responsible for the origin of imprinting. Imprinted gene expression represents the outcome of an intragenomic evolutionary conflict, where natural selection favors different expression strategies for maternally and paternally inherited alleles. This conflict is reasonably well understood in the context of the early growth effects of imprinted genes, where paternally inherited alleles are selected to place a greater demand on maternal resources than are maternally inherited alleles. Less well understood are the origins of imprinted gene expression in the brain, and their effects on cognition and behavior. This chapter reviews the genetic diseases that are associated with imprinted genes, framed in terms of the evolutionary pressures acting on gene expression at those loci. We begin by reviewing the phenomenon and evolutionary origins of genomic imprinting. We then discuss diseases that are associated with genetic or epigenetic defects at particular imprinted loci, many of which are associated with abnormalities in growth and/or feeding behaviors that can be understood in terms of the asymmetric pressures of natural selection on maternally and paternally inherited alleles. We next described the evidence for imprinted gene effects on adult cognition and behavior, and the possible role of imprinted genes in the etiology of certain major psychiatric disorders. Finally, we conclude with a discussion of how imprinting, and the evolutionary-genetic conflicts that underlie it, may enhance both the frequency and morbidity of certain types of diseases.
Collapse
|
42
|
CTCF-dependent chromatin bias constitutes transient epigenetic memory of the mother at the H19-Igf2 imprinting control region in prospermatogonia. PLoS Genet 2010; 6:e1001224. [PMID: 21124827 PMCID: PMC2991272 DOI: 10.1371/journal.pgen.1001224] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2010] [Accepted: 10/27/2010] [Indexed: 12/23/2022] Open
Abstract
Genomic imprints—parental allele-specific DNA methylation marks at the differentially methylated regions (DMRs) of imprinted genes—are erased and reestablished in germ cells according to the individual's sex. Imprint establishment at paternally methylated germ line DMRs occurs in fetal male germ cells. In prospermatogonia, the two unmethylated alleles exhibit different rates of de novo methylation at the H19/Igf2 imprinting control region (ICR) depending on parental origin. We investigated the nature of this epigenetic memory using bisulfite sequencing and allele-specific ChIP–SNuPE assays. We found that the chromatin composition in fetal germ cells was biased at the ICR between the two alleles with the maternally inherited allele exhibiting more H3K4me3 and less H3K9me3 than the paternally inherited allele. We determined genetically that the chromatin bias, and also the delayed methylation establishment in the maternal allele, depended on functional CTCF insulator binding sites in the ICR. Our data suggest that, in primordial germ cells, maternally inherited allele-specific CTCF binding sets up allele-specific chromatin differences at the ICR. The erasure of these allele-specific chromatin marks is not complete before the process of de novo methylation imprint establishment begins. CTCF–dependent allele-specific chromatin composition imposes a maternal allele-specific delay on de novo methylation imprint establishment at the H19/Igf2 ICR in prospermatogonia. Allele-specific DNA methylation is considered the primary mark that distinguishes the parental alleles of imprinted genes. Whereas allele-specific chromatin also exists at imprinted genes in the soma, this has not been assessed in the germ line. It will be important to understand what extent the chromatin composition provides clues in the germ line to the erasure and establishment of methylation imprints. Our novel methods provide the sensitivity required to answer these questions. Our results argue that the erasure of the DNA methylation imprint is complete before, and therefore does not depend on, the erasure of allele-specific chromatin marks at the H19/Igf2 imprint control region. Additionally, we show that incomplete erasure of the allele-specific chromatin is responsible for the delayed DNA methylation imprint establishment of the maternal ICR allele in prospermatogonia. The chromatin bias—the transient epigenetic memory of the mother—in fetal germ cells depends on functional CTCF insulator binding sites in this imprint control region.
Collapse
|
43
|
Lee DH, Singh P, Tsark WMK, Szabó PE. Complete biallelic insulation at the H19/Igf2 imprinting control region position results in fetal growth retardation and perinatal lethality. PLoS One 2010; 5:e12630. [PMID: 20838620 PMCID: PMC2935888 DOI: 10.1371/journal.pone.0012630] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2010] [Accepted: 08/16/2010] [Indexed: 11/18/2022] Open
Abstract
Background The H19/Igf2 imprinting control region (ICR) functions as an insulator exclusively in the unmethylated maternal allele, where enhancer-blocking by CTCF protein prevents the interaction between the Igf2 promoter and the distant enhancers. DNA methylation inhibits CTCF binding in the paternal ICR allele. Two copies of the chicken β-globin insulator (ChβGI)2 are capable of substituting for the enhancer blocking function of the ICR. Insulation, however, now also occurs upon paternal inheritance, because unlike the H19 ICR, the (ChβGI)2 does not become methylated in fetal male germ cells. The (ChβGI)2 is a composite insulator, exhibiting enhancer blocking by CTCF and chromatin barrier functions by USF1 and VEZF1. We asked the question whether these barrier proteins protected the (ChβGI)2 sequences from methylation in the male germ line. Methodology/Principal Findings We genetically dissected the ChβGI in the mouse by deleting the binding sites USF1 and VEZF1. The methylation of the mutant versus normal (ChβGI)2 significantly increased from 11% to 32% in perinatal male germ cells, suggesting that the barrier proteins did have a role in protecting the (ChβGI)2 from methylation in the male germ line. Contrary to the H19 ICR, however, the mutant (mChβGI)2 lacked the potential to attain full de novo methylation in the germ line and to maintain methylation in the paternal allele in the soma, where it consequently functioned as a biallelic insulator. Unexpectedly, a stricter enhancer blocking was achieved by CTCF alone than by a combination of the CTCF, USF1 and VEZF1 sites, illustrated by undetectable Igf2 expression upon paternal transmission. Conclusions/Significance In this in vivo model, hypomethylation at the ICR position together with fetal growth retardation mimicked the human Silver-Russell syndrome. Importantly, late fetal/perinatal death occurred arguing that strict biallelic insulation at the H19/Igf2 ICR position is not tolerated in development.
Collapse
Affiliation(s)
- Dong-Hoon Lee
- Department of Molecular and Cellular Biology, City of Hope National Medical Center, Duarte, California, United States of America
| | - Purnima Singh
- Department of Molecular and Cellular Biology, City of Hope National Medical Center, Duarte, California, United States of America
| | - Walter M. K. Tsark
- Transgenic Mouse Facility, City of Hope National Medical Center, Duarte, California, United States of America
| | - Piroska E. Szabó
- Department of Molecular and Cellular Biology, City of Hope National Medical Center, Duarte, California, United States of America
- * E-mail:
| |
Collapse
|
44
|
Singh P, Cho J, Tsai SY, Rivas GE, Larson GP, Szabó PE. Coordinated allele-specific histone acetylation at the differentially methylated regions of imprinted genes. Nucleic Acids Res 2010; 38:7974-90. [PMID: 20693536 PMCID: PMC3001058 DOI: 10.1093/nar/gkq680] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Genomic imprinting is an epigenetic inheritance system characterized by parental allele-specific gene expression. Allele-specific DNA methylation and chromatin composition are two epigenetic modification systems that control imprinted gene expression. To get a general assessment of histone lysine acetylation at imprinted genes we measured allele-specific acetylation of a wide range of lysine residues, H3K4, H3K18, H3K27, H3K36, H3K79, H3K64, H4K5, H4K8, H4K12, H2AK5, H2BK12, H2BK16 and H2BK46 at 11 differentially methylated regions (DMRs) in reciprocal mouse crosses using multiplex chromatin immunoprecipitation SNuPE assays. Histone acetylation marks generally distinguished the methylation-free alleles from methylated alleles at DMRs in mouse embryo fibroblasts and embryos. Acetylated lysines that are typically found at transcription start sites exhibited stronger allelic bias than acetylated histone residues in general. Maternally methylated DMRs, that usually overlap with promoters exhibited higher levels of acetylation and a 10% stronger allele-specific bias than paternally methylated DMRs that reside in intergenic regions. Along the H19/Igf2 imprinted domain, allele-specific acetylation at each lysine residue depended on functional CTCF binding sites in the imprinting control region. Our results suggest that many different histone acetyltransferase and histone deacetylase enzymes must act in concert in setting up and maintaining reciprocal parental allelic histone acetylation at DMRs.
Collapse
Affiliation(s)
- Purnima Singh
- Department of Molecular and Cellular Biology, City of Hope National Medical Center, Duarte, CA 91010, USA
| | | | | | | | | | | |
Collapse
|
45
|
Ohlsson R, Bartkuhn M, Renkawitz R. CTCF shapes chromatin by multiple mechanisms: the impact of 20 years of CTCF research on understanding the workings of chromatin. Chromosoma 2010; 119:351-60. [PMID: 20174815 PMCID: PMC2910314 DOI: 10.1007/s00412-010-0262-0] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Revised: 01/17/2010] [Accepted: 01/19/2010] [Indexed: 11/30/2022]
Abstract
More than 10(9) base pairs of the genome in higher eucaryotes are positioned in the interphase nucleus such that gene activation, gene repression, remote gene regulation by enhancer elements, and reading as well as adjusting epigenetic marks are possible. One important structural and functional component of chromatin organization is the zinc finger factor CTCF. Two decades of research has advanced the understanding of the fundamental role that CTCF plays in regulating such a vast expanse of DNA.
Collapse
Affiliation(s)
- Rolf Ohlsson
- Institute for Microbiology, Tumor- and Cellbiology (MTC), Karolinska Institute, Stockholm, Sweden
| | - Marek Bartkuhn
- Institute for Genetics, Justus-Liebig-University, 35392 Giessen, Germany
| | - Rainer Renkawitz
- Institute for Genetics, Justus-Liebig-University, 35392 Giessen, Germany
| |
Collapse
|
46
|
Bergström R, Savary K, Morén A, Guibert S, Heldin CH, Ohlsson R, Moustakas A. Transforming growth factor beta promotes complexes between Smad proteins and the CCCTC-binding factor on the H19 imprinting control region chromatin. J Biol Chem 2010; 285:19727-37. [PMID: 20427289 PMCID: PMC2888383 DOI: 10.1074/jbc.m109.088385] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Whether signal transduction pathways regulate epigenetic states in response to environmental cues remains poorly understood. We demonstrate here that Smad3, signaling downstream of transforming growth factor β, interacts with the zinc finger domain of CCCTC-binding factor (CTCF), a nuclear protein known to act as “the master weaver of the genome.” This interaction occurs via the Mad homology 1 domain of Smad3. Although Smad2 and Smad4 fail to interact, an alternatively spliced form of Smad2 lacking exon 3 interacts with CTCF. CTCF does not perturb well established transforming growth factor β gene responses. However, Smads and CTCF co-localize to the H19 imprinting control region (ICR), which emerges as an insulator in cis and regulator of transcription and replication in trans via direct CTCF binding to the ICR. Smad recruitment to the ICR requires intact CTCF binding to this locus. Smad2/3 binding to the ICR requires Smad4, which potentially provides stability to the complex. Because the CTCF-Smad complex is not essential for the chromatin insulator function of the H19 ICR, we propose that it can play a role in chromatin cross-talk organized by the H19 ICR.
Collapse
Affiliation(s)
- Rosita Bergström
- Ludwig Institute for Cancer Research, Uppsala University, SE-751 24 Uppsala, Sweden
| | | | | | | | | | | | | |
Collapse
|
47
|
Allele-specific H3K79 Di- versus trimethylation distinguishes opposite parental alleles at imprinted regions. Mol Cell Biol 2010; 30:2693-707. [PMID: 20351169 DOI: 10.1128/mcb.01537-09] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Imprinted gene expression corresponds to parental allele-specific DNA CpG methylation and chromatin composition. Histone tail covalent modifications have been extensively studied, but it is not known whether modifications in the histone globular domains can also discriminate between the parental alleles. Using multiplex chromatin immunoprecipitation-single nucleotide primer extension (ChIP-SNuPE) assays, we measured the allele-specific enrichment of H3K79 methylation and H4K91 acetylation along the H19/Igf2 imprinted domain. Whereas H3K79me1, H3K79me2, and H4K91ac displayed a paternal-specific enrichment at the paternally expressed Igf2 locus, H3K79me3 was paternally biased at the maternally expressed H19 locus, including the paternally methylated imprinting control region (ICR). We found that these allele-specific differences depended on CTCF binding in the maternal ICR allele. We analyzed an additional 11 differentially methylated regions (DMRs) and found that, in general, H3K79me3 was associated with the CpG-methylated alleles, whereas H3K79me1, H3K79me2, and H4K91ac enrichment was specific to the unmethylated alleles. Our data suggest that allele-specific differences in the globular histone domains may constitute a layer of the "histone code" at imprinted genes.
Collapse
|
48
|
Matsuzaki H, Okamura E, Fukamizu A, Tanimoto K. CTCF binding is not the epigenetic mark that establishes post-fertilization methylation imprinting in the transgenic H19 ICR. Hum Mol Genet 2010; 19:1190-8. [PMID: 20047949 DOI: 10.1093/hmg/ddp589] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Hitomi Matsuzaki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | | | | | | |
Collapse
|
49
|
Abstract
The multifunctional zinc-finger protein CCCTC-binding factor (CTCF) is a very strong candidate for the role of coordinating the expression level of coding sequences with their three-dimensional position in the nucleus, apparently responding to a "code" in the DNA itself. Dynamic interactions between chromatin fibers in the context of nuclear architecture have been implicated in various aspects of genome functions. However, the molecular basis of these interactions still remains elusive and is a subject of intense debate. Here we discuss the nature of CTCF-DNA interactions, the CTCF-binding specificity to its binding sites and the relationship between CTCF and chromatin, and we examine data linking CTCF with gene regulation in the three-dimensional nuclear space. We discuss why these features render CTCF a very strong candidate for the role and propose a unifying model, the "CTCF code," explaining the mechanistic basis of how the information encrypted in DNA may be interpreted by CTCF into diverse nuclear functions.
Collapse
Affiliation(s)
- Rolf Ohlsson
- Department of Microbiology, Tumor and Cell Biology, Nobels väg 16, Box 280, Karolinska Institute, SE-171 77 Stockholm, Sweden
| | - Victor Lobanenkov
- Molecular Pathology Section, Laboratory of Immunopathology, National Institute of Allergy and Infectious Diseases, National Institutes of Health (LIP/NIAID/NIH), Twinbrook Building, Room 1329, MSC-8152, 5640 Fisher Lane, Rockville, MD 20852, USA
| | - Elena Klenova
- Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ, UK
| |
Collapse
|
50
|
|