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Morgan RK, Wang K, Svoboda LK, Rygiel CA, Lalancette C, Cavalcante R, Bartolomei MS, Prasasya R, Neier K, Perera BPU, Jones TR, Colacino JA, Sartor MA, Dolinoy DC. Effects of Developmental Lead and Phthalate Exposures on DNA Methylation in Adult Mouse Blood, Brain, and Liver: A Focus on Genomic Imprinting by Tissue and Sex. ENVIRONMENTAL HEALTH PERSPECTIVES 2024; 132:67003. [PMID: 38833407 DOI: 10.1289/ehp14074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
BACKGROUND Maternal exposure to environmental chemicals can cause adverse health effects in offspring. Mounting evidence supports that these effects are influenced, at least in part, by epigenetic modifications. It is unknown whether epigenetic changes in surrogate tissues such as the blood are reflective of similar changes in target tissues such as cortex or liver. OBJECTIVE We examined tissue- and sex-specific changes in DNA methylation (DNAm) associated with human-relevant lead (Pb) and di(2-ethylhexyl) phthalate (DEHP) exposure during perinatal development in cerebral cortex, blood, and liver. METHODS Female mice were exposed to human relevant doses of either Pb (32 ppm ) via drinking water or DEHP (5 mg / kg-day ) via chow for 2 weeks prior to mating through offspring weaning. Whole genome bisulfite sequencing (WGBS) was utilized to examine DNAm changes in offspring cortex, blood, and liver at 5 months of age. Metilene and methylSig were used to identify differentially methylated regions (DMRs). Annotatr and ChIP-enrich were used for genomic annotations and gene set enrichment tests of DMRs, respectively. RESULTS The cortex contained the majority of DMRs associated with Pb (66%) and DEHP (57%) exposure. The cortex also contained the greatest degree of overlap in DMR signatures between sexes (n = 13 and 8 DMRs with Pb and DEHP exposure, respectively) and exposure types (n = 55 and 39 DMRs in males and females, respectively). In all tissues, detected DMRs were preferentially found at genomic regions associated with gene expression regulation (e.g., CpG islands and shores, 5' UTRs, promoters, and exons). An analysis of GO terms associated with DMR-containing genes identified imprinted genes to be impacted by both Pb and DEHP exposure. Of these, Gnas and Grb10 contained DMRs across tissues, sexes, and exposures, with some signatures replicated between target and surrogate tissues. DMRs were enriched in the imprinting control regions (ICRs) of Gnas and Grb10, and we again observed a replication of DMR signatures between blood and target tissues. Specifically, we observed hypermethylation of the Grb10 ICR in both blood and liver of Pb-exposed male animals. CONCLUSIONS These data provide preliminary evidence that imprinted genes may be viable candidates in the search for epigenetic biomarkers of toxicant exposure in target tissues. Additional research is needed on allele- and developmental stage-specific effects, as well as whether other imprinted genes provide additional examples of this relationship. https://doi.org/10.1289/EHP14074.
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Affiliation(s)
- Rachel K Morgan
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Kai Wang
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Laurie K Svoboda
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Christine A Rygiel
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Claudia Lalancette
- Epigenomics Core, School of Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Raymond Cavalcante
- Epigenomics Core, School of Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Marisa S Bartolomei
- Department of Cell and Developmental Biology, Center of Excellence in Environmental Toxicology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Rexxi Prasasya
- Department of Cell and Developmental Biology, Center of Excellence in Environmental Toxicology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kari Neier
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Bambarendage P U Perera
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Tamara R Jones
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Justin A Colacino
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
- Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Dana C Dolinoy
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
- Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
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2
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Xie G, Si Q, Zhang G, Fan Y, Li Q, Leng P, Qiao F, Liang S, Yu R, Wang Y. The role of imprinting genes' loss of imprints in cancers and their clinical implications. Front Oncol 2024; 14:1365474. [PMID: 38812777 PMCID: PMC11133587 DOI: 10.3389/fonc.2024.1365474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 04/23/2024] [Indexed: 05/31/2024] Open
Abstract
Genomic imprinting plays an important role in the growth and development of mammals. When the original imprint status of these genes is lost, known as loss of imprinting (LOI), it may affect growth, neurocognitive development, metabolism, and even tumor susceptibility. The LOI of imprint genes has gradually been found not only as an early event in tumorigenesis, but also to be involved in progression. More than 120 imprinted genes had been identified in humans. In this review, we summarized the most studied LOI of two gene clusters and 13 single genes in cancers. We focused on the roles they played, that is, as growth suppressors and anti-apoptosis agents, sustaining proliferative signaling or inducing angiogenesis; the molecular pathways they regulated; and especially their clinical significance. It is notable that 12 combined forms of multi-genes' LOI, 3 of which have already been used as diagnostic models, achieved good sensitivity, specificity, and accuracy. In addition, the methods used for LOI detection in existing research are classified into detection of biallelic expression (BAE), differentially methylated regions (DMRs), methylation, and single-nucleotide polymorphisms (SNPs). These all indicated that the detection of imprinting genes' LOI has potential clinical significance in cancer diagnosis, treatment, and prognosis.
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Affiliation(s)
- Guojing Xie
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Qin Si
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Guangjie Zhang
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Department of Clinical Laboratory, Chengdu Fifth People’s Hospital, Chengdu, China
| | - Yu Fan
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Sichuan Key Laboratory of Medical Molecular Testing, Chengdu, China
| | - Qinghua Li
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Ping Leng
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Sichuan Key Laboratory of Medical Molecular Testing, Chengdu, China
| | - Fengling Qiao
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Sichuan Key Laboratory of Medical Molecular Testing, Chengdu, China
| | - Simin Liang
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Rong Yu
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Sichuan Key Laboratory of Medical Molecular Testing, Chengdu, China
| | - Yingshuang Wang
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Sichuan Key Laboratory of Medical Molecular Testing, Chengdu, China
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3
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Ferrer J, Dimitrova N. Transcription regulation by long non-coding RNAs: mechanisms and disease relevance. Nat Rev Mol Cell Biol 2024; 25:396-415. [PMID: 38242953 PMCID: PMC11045326 DOI: 10.1038/s41580-023-00694-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/11/2023] [Indexed: 01/21/2024]
Abstract
Long non-coding RNAs (lncRNAs) outnumber protein-coding transcripts, but their functions remain largely unknown. In this Review, we discuss the emerging roles of lncRNAs in the control of gene transcription. Some of the best characterized lncRNAs have essential transcription cis-regulatory functions that cannot be easily accomplished by DNA-interacting transcription factors, such as XIST, which controls X-chromosome inactivation, or imprinted lncRNAs that direct allele-specific repression. A growing number of lncRNA transcription units, including CHASERR, PVT1 and HASTER (also known as HNF1A-AS1) act as transcription-stabilizing elements that fine-tune the activity of dosage-sensitive genes that encode transcription factors. Genetic experiments have shown that defects in such transcription stabilizers often cause severe phenotypes. Other lncRNAs, such as lincRNA-p21 (also known as Trp53cor1) and Maenli (Gm29348) contribute to local activation of gene transcription, whereas distinct lncRNAs influence gene transcription in trans. We discuss findings of lncRNAs that elicit a function through either activation of their transcription, transcript elongation and processing or the lncRNA molecule itself. We also discuss emerging evidence of lncRNA involvement in human diseases, and their potential as therapeutic targets.
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Affiliation(s)
- Jorge Ferrer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain.
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.
| | - Nadya Dimitrova
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.
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4
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Tian H, Luan P, Liu Y, Li G. Tet-mediated DNA methylation dynamics affect chromosome organization. Nucleic Acids Res 2024; 52:3654-3666. [PMID: 38300758 DOI: 10.1093/nar/gkae054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 02/03/2024] Open
Abstract
DNA Methylation is a significant epigenetic modification that can modulate chromosome states, but its role in orchestrating chromosome organization has not been well elucidated. Here we systematically assessed the effects of DNA Methylation on chromosome organization with a multi-omics strategy to capture DNA Methylation and high-order chromosome interaction simultaneously on mouse embryonic stem cells with DNA methylation dioxygenase Tet triple knock-out (Tet-TKO). Globally, upon Tet-TKO, we observed weakened compartmentalization, corresponding to decreased methylation differences between CpG island (CGI) rich and poor domains. Tet-TKO could also induce hypermethylation for the CTCF binding peaks in TAD boundaries and chromatin loop anchors. Accordingly, CTCF peak generally weakened upon Tet-TKO, which results in weakened TAD structure and depletion of long-range chromatin loops. Genes that lost enhancer-promoter looping upon Tet-TKO showed DNA hypermethylation in their gene bodies, which may compensate for the disruption of gene expression. We also observed distinct effects of Tet1 and Tet2 on chromatin organization and increased DNA methylation correlation on spatially interacted fragments upon Tet inactivation. Our work showed the broad effects of Tet inactivation and DNA methylation dynamics on chromosome organization.
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Affiliation(s)
- Hao Tian
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics, Peking University, Beijing 100871, China
| | - Pengfei Luan
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Yaping Liu
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Guoqiang Li
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics, Peking University, Beijing 100871, China
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5
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Rengifo Rojas C, Cercy J, Perillous S, Gonthier-Guéret C, Montibus B, Maupetit-Méhouas S, Espinadel A, Dupré M, Hong CC, Hata K, Nakabayashi K, Plagge A, Bouschet T, Arnaud P, Vaillant I, Court F. Biallelic non-productive enhancer-promoter interactions precede imprinted expression of Kcnk9 during mouse neural commitment. HGG ADVANCES 2024; 5:100271. [PMID: 38297831 PMCID: PMC10869267 DOI: 10.1016/j.xhgg.2024.100271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/18/2023] [Accepted: 01/23/2024] [Indexed: 02/02/2024] Open
Abstract
It is only partially understood how constitutive allelic methylation at imprinting control regions (ICRs) interacts with other regulation levels to drive timely parental allele-specific expression along large imprinted domains. The Peg13-Kcnk9 domain is an imprinted domain with important brain functions. To gain insights into its regulation during neural commitment, we performed an integrative analysis of its allele-specific epigenetic, transcriptomic, and cis-spatial organization using a mouse stem cell-based corticogenesis model that recapitulates the control of imprinted gene expression during neurodevelopment. We found that, despite an allelic higher-order chromatin structure associated with the paternally CTCF-bound Peg13 ICR, enhancer-Kcnk9 promoter contacts occurred on both alleles, although they were productive only on the maternal allele. This observation challenges the canonical model in which CTCF binding isolates the enhancer and its target gene on either side and suggests a more nuanced role for allelic CTCF binding at some ICRs.
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Affiliation(s)
- Cecilia Rengifo Rojas
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Jil Cercy
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Sophie Perillous
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Céline Gonthier-Guéret
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Bertille Montibus
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Stéphanie Maupetit-Méhouas
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Astrid Espinadel
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Marylou Dupré
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Charles C Hong
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan; Department of Human Molecular Genetics, Gunma University Graduate School of Medicine 3-39-22 Showa, Maebashi, Gunma 371-8511, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan
| | - Antonius Plagge
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Tristan Bouschet
- Institut de Génomique Fonctionnelle, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Philippe Arnaud
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France.
| | - Isabelle Vaillant
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France.
| | - Franck Court
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France.
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6
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Argentato PP, Marchesi JAP, Dejani NN, Nakandakare PY, Teles LDFDS, Batista LPR, Leitão MPC, Luzia LA, Ramos ES, Rondó PH. The relationship between obesity-related H19DMR methylation and H19 and IGF2 gene expression on offspring growth and body composition. Front Nutr 2023; 10:1170411. [PMID: 37810933 PMCID: PMC10552537 DOI: 10.3389/fnut.2023.1170411] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023] Open
Abstract
Background and objective Imprinted genes are important for the offspring development. To assess the relationship between obesity-related H19DMR methylation and H19 and IGF2 gene expression and offspring growth and body composition. Methods Thirty-nine overweight/obese and 25 normal weight pregnant women were selected from the "Araraquara Cohort Study" according to their pre-pregnancy BMI. Fetal growth and body composition and newborn growth were assessed, respectively, by ultrasound and anthropometry. The methylation of H19DMR in maternal blood, cord blood, maternal decidua and placental villi tissues was evaluated by methylation-sensitive restriction endonuclease qPCR, and H19 and IGF2 expression by relative real-time PCR quantification. Multiple linear regression models explored the associations of DNA methylation and gene expression with maternal, fetal, and newborn parameters. Results H19DMR was less methylated in maternal blood of the overweight/obese group. There were associations of H19DMR methylation in cord blood with centiles of fetal biparietal diameter (BPD) and abdominal subcutaneous fat thickness and newborn head circumference (HC); H19DMR methylation in maternal decidua with fetal occipitofrontal diameter (OFD), HC, and length; H19DMR methylation in placental villi with fetal OFD, HC and abdominal subcutaneous fat thickness and with newborn HC. H19 expression in maternal decidua was associated with fetal BPD and femur length centiles and in placental villi with fetal OFD and subcutaneous arm fat. IGF2 expression in maternal decidua was associated with fetal BPD and in placental villi with fetal OFD. Conclusion To our knowledge, this is the first study to demonstrate associations of imprinted genes variations at the maternal-fetal interface of the placenta and in cord blood with fetal body composition, supporting the involvement of epigenetic mechanisms in offspring growth and body composition.
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Affiliation(s)
- Perla Pizzi Argentato
- Nutrition Department, School of Public Health, University of São Paulo, São Paulo, Brazil
| | | | - Naiara Naiana Dejani
- Nutrition Department, School of Public Health, University of São Paulo, São Paulo, Brazil
| | | | | | | | | | - Liania Alves Luzia
- Nutrition Department, School of Public Health, University of São Paulo, São Paulo, Brazil
| | - Ester Silveira Ramos
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Patricia Helen Rondó
- Nutrition Department, School of Public Health, University of São Paulo, São Paulo, Brazil
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7
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Stricker SH. Folding makes an imprint. Genes Dev 2023; 37:779-780. [PMID: 37821108 PMCID: PMC10620038 DOI: 10.1101/gad.351216.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Imprinted gene clusters are confined genomic regions containing genes with parent-of-origin-dependent transcriptional activity. In this issue of Genes & Development, Loftus and colleagues (pp. 829-843) made use of an insightful combination of descriptive approaches, genetic manipulations, and epigenome-editing approaches to show that differences in nuclear topology precede the onset of imprinted expression at the Peg13-Kcnk9 locus. Furthermore, the investigators provide data in line with a model suggesting that parent-of-origin-specific topological differences could be responsible for parent-of-origin-specific enhancer activity and thus imprinted expression.
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Affiliation(s)
- Stefan H Stricker
- Reprogramming and Regeneration, Biomedical Center (BMC), Physiological Genomics, Faculty of Medicine, Ludwig Maximilian University (LMU) Munich, Planegg-Martinsried 82152, Germany; Epigenetic Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, Planegg-Martinsried 82152, Germany
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8
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Loftus D, Bae B, Whilden CM, Whipple AJ. Allelic chromatin structure precedes imprinted expression of Kcnk9 during neurogenesis. Genes Dev 2023; 37:829-843. [PMID: 37821107 PMCID: PMC10620047 DOI: 10.1101/gad.350896.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 09/18/2023] [Indexed: 10/13/2023]
Abstract
Differences in chromatin state inherited from the parental gametes influence the regulation of maternal and paternal alleles in offspring. This phenomenon, known as genomic imprinting, results in genes preferentially transcribed from one parental allele. While local epigenetic factors such as DNA methylation are known to be important for the establishment of imprinted gene expression, less is known about the mechanisms by which differentially methylated regions (DMRs) lead to differences in allelic expression across broad stretches of chromatin. Allele-specific higher-order chromatin structure has been observed at multiple imprinted loci, consistent with the observation of allelic binding of the chromatin-organizing factor CTCF at multiple DMRs. However, whether allelic chromatin structure impacts allelic gene expression is not known for most imprinted loci. Here we characterize the mechanisms underlying brain-specific imprinted expression of the Peg13-Kcnk9 locus, an imprinted region associated with intellectual disability. We performed region capture Hi-C on mouse brains from reciprocal hybrid crosses and found imprinted higher-order chromatin structure caused by the allelic binding of CTCF to the Peg13 DMR. Using an in vitro neuron differentiation system, we showed that imprinted chromatin structure precedes imprinted expression at the locus. Additionally, activation of a distal enhancer induced imprinted expression of Kcnk9 in an allelic chromatin structure-dependent manner. This work provides a high-resolution map of imprinted chromatin structure and demonstrates that chromatin state established in early development can promote imprinted expression upon differentiation.
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Affiliation(s)
- Daniel Loftus
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Bongmin Bae
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Courtney M Whilden
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Amanda J Whipple
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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9
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Senapati S, Irshad IU, Sharma AK, Kumar H. Fundamental insights into the correlation between chromosome configuration and transcription. Phys Biol 2023; 20:051002. [PMID: 37467757 DOI: 10.1088/1478-3975/ace8e5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 07/19/2023] [Indexed: 07/21/2023]
Abstract
Eukaryotic chromosomes exhibit a hierarchical organization that spans a spectrum of length scales, ranging from sub-regions known as loops, which typically comprise hundreds of base pairs, to much larger chromosome territories that can encompass a few mega base pairs. Chromosome conformation capture experiments that involve high-throughput sequencing methods combined with microscopy techniques have enabled a new understanding of inter- and intra-chromosomal interactions with unprecedented details. This information also provides mechanistic insights on the relationship between genome architecture and gene expression. In this article, we review the recent findings on three-dimensional interactions among chromosomes at the compartment, topologically associating domain, and loop levels and the impact of these interactions on the transcription process. We also discuss current understanding of various biophysical processes involved in multi-layer structural organization of chromosomes. Then, we discuss the relationships between gene expression and genome structure from perturbative genome-wide association studies. Furthermore, for a better understanding of how chromosome architecture and function are linked, we emphasize the role of epigenetic modifications in the regulation of gene expression. Such an understanding of the relationship between genome architecture and gene expression can provide a new perspective on the range of potential future discoveries and therapeutic research.
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Affiliation(s)
- Swayamshree Senapati
- School of Basic Sciences, Indian Institute of Technology, Bhubaneswar, Argul, Odisha 752050, India
| | - Inayat Ullah Irshad
- Department of Physics, Indian Institute of Technology, Jammu, Jammu 181221, India
| | - Ajeet K Sharma
- Department of Physics, Indian Institute of Technology, Jammu, Jammu 181221, India
- Department of Biosciences and Bioengineering, Indian Institute of Technology Jammu, Jammu 181221, India
| | - Hemant Kumar
- School of Basic Sciences, Indian Institute of Technology, Bhubaneswar, Argul, Odisha 752050, India
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10
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Ye B, Yu M, Yue M, Yin M, Zhang C, Wang Q, Ding X, Shen W, Zhao Z. Role of PDLIM1 in hepatic stellate cell activation and liver fibrosis progression. Sci Rep 2023; 13:10946. [PMID: 37414929 PMCID: PMC10326060 DOI: 10.1038/s41598-023-38144-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 07/04/2023] [Indexed: 07/08/2023] Open
Abstract
Liver fibrosis is caused by chronic hepatic injury and may lead to cirrhosis, and even hepatocellular carcinoma. When hepatic stellate cells (HSCs) are activated by liver injury, they transdifferentiate into myofibroblasts, which secrete extracellular matrix proteins that generate the fibrous scar. Therefore, it is extremely urgent to find safe and effective drugs for HSCs activation treatment to prevent liver against fibrosis. Here, we reported that PDZ and LIM domain protein 1 (PDLIM1), a highly conserved cytoskeleton organization regulator, was significantly up-regulated in fibrotic liver tissues and TGF-β-treated HSC-T6 cells. Through transcriptome analysis, we found that knockdown of PDLIM1 resulted in a significant downregulation of genes related to inflammation and immune-related pathways in HSC-T6 cells. Moreover, PDLIM1 knockdown significantly inhibited the activation of HSC-T6 cells and the trans-differentiation of HSC-T6 cells into myofibroblasts. Mechanistically, PDLIM1 is involved in the regulation of TGF-β-mediated signaling pathways in HSCs activation. Thus, targeting PDLIM1 may provide an alternative method to suppress HSCs activation during liver injury. CCCTC-binding factor (CTCF), a master regulator of genome architecture, is upregulated during HSCs activation. PDLIM1 knockdown also indirectly reduced CTCF protein expression, however, CTCF binding to chromatin was not significantly altered by CUT&Tag analysis. We speculate that CTCF may cooperate with PDLIM1 to activate HSCs in other ways. Our results suggest that PDLIM1 can accelerate the activation of HSCs and liver fibrosis progression and could be a potential biomarker for monitoring response to anti-fibrotic therapy.
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Affiliation(s)
- Bingyu Ye
- State Key Laboratory of Cell Differentiation and Regulation, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China.
| | - Mengli Yu
- State Key Laboratory of Cell Differentiation and Regulation, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Meijuan Yue
- State Key Laboratory of Cell Differentiation and Regulation, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Man Yin
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chunyan Zhang
- State Key Laboratory of Cell Differentiation and Regulation, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Qiwen Wang
- State Key Laboratory of Cell Differentiation and Regulation, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Xinru Ding
- State Key Laboratory of Cell Differentiation and Regulation, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Wenlong Shen
- Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Fengtai District, Beijing, 100071, China.
| | - Zhihu Zhao
- Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Fengtai District, Beijing, 100071, China.
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Pandupuspitasari NS, Khan FA, Huang C, Ali A, Yousaf MR, Shakeel F, Putri EM, Negara W, Muktiani A, Prasetiyono BWHE, Kustiawan L, Wahyuni DS. Recent advances in chromosome capture techniques unraveling 3D genome architecture in germ cells, health, and disease. Funct Integr Genomics 2023; 23:214. [PMID: 37386239 DOI: 10.1007/s10142-023-01146-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 06/16/2023] [Accepted: 06/20/2023] [Indexed: 07/01/2023]
Abstract
In eukaryotes, the genome does not emerge in a specific shape but rather as a hierarchial bundle within the nucleus. This multifaceted genome organization consists of multiresolution cellular structures, such as chromosome territories, compartments, and topologically associating domains, which are frequently defined by architecture, design proteins including CTCF and cohesin, and chromatin loops. This review briefly discusses the advances in understanding the basic rules of control, chromatin folding, and functional areas in early embryogenesis. With the use of chromosome capture techniques, the latest advancements in technologies for visualizing chromatin interactions come close to revealing 3D genome formation frameworks with incredible detail throughout all genomic levels, including at single-cell resolution. The possibility of detecting variations in chromatin architecture might open up new opportunities for disease diagnosis and prevention, infertility treatments, therapeutic approaches, desired exploration, and many other application scenarios.
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Affiliation(s)
- Nuruliarizki Shinta Pandupuspitasari
- Laboratory of Animal Nutrition and Feed Science, Animal Science Department, Faculty of Animal and Agricultural Sciences, Universitas Diponegoro, Semarang, Indonesia.
| | - Faheem Ahmed Khan
- Research Center for Animal Husbandry, National Research and Innovation Agency, Bogor, Indonesia
| | - Chunjie Huang
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, 226001, China
| | - Azhar Ali
- Laboratory of Molecular Biology and Genomics, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Muhammad Rizwan Yousaf
- Laboratory of Molecular Biology and Genomics, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Farwa Shakeel
- Laboratory of Molecular Biology and Genomics, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Ezi Masdia Putri
- Research Center for Animal Husbandry, National Research and Innovation Agency, Bogor, Indonesia
| | - Windu Negara
- Research Center for Animal Husbandry, National Research and Innovation Agency, Bogor, Indonesia
| | - Anis Muktiani
- Laboratory of Animal Nutrition and Feed Science, Animal Science Department, Faculty of Animal and Agricultural Sciences, Universitas Diponegoro, Semarang, Indonesia
| | - Bambang Waluyo Hadi Eko Prasetiyono
- Laboratory of Feed Technology, Animal Science Department, Faculty of Animal and Agricultural Sciences Universitas Diponegoro, Semarang, Indonesia
| | - Limbang Kustiawan
- Laboratory of Animal Nutrition and Feed Science, Animal Science Department, Faculty of Animal and Agricultural Sciences, Universitas Diponegoro, Semarang, Indonesia
| | - Dimar Sari Wahyuni
- Research Center for Animal Husbandry, National Research and Innovation Agency, Bogor, Indonesia
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12
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Loftus D, Bae B, Whilden CM, Whipple AJ. Allelic chromatin structure primes imprinted expression of Kcnk9 during neurogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.09.544389. [PMID: 37333073 PMCID: PMC10274912 DOI: 10.1101/2023.06.09.544389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Differences in chromatin state inherited from the parental gametes influence the regulation of maternal and paternal alleles in offspring. This phenomenon, known as genomic imprinting, results in genes preferentially transcribed from one parental allele. While local epigenetic factors such as DNA methylation are known to be important for the establishment of imprinted gene expression, less is known about the mechanisms by which differentially methylated regions (DMRs) lead to differences in allelic expression across broad stretches of chromatin. Allele-specific higher-order chromatin structure has been observed at multiple imprinted loci, consistent with the observation of allelic binding of the chromatin-organizing factor CTCF at multiple DMRs. However, whether allelic chromatin structure impacts allelic gene expression is not known for most imprinted loci. Here we characterize the mechanisms underlying brain-specific imprinted expression of the Peg13-Kcnk9 locus, an imprinted region associated with intellectual disability. We performed region capture Hi-C on mouse brain from reciprocal hybrid crosses and found imprinted higher-order chromatin structure caused by the allelic binding of CTCF to the Peg13 DMR. Using an in vitro neuron differentiation system, we show that on the maternal allele enhancer-promoter contacts formed early in development prime the brain-specific potassium leak channel Kcnk9 for maternal expression prior to neurogenesis. In contrast, these enhancer-promoter contacts are blocked by CTCF on the paternal allele, preventing paternal Kcnk9 activation. This work provides a high-resolution map of imprinted chromatin structure and demonstrates that chromatin state established in early development can promote imprinted expression upon differentiation.
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Affiliation(s)
- Daniel Loftus
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138 USA
| | - Bongmin Bae
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138 USA
| | - Courtney M. Whilden
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138 USA
| | - Amanda J. Whipple
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138 USA
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13
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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.
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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
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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
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14
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Hu Y, Yuan S, Du X, Liu J, Zhou W, Wei F. Comparative analysis reveals epigenomic evolution related to species traits and genomic imprinting in mammals. Innovation (N Y) 2023; 4:100434. [PMID: 37215528 PMCID: PMC10196708 DOI: 10.1016/j.xinn.2023.100434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 04/25/2023] [Indexed: 05/24/2023] Open
Abstract
DNA methylation is an epigenetic modification that plays a crucial role in various regulatory processes, including gene expression regulation, transposable element repression, and genomic imprinting. However, most studies on DNA methylation have been conducted in humans and other model species, whereas the dynamics of DNA methylation across mammals remain poorly explored, limiting our understanding of epigenomic evolution in mammals and the evolutionary impacts of conserved and lineage-specific DNA methylation. Here, we generated and gathered comparative epigenomic data from 13 mammalian species, including two marsupial species, to demonstrate that DNA methylation plays critical roles in several aspects of gene evolution and species trait evolution. We found that the species-specific DNA methylation of promoters and noncoding elements correlates with species-specific traits such as body patterning, indicating that DNA methylation might help establish or maintain interspecies differences in gene regulation that shape phenotypes. For a broader view, we investigated the evolutionary histories of 88 known imprinting control regions across mammals to identify their evolutionary origins. By analyzing the features of known and newly identified potential imprints in all studied mammals, we found that genomic imprinting may function in embryonic development through the binding of specific transcription factors. Our findings show that DNA methylation and the complex interaction between the genome and epigenome have a significant impact on mammalian evolution, suggesting that evolutionary epigenomics should be incorporated to develop a unified evolutionary theory.
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Affiliation(s)
- Yisi Hu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Shenli Yuan
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xin Du
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiang Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenliang Zhou
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Fuwen Wei
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
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15
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Smits WK, Vermeulen C, Hagelaar R, Kimura S, Vroegindeweij EM, Buijs-Gladdines JGCAM, van de Geer E, Verstegen MJAM, Splinter E, van Reijmersdal SV, Buijs A, Galjart N, van Eyndhoven W, van Min M, Kuiper R, Kemmeren P, Mullighan CG, de Laat W, Meijerink JPP. Elevated enhancer-oncogene contacts and higher oncogene expression levels by recurrent CTCF inactivating mutations in acute T cell leukemia. Cell Rep 2023; 42:112373. [PMID: 37060567 PMCID: PMC10750298 DOI: 10.1016/j.celrep.2023.112373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 03/18/2023] [Accepted: 03/23/2023] [Indexed: 04/16/2023] Open
Abstract
Monoallelic inactivation of CCCTC-binding factor (CTCF) in human cancer drives altered methylated genomic states, altered CTCF occupancy at promoter and enhancer regions, and deregulated global gene expression. In patients with T cell acute lymphoblastic leukemia (T-ALL), we find that acquired monoallelic CTCF-inactivating events drive subtle and local genomic effects in nearly half of t(5; 14) (q35; q32.2) rearranged patients, especially when CTCF-binding sites are preserved in between the BCL11B enhancer and the TLX3 oncogene. These solitary intervening sites insulate TLX3 from the enhancer by inducing competitive looping to multiple binding sites near the TLX3 promoter. Reduced CTCF levels or deletion of the intervening CTCF site abrogates enhancer insulation by weakening competitive looping while favoring TLX3 promoter to BCL11B enhancer looping, which elevates oncogene expression levels and leukemia burden.
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Affiliation(s)
- Willem K Smits
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Carlo Vermeulen
- Oncode Institute, Utrecht, the Netherlands; Hubrecht Institute-KNAW, Utrecht, the Netherlands; Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Rico Hagelaar
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Shunsuke Kimura
- Laboratory of Pathology, St. Jude's Children's Research Hospital, Memphis TN, USA
| | | | | | - Ellen van de Geer
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Marjon J A M Verstegen
- Oncode Institute, Utrecht, the Netherlands; Hubrecht Institute-KNAW, Utrecht, the Netherlands
| | | | | | - Arjan Buijs
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Niels Galjart
- Department of Cell Biology, Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands
| | | | | | - Roland Kuiper
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands; Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Patrick Kemmeren
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Charles G Mullighan
- Laboratory of Pathology, St. Jude's Children's Research Hospital, Memphis TN, USA
| | - Wouter de Laat
- Oncode Institute, Utrecht, the Netherlands; Hubrecht Institute-KNAW, Utrecht, the Netherlands
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16
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Richer S, Tian Y, Schoenfelder S, Hurst L, Murrell A, Pisignano G. Widespread allele-specific topological domains in the human genome are not confined to imprinted gene clusters. Genome Biol 2023; 24:40. [PMID: 36869353 PMCID: PMC9983196 DOI: 10.1186/s13059-023-02876-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 02/13/2023] [Indexed: 03/05/2023] Open
Abstract
BACKGROUND There is widespread interest in the three-dimensional chromatin conformation of the genome and its impact on gene expression. However, these studies frequently do not consider parent-of-origin differences, such as genomic imprinting, which result in monoallelic expression. In addition, genome-wide allele-specific chromatin conformation associations have not been extensively explored. There are few accessible bioinformatic workflows for investigating allelic conformation differences and these require pre-phased haplotypes which are not widely available. RESULTS We developed a bioinformatic pipeline, "HiCFlow," that performs haplotype assembly and visualization of parental chromatin architecture. We benchmarked the pipeline using prototype haplotype phased Hi-C data from GM12878 cells at three disease-associated imprinted gene clusters. Using Region Capture Hi-C and Hi-C data from human cell lines (1-7HB2, IMR-90, and H1-hESCs), we can robustly identify the known stable allele-specific interactions at the IGF2-H19 locus. Other imprinted loci (DLK1 and SNRPN) are more variable and there is no "canonical imprinted 3D structure," but we could detect allele-specific differences in A/B compartmentalization. Genome-wide, when topologically associating domains (TADs) are unbiasedly ranked according to their allele-specific contact frequencies, a set of allele-specific TADs could be defined. These occur in genomic regions of high sequence variation. In addition to imprinted genes, allele-specific TADs are also enriched for allele-specific expressed genes. We find loci that have not previously been identified as allele-specific expressed genes such as the bitter taste receptors (TAS2Rs). CONCLUSIONS This study highlights the widespread differences in chromatin conformation between heterozygous loci and provides a new framework for understanding allele-specific expressed genes.
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Affiliation(s)
- Stephen Richer
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Yuan Tian
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
- UCL Cancer Institute, University College London, Paul O'Gorman Building, London, UK
| | | | - Laurence Hurst
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Adele Murrell
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
| | - Giuseppina Pisignano
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
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17
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Ye B, Shen W, Li Y, Wang D, Zhang Y, Li P, Yin M, Wang Y, Xie D, Shi S, Yao T, Chen J, Xu P, Zhao Z. FAIRE-MS reveals mitotic retention of transcriptional regulators on a proteome-wide scale. FASEB J 2023; 37:e22724. [PMID: 36583687 DOI: 10.1096/fj.202201038rrr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 12/01/2022] [Accepted: 12/08/2022] [Indexed: 12/31/2022]
Abstract
Mitosis entails global and dramatic alterations, such as higher-order chromatin organization disruption, concomitant with global transcription downregulation. Cells reliably re-establishing gene expression patterns upon mitotic exit and maintaining cellular identities remain poorly understood. Previous studies indicated that certain transcription factors (TFs) remain associated with individual loci during mitosis and serve as mitotic bookmarkers. However, it is unclear which regulatory factors remain bound to the compacted mitotic chromosomes. We developed formaldehyde-assisted isolation of regulatory elements-coupled mass spectrometry (FAIRE-MS) that combines FAIRE-based open chromatin-associated protein pull-down and mass spectrometry (MS) to quantify the open chromatin-associated proteome during the interphase and mitosis. We identified 189 interphase and mitosis maintained (IM) regulatory factors using FAIRE-MS and found intrinsically disordered proteins and regions (IDP(R)s) are highly enriched, which plays a crucial role in liquid-liquid phase separation (LLPS) and chromatin organization during the cell cycle. Notably, in these IDP(R)s, we identified mitotic bookmarkers, such as CEBPB, HMGB1, and TFAP2A, and several factors, including MAX, HMGB3, hnRNP A2/B1, FUS, hnRNP D, and TIAL1, which are at least partially bound to the mitotic chromosome. Furthermore, it will be essential to study whether these IDP(R)s through LLPS helps cells transit from mitosis to the G1 phase during the cell cycle.
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Affiliation(s)
- Bingyu Ye
- Beijing Institute of Biotechnology, Beijing, China.,State Key Laboratory of Cell Differentiation and Regulation, College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Wenlong Shen
- Beijing Institute of Biotechnology, Beijing, China
| | - Yanchang Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Institute of Lifeomics, Beijing, China
| | - Dong Wang
- Beijing Institute of Biotechnology, Beijing, China
| | - Yan Zhang
- Beijing Institute of Biotechnology, Beijing, China
| | - Ping Li
- Beijing Institute of Biotechnology, Beijing, China
| | - Man Yin
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yahao Wang
- Beijing Institute of Biotechnology, Beijing, China
| | - Dejian Xie
- Beijing Institute of Biotechnology, Beijing, China
| | - Shu Shi
- Beijing Institute of Biotechnology, Beijing, China
| | - Tao Yao
- Beijing Institute of Biotechnology, Beijing, China
| | - Juncai Chen
- Beijing Institute of Biotechnology, Beijing, China
| | - Ping Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Institute of Lifeomics, Beijing, China
| | - Zhihu Zhao
- Beijing Institute of Biotechnology, Beijing, China
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18
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Zhao J, Huai J. Role of primary aging hallmarks in Alzheimer´s disease. Theranostics 2023; 13:197-230. [PMID: 36593969 PMCID: PMC9800733 DOI: 10.7150/thno.79535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 11/15/2022] [Indexed: 12/03/2022] Open
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disease, which severely threatens the health of the elderly and causes significant economic and social burdens. The causes of AD are complex and include heritable but mostly aging-related factors. The primary aging hallmarks include genomic instability, telomere wear, epigenetic changes, and loss of protein stability, which play a dominant role in the aging process. Although AD is closely associated with the aging process, the underlying mechanisms involved in AD pathogenesis have not been well characterized. This review summarizes the available literature about primary aging hallmarks and their roles in AD pathogenesis. By analyzing published literature, we attempted to uncover the possible mechanisms of aberrant epigenetic markers with related enzymes, transcription factors, and loss of proteostasis in AD. In particular, the importance of oxidative stress-induced DNA methylation and DNA methylation-directed histone modifications and proteostasis are highlighted. A molecular network of gene regulatory elements that undergoes a dynamic change with age may underlie age-dependent AD pathogenesis, and can be used as a new drug target to treat AD.
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19
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Gaspar AD, Cuddapah S. Nickel-induced alterations to chromatin structure and function. Toxicol Appl Pharmacol 2022; 457:116317. [PMID: 36400264 PMCID: PMC9722551 DOI: 10.1016/j.taap.2022.116317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/17/2022]
Abstract
Nickel (Ni), a heavy metal is prevalent in the atmosphere due to both natural and anthropogenic activities. Ni is a carcinogen implicated in the development of lung and nasal cancers in humans. Furthermore, Ni exposure is associated with a number of chronic lung diseases in humans including asthma, chronic bronchitis, emphysema, pulmonary fibrosis, pulmonary edema and chronic obstructive pulmonary disease (COPD). While Ni compounds are weak mutagens, a number of studies have demonstrated the potential of Ni to alter the epigenome, suggesting epigenomic dysregulation as an important underlying cause for its pathogenicity. In the eukaryotic nucleus, the DNA is organized in a three-dimensional (3D) space through assembly of higher order chromatin structures. Such an organization is critically important for transcription and other biological activities. Accumulating evidence suggests that by negatively affecting various cellular regulatory processes, Ni could potentially affect chromatin organization. In this review, we discuss the role of Ni in altering the chromatin architecture, which potentially plays a major role in Ni pathogenicity.
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Affiliation(s)
- Adrian Domnic Gaspar
- Division of Environmental Medicine, Department of Medicine, New York University Grossman School of Medicine, New York, NY 10010, USA
| | - Suresh Cuddapah
- Division of Environmental Medicine, Department of Medicine, New York University Grossman School of Medicine, New York, NY 10010, USA.
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20
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A Tremendous Reorganization Journey for the 3D Chromatin Structure from Gametes to Embryos. Genes (Basel) 2022; 13:genes13101864. [PMID: 36292750 PMCID: PMC9602195 DOI: 10.3390/genes13101864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 10/02/2022] [Accepted: 10/12/2022] [Indexed: 11/04/2022] Open
Abstract
The 3D chromatin structure within the nucleus is important for gene expression regulation and correct developmental programs. Recently, the rapid development of low-input chromatin conformation capture technologies has made it possible to study 3D chromatin structures in gametes, zygotes and early embryos in a variety of species, including flies, vertebrates and mammals. There are distinct 3D chromatin structures within the male and female gametes. Following the fertilization of male and female gametes, fertilized eggs undergo drastic epigenetic reprogramming at multi levels, including the 3D chromatin structure, to convert the terminally differentiated gamete state into the totipotent state, which can give rise to an individual. However, to what extent the 3D chromatin structure reorganization is evolutionarily conserved and what the underlying mechanisms are for the tremendous reorganization in early embryos remain elusive. Here, we review the latest findings on the 3D chromatin structure reorganization during embryogenesis, and discuss the convergent and divergent reprogramming patterns and key molecular mechanisms for the 3D chromatin structure reorganization from gametes to embryos in different species. These findings shed light on how the 3D chromatin structure reorganization contribute to embryo development in different species. The findings also indicate the role of the 3D chromatin structure on the acquisition of totipotent developmental potential.
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21
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Kaplun DS, Kaluzhny DN, Prokhortchouk EB, Zhenilo SV. DNA Methylation: Genomewide Distribution, Regulatory Mechanism and Therapy Target. Acta Naturae 2022; 14:4-19. [PMID: 36694897 PMCID: PMC9844086 DOI: 10.32607/actanaturae.11822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 11/29/2022] [Indexed: 01/22/2023] Open
Abstract
DNA methylation is the most important epigenetic modification involved in the regulation of transcription, imprinting, establishment of X-inactivation, and the formation of a chromatin structure. DNA methylation in the genome is often associated with transcriptional repression and the formation of closed heterochromatin. However, the results of genome-wide studies of the DNA methylation pattern and transcriptional activity of genes have nudged us toward reconsidering this paradigm, since the promoters of many genes remain active despite their methylation. The differences in the DNA methylation distribution in normal and pathological conditions allow us to consider methylation as a diagnostic marker or a therapy target. In this regard, the need to investigate the factors affecting DNA methylation and those involved in its interpretation becomes pressing. Recently, a large number of protein factors have been uncovered, whose ability to bind to DNA depends on their methylation. Many of these proteins act not only as transcriptional activators or repressors, but also affect the level of DNA methylation. These factors are considered potential therapeutic targets for the treatment of diseases resulting from either a change in DNA methylation or a change in the interpretation of its methylation level. In addition to protein factors, a secondary DNA structure can also affect its methylation and can be considered as a therapy target. In this review, the latest research into the DNA methylation landscape in the genome has been summarized to discuss why some DNA regions avoid methylation and what factors can affect its level or interpretation and, therefore, can be considered a therapy target.
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Affiliation(s)
- D. S. Kaplun
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071 Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119071 Russia
| | - D. N. Kaluzhny
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - E. B. Prokhortchouk
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071 Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119071 Russia
| | - S. V. Zhenilo
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071 Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119071 Russia
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22
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Zhang S, Plummer D, Lu L, Cui J, Xu W, Wang M, Liu X, Prabhakar N, Shrinet J, Srinivasan D, Fraser P, Li Y, Li J, Jin F. DeepLoop robustly maps chromatin interactions from sparse allele-resolved or single-cell Hi-C data at kilobase resolution. Nat Genet 2022; 54:1013-1025. [PMID: 35817982 PMCID: PMC10082397 DOI: 10.1038/s41588-022-01116-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 05/30/2022] [Indexed: 11/09/2022]
Abstract
Mapping chromatin loops from noisy Hi-C heatmaps remains a major challenge. Here we present DeepLoop, which performs rigorous bias correction followed by deep-learning-based signal enhancement for robust chromatin interaction mapping from low-depth Hi-C data. DeepLoop enables loop-resolution, single-cell Hi-C analysis. It also achieves a cross-platform convergence between different Hi-C protocols and micrococcal nuclease (micro-C). DeepLoop allowed us to map the genetic and epigenetic determinants of allele-specific chromatin interactions in the human genome. We nominate new loci with allele-specific interactions governed by imprinting or allelic DNA methylation. We also discovered that, in the inactivated X chromosome (Xi), local loops at the DXZ4 'megadomain' boundary escape X-inactivation but the FIRRE 'superloop' locus does not. Importantly, DeepLoop can pinpoint heterozygous single-nucleotide polymorphisms and large structure variants that cause allelic chromatin loops, many of which rewire enhancers with transcription consequences. Taken together, DeepLoop expands the use of Hi-C to provide loop-resolution insights into the genetics of the three-dimensional genome.
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Affiliation(s)
- Shanshan Zhang
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.,The Biomedical Sciences Training Program, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Dylan Plummer
- Department of Computer and Data Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Leina Lu
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Jian Cui
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Wanying Xu
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.,The Biomedical Sciences Training Program, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Miao Wang
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Xiaoxiao Liu
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Nachiketh Prabhakar
- Department of Computer and Data Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Jatin Shrinet
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Divyaa Srinivasan
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Peter Fraser
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Yan Li
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
| | - Jing Li
- Department of Computer and Data Sciences, Case Western Reserve University, Cleveland, OH, USA. .,Department of Population and Quantitative Health Sciences, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA.
| | - Fulai Jin
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA. .,Department of Computer and Data Sciences, Case Western Reserve University, Cleveland, OH, USA. .,Department of Population and Quantitative Health Sciences, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA.
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23
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Papadogkonas G, Papamatheakis DA, Spilianakis C. 3D Genome Organization as an Epigenetic Determinant of Transcription Regulation in T Cells. Front Immunol 2022; 13:921375. [PMID: 35812421 PMCID: PMC9257000 DOI: 10.3389/fimmu.2022.921375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/26/2022] [Indexed: 12/12/2022] Open
Abstract
In the heart of innate and adaptive immunity lies the proper spatiotemporal development of several immune cell lineages. Multiple studies have highlighted the necessity of epigenetic and transcriptional regulation in cell lineage specification. This mode of regulation is mediated by transcription factors and chromatin remodelers, controlling developmentally essential gene sets. The core of transcription and epigenetic regulation is formulated by different epigenetic modifications determining gene expression. Apart from “classic” epigenetic modifications, 3D chromatin architecture is also purported to exert fundamental roles in gene regulation. Chromatin conformation both facilitates cell-specific factor binding at specified regions and is in turn modified as such, acting synergistically. The interplay between global and tissue-specific protein factors dictates the epigenetic landscape of T and innate lymphoid cell (ILC) lineages. The expression of global genome organizers such as CTCF, YY1, and the cohesin complexes, closely cooperate with tissue-specific factors to exert cell type-specific gene regulation. Special AT-rich binding protein 1 (SATB1) is an important tissue-specific genome organizer and regulator controlling both long- and short-range chromatin interactions. Recent indications point to SATB1’s cooperation with the aforementioned factors, linking global to tissue-specific gene regulation. Changes in 3D genome organization are of vital importance for proper cell development and function, while disruption of this mechanism can lead to severe immuno-developmental defects. Newly emerging data have inextricably linked chromatin architecture deregulation to tissue-specific pathophysiological phenotypes. The combination of these findings may shed light on the mechanisms behind pathological conditions.
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Affiliation(s)
- George Papadogkonas
- Department of Biology, University of Crete, Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Greece
| | - Dionysios-Alexandros Papamatheakis
- Department of Biology, University of Crete, Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Greece
| | - Charalampos Spilianakis
- Department of Biology, University of Crete, Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Greece
- *Correspondence: Charalampos Spilianakis,
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24
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IGF2: Development, Genetic and Epigenetic Abnormalities. Cells 2022; 11:cells11121886. [PMID: 35741015 PMCID: PMC9221339 DOI: 10.3390/cells11121886] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/04/2022] [Accepted: 06/06/2022] [Indexed: 02/07/2023] Open
Abstract
In the 30 years since the first report of parental imprinting in insulin-like growth factor 2 (Igf2) knockout mouse models, we have learnt much about the structure of this protein, its role and regulation. Indeed, many animal and human studies involving innovative techniques have shed light on the complex regulation of IGF2 expression. The physiological roles of IGF-II have also been documented, revealing pleiotropic tissue-specific and developmental-stage-dependent action. Furthermore, in recent years, animal studies have highlighted important interspecies differences in IGF-II function, gene expression and regulation. The identification of human disorders due to impaired IGF2 gene expression has also helped to elucidate the major role of IGF-II in growth and in tumor proliferation. The Silver-Russell and Beckwith-Wiedemann syndromes are the most representative imprinted disorders, as they constitute both phenotypic and molecular mirrors of IGF2-linked abnormalities. The characterization of patients with either epigenetic or genetic defects altering IGF2 expression has confirmed the central role of IGF-II in human growth regulation, particularly before birth, and its effects on broader body functions, such as metabolism or tumor susceptibility. Given the long-term health impact of these rare disorders, it is important to understand the consequences of IGF2 defects in these patients.
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25
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Kamrani S, Amirchaghmaghi E, Ghaffari F, Shahhoseini M, Ghaedi K. Altered gene expression of VEGF, IGFs and H19 lncRNA and epigenetic profile of H19-DMR region in endometrial tissues of women with endometriosis. Reprod Health 2022; 19:100. [PMID: 35459174 PMCID: PMC9034598 DOI: 10.1186/s12978-022-01406-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 04/06/2022] [Indexed: 12/03/2022] Open
Abstract
Background Endometriosis, as chronic estrogen-dependent disease, is defined by the presence of endometrial-like tissue outside the uterus. Proliferation of endometrial tissue and neoangiogenesis are critical factors in development of endometriosis. Hence, vascular endothelial growth factor (VEGF) as well as insulin‐like growth factor 1 and 2 (IGF1, 2) may be involved as inducers of cellular proliferation or neoangiogenesis. Imprinted long noncoding RNA H19 (lncRNA H19) has been suggested to be involved in pathogenesis of endometriosis via regulation of cellular proliferation and differentiation. Epigenetic aberrations appear to play an important role in its pathogenesis. The present study was designed to elucidate VEGF, IGF1, IGF2 and H19 lncRNA genes expression and epigenetic alterations of differentially methylated region (DMR) of H19 (H19-DMR) regulatory region in endometrial tissues of patients with endometriosis, in comparison with control women. Methods In this case–control study, 24 women with and without endometriosis were studied for the relative expression of VEGF, IGF1, IGF2 and H19 lncRNA genes using real-time polymerase chain reaction (PCR) technique. Occupancy of the MeCP2 on DMR region of H19 gene was assessed using chromatin immunoprecipitation (ChIP), followed by real-time PCR. Results Genes expression profile of H19, IGF1 and IGF2 was decreased in eutopic and ectopic endometrial tissues of endometriosis group, compared to the control tissues. Decreased expression of H19 in ectopic samples was significant in comparison with the controls (P < 0.05). Gene expression of VEGF was increased in eutopic tissues of endometriosis group, compared to control group. Whereas its expression level was lower in ectopic lesions versus eutopic and control endometrial samples. ChIP analysis revealed significant and nearly significant hypomethylation of H19-DMR region II in eutopic and ectopic samples, compared to the control group respectively. This epigenetic change was aligned with expression of IGF2. While methylation of H19-DMR region I was not significantly different between the eutopic, ectopic and control endometrial samples. Conclusion These data showed that VEGF, IGF1, IGF2 and H19 lncRNA genes expression and epigenetic alterations of H19 lncRNA have dynamic role in the pathogenesis of endometriosis, specifically in the way that hypomethylation of H19-DMR region II can be involved in IGF2 dysregulation in endometriosis.
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Affiliation(s)
- Sedigheh Kamrani
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Hezar Jerib Ave, Azadi Square, Isfahan, Iran
| | - Elham Amirchaghmaghi
- Department of Endocrinology and Female Infertility, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran.,Department of Regenerative Biomedicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Firouzeh Ghaffari
- Department of Endocrinology and Female Infertility, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Maryam Shahhoseini
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, P.O.Box: 19395-4644, Tehran, Iran. .,Reproductive Epidemiology Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran. .,Department of Cell and Molecular Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran.
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Hezar Jerib Ave, Azadi Square, Isfahan, Iran.
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26
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Bencivenga D, Stampone E, Vastante A, Barahmeh M, Della Ragione F, Borriello A. An Unanticipated Modulation of Cyclin-Dependent Kinase Inhibitors: The Role of Long Non-Coding RNAs. Cells 2022; 11:cells11081346. [PMID: 35456025 PMCID: PMC9028986 DOI: 10.3390/cells11081346] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/08/2022] [Accepted: 04/11/2022] [Indexed: 12/13/2022] Open
Abstract
It is now definitively established that a large part of the human genome is transcribed. However, only a scarce percentage of the transcriptome (about 1.2%) consists of RNAs that are translated into proteins, while the large majority of transcripts include a variety of RNA families with different dimensions and functions. Within this heterogeneous RNA world, a significant fraction consists of sequences with a length of more than 200 bases that form the so-called long non-coding RNA family. The functions of long non-coding RNAs range from the regulation of gene transcription to the changes in DNA topology and nucleosome modification and structural organization, to paraspeckle formation and cellular organelles maturation. This review is focused on the role of long non-coding RNAs as regulators of cyclin-dependent kinase inhibitors’ (CDKIs) levels and activities. Cyclin-dependent kinases are enzymes necessary for the tuned progression of the cell division cycle. The control of their activity takes place at various levels. Among these, interaction with CDKIs is a vital mechanism. Through CDKI modulation, long non-coding RNAs implement control over cellular physiology and are associated with numerous pathologies. However, although there are robust data in the literature, the role of long non-coding RNAs in the modulation of CDKIs appears to still be underestimated, as well as their importance in cell proliferation control.
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27
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The Role of DNA Methylation and DNA Methyltransferases in Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:317-348. [DOI: 10.1007/978-3-031-11454-0_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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28
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Oh HJ, Aguilar R, Kesner B, Lee HG, Kriz AJ, Chu HP, Lee JT. Jpx RNA regulates CTCF anchor site selection and formation of chromosome loops. Cell 2021; 184:6157-6173.e24. [PMID: 34856126 DOI: 10.1016/j.cell.2021.11.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 09/22/2021] [Accepted: 11/09/2021] [Indexed: 01/24/2023]
Abstract
Chromosome loops shift dynamically during development, homeostasis, and disease. CCCTC-binding factor (CTCF) is known to anchor loops and construct 3D genomes, but how anchor sites are selected is not yet understood. Here, we unveil Jpx RNA as a determinant of anchor selectivity. Jpx RNA targets thousands of genomic sites, preferentially binding promoters of active genes. Depleting Jpx RNA causes ectopic CTCF binding, massive shifts in chromosome looping, and downregulation of >700 Jpx target genes. Without Jpx, thousands of lost loops are replaced by de novo loops anchored by ectopic CTCF sites. Although Jpx controls CTCF binding on a genome-wide basis, it acts selectively at the subset of developmentally sensitive CTCF sites. Specifically, Jpx targets low-affinity CTCF motifs and displaces CTCF protein through competitive inhibition. We conclude that Jpx acts as a CTCF release factor and shapes the 3D genome by regulating anchor site usage.
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Affiliation(s)
- Hyun Jung Oh
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Rodrigo Aguilar
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Barry Kesner
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Hun-Goo Lee
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Andrea J Kriz
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Hsueh-Ping Chu
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02114, USA.
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29
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Patel D, Patel M, Datta S, Singh U. CGGBP1-dependent CTCF-binding sites restrict ectopic transcription. Cell Cycle 2021; 20:2387-2401. [PMID: 34585631 PMCID: PMC8794514 DOI: 10.1080/15384101.2021.1982508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/25/2021] [Accepted: 09/14/2021] [Indexed: 10/20/2022] Open
Abstract
Binding sites of the chromatin regulator protein CTCF function as important landmarks in the human genome. The recently characterized CTCF-binding sites at LINE-1 repeats depend on another repeat-regulatory protein CGGBP1. These CGGBP1-dependent CTCF-binding sites serve as potential barrier elements for epigenetic marks such as H3K9me3. Such CTCF-binding sites are associated with asymmetric H3K9me3 levels as well as RNA levels in their flanks. The functions of these CGGBP1-dependent CTCF-binding sites remain unknown. By performing targeted studies on candidate CGGBP1-dependent CTCF-binding sites cloned in an SV40 promoter-enhancer episomal system we show that these regions act as inhibitors of ectopic transcription from the SV40 promoter. CGGBP1-dependent CTCF-binding sites that recapitulate their genomic function of loss of CTCF binding upon CGGBP1 depletion and H3K9me3 asymmetry in immediate flanks are also the ones that show the strongest inhibition of ectopic transcription. By performing a series of strand-specific reverse transcription PCRs we demonstrate that this ectopic transcription results in the synthesis of RNA from the SV40 promoter in a direction opposite to the downstream reporter gene in a strand-specific manner. The unleashing of the bidirectionality of the SV40 promoter activity and a breach of the transcription barrier seems to depend on depletion of CGGBP1 and loss of CTCF binding proximal to the SV40 promoter. RNA-sequencing reveals that CGGBP1-regulated CTCF-binding sites act as barriers to transcription at multiple locations genome-wide. These findings suggest a role of CGGBP1-dependent binding sites in restricting ectopic transcription.
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Affiliation(s)
- Divyesh Patel
- HoMeCell Lab, Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, India
- Research Programs Unit, Applied Tumor Genomics Program, Faculty of Medicine, University of Helsinki, Biomedicum, Helsinki, Finland
| | - Manthan Patel
- HoMeCell Lab, Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, India
| | - Subhamoy Datta
- HoMeCell Lab, Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, India
| | - Umashankar Singh
- HoMeCell Lab, Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, India
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30
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Kang J, Kim YW, Park S, Kang Y, Kim A. Multiple CTCF sites cooperate with each other to maintain a TAD for enhancer-promoter interaction in the β-globin locus. FASEB J 2021; 35:e21768. [PMID: 34245617 DOI: 10.1096/fj.202100105rr] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 06/11/2021] [Accepted: 06/15/2021] [Indexed: 01/01/2023]
Abstract
Insulators are cis-regulatory elements that block enhancer activity and prevent heterochromatin spreading. The binding of CCCTC-binding factor (CTCF) protein is essential for insulators to play the roles in a chromatin context. The β-globin locus, consisting of multiple genes and enhancers, is flanked by two insulators 3'HS1 and HS5. However, it has been reported that the absence of these insulators did not affect the β-globin transcription. To explain the unexpected finding, we have deleted a CTCF motif at 3'HS1 or HS5 in the human β-globin locus and analyzed chromatin interactions around the locus. It was found that a topologically associating domain (TAD) containing the β-globin locus is maintained by neighboring CTCF sites in the CTCF motif-deleted loci. The additional deletions of neighboring CTCF motifs disrupted the β-globin TAD, resulting in decrease of the β-globin transcription. Chromatin interactions of the β-globin enhancers with gene promoter were weakened in the multiple CTCF motifs-deleted loci, even though the enhancers have still active chromatin features such as histone H3K27ac and histone H3 depletion. Genome-wide analysis using public CTCF ChIA-PET and ChIP-seq data showed that chromatin domains possessing multiple CTCF binding sites tend to contain super-enhancers like the β-globin enhancers. Taken together, our results show that multiple CTCF sites surrounding the β-globin locus cooperate with each other to maintain a TAD. The β-globin TAD appears to provide a compact spatial environment that enables enhancers to interact with promoter.
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Affiliation(s)
- Jin Kang
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan, Korea
| | - Yea Woon Kim
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan, Korea
| | - Seongwon Park
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan, Korea
| | - Yujin Kang
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan, Korea
| | - AeRi Kim
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan, Korea
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31
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Large parental differences in chromatin organization in pancreatic beta cell line explaining diabetes susceptibility effects. Nat Commun 2021; 12:4338. [PMID: 34267199 PMCID: PMC8282625 DOI: 10.1038/s41467-021-24635-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 06/28/2021] [Indexed: 12/26/2022] Open
Abstract
Previous GWAS studies identified non-coding loci with parent-of-origin-specific effects on Type 2 diabetes susceptibility. Here we report the molecular basis for one such locus near the KRTAP5-6 gene on chromosome 11. We determine the pattern of long-range contacts between an enhancer in this locus and the human INS promoter 460 kb away, in the human pancreatic β-cell line, EndoC-βH1. 3C long range contact experiments distinguish contacts on the two sister chromosomes. Coupling with allele-specific SNPs allows construction of maps revealing marked differences in organization of the two sister chromosomes in the entire region between KRTAP5-6 and INS. Further mapping distinguishes maternal and paternal alleles. This reveals a domain of parent-of-origin-specific chromatin structure extending in the telomeric direction from the INS locus. This suggests more generally that imprinted loci may extend their influence over gene expression beyond those loci through long range chromatin structure, resulting in parent-of-origin-biased expression patterns over great distances. A SNP distant from the human insulin (INS) gene near the KRTAP5-6 gene confers increased susceptibility to type 2 diabetes when present on the paternal allele while decreased susceptibility when on the maternal allele. Here the authors show that long-range contacts between the INS locus and the KRTAP5-6 gene locus distinguish paternal and maternal alleles.
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32
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Naveh NSS, Deegan DF, Huhn J, Traxler E, Lan Y, Weksberg R, Ganguly A, Engel N, Kalish JM. The role of CTCF in the organization of the centromeric 11p15 imprinted domain interactome. Nucleic Acids Res 2021; 49:6315-6330. [PMID: 34107024 PMCID: PMC8216465 DOI: 10.1093/nar/gkab475] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 04/22/2021] [Accepted: 05/20/2021] [Indexed: 02/06/2023] Open
Abstract
DNA methylation, chromatin-binding proteins, and DNA looping are common components regulating genomic imprinting which leads to parent-specific monoallelic gene expression. Loss of methylation (LOM) at the human imprinting center 2 (IC2) on chromosome 11p15 is the most common cause of the imprinting overgrowth disorder Beckwith-Wiedemann Syndrome (BWS). Here, we report a familial transmission of a 7.6 kB deletion that ablates the core promoter of KCNQ1. This structural alteration leads to IC2 LOM and causes recurrent BWS. We find that occupancy of the chromatin organizer CTCF is disrupted proximal to the deletion, which causes chromatin architecture changes both in cis and in trans. We also profile the chromatin architecture of IC2 in patients with sporadic BWS caused by isolated LOM to identify conserved features of IC2 regulatory disruption. A strong interaction between CTCF sites around KCNQ1 and CDKN1C likely drive their expression on the maternal allele, while a weaker interaction involving the imprinting control region element may impede this connection and mediate gene silencing on the paternal allele. We present an imprinting model in which KCNQ1 transcription is necessary for appropriate CTCF binding and a novel chromatin conformation to drive allele-specific gene expression.
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Affiliation(s)
- Natali S Sobel Naveh
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Daniel F Deegan
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, PA 19140, USA
| | - Jacklyn Huhn
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, PA 19140, USA
| | - Emily Traxler
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yemin Lan
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rosanna Weksberg
- Division of Clinical and Metabolic Genetics, Genetics and Genome Biology, Hospital for Sick Children, and Institute of Medical Science, University of Toronto, Toronto, Canada
| | - Arupa Ganguly
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nora Engel
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, PA 19140, USA
| | - Jennifer M Kalish
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
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33
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Davidson IF, Peters JM. Genome folding through loop extrusion by SMC complexes. Nat Rev Mol Cell Biol 2021; 22:445-464. [PMID: 33767413 DOI: 10.1038/s41580-021-00349-7] [Citation(s) in RCA: 196] [Impact Index Per Article: 65.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/03/2021] [Indexed: 02/02/2023]
Abstract
Genomic DNA is folded into loops and topologically associating domains (TADs), which serve important structural and regulatory roles. It has been proposed that these genomic structures are formed by a loop extrusion process, which is mediated by structural maintenance of chromosomes (SMC) protein complexes. Recent single-molecule studies have shown that the SMC complexes condensin and cohesin are indeed able to extrude DNA into loops. In this Review, we discuss how the loop extrusion hypothesis can explain key features of genome architecture; cellular functions of loop extrusion, such as separation of replicated DNA molecules, facilitation of enhancer-promoter interactions and immunoglobulin gene recombination; and what is known about the mechanism of loop extrusion and its regulation, for example, by chromatin boundaries that depend on the DNA binding protein CTCF. We also discuss how the loop extrusion hypothesis has led to a paradigm shift in our understanding of both genome architecture and the functions of SMC complexes.
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Affiliation(s)
- Iain F Davidson
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.
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34
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Wu J, Nagy LE, Wang L. The long and the small collide: LncRNAs and small heterodimer partner (SHP) in liver disease. Mol Cell Endocrinol 2021; 528:111262. [PMID: 33781837 PMCID: PMC8087644 DOI: 10.1016/j.mce.2021.111262] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/20/2021] [Accepted: 03/22/2021] [Indexed: 02/08/2023]
Abstract
Long non-coding RNAs (lncRNAs) are a large and diverse class of RNA molecules that are transcribed but not translated into proteins, with a length of more than 200 nucleotides. LncRNAs are involved in gene expression and regulation. The abnormal expression of lncRNAs is associated with disease pathogenesis. Small heterodimer partner (SHP, NR0B2) is a unique orphan nuclear receptor that plays a pivotal role in many biological processes by acting as a transcriptional repressor. In this review, we present the critical roles of SHP and summarize recent findings demonstrating the regulation between lncRNAs and SHP in liver disease.
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Affiliation(s)
- Jianguo Wu
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, USA.
| | - Laura E Nagy
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Department of Gastroenterology and Hepatology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, USA
| | - Li Wang
- Independent Researcher, Tucson, AZ, USA
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Yang Z, Zhang T, Han S, Kusumanchi P, Huda N, Jiang Y, Liangpunsakul S. Long noncoding RNA H19 - a new player in the pathogenesis of liver diseases. Transl Res 2021; 230:139-150. [PMID: 33227504 PMCID: PMC9330166 DOI: 10.1016/j.trsl.2020.11.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 11/05/2020] [Accepted: 11/17/2020] [Indexed: 12/12/2022]
Abstract
The liver is a vital organ that controls glucose and lipid metabolism, hormone regulation, and bile secretion. Liver injury can occur from various insults such as viruses, metabolic diseases, and alcohol, which lead to acute and chronic liver diseases. Recent studies have demonstrated the implications of long noncoding RNAs (lncRNAs) in the pathogenesis of liver diseases. These newly discovered lncRNAs have various functions attributing to many cellular biological processes via distinct and diverse mechanisms. LncRNA H19, one of the first lncRNAs being identified, is highly expressed in fetal liver but not in adult normal liver. Its expression, however, is increased in liver diseases with various etiologies. In this review, we focused on the roles of H19 in the pathogenesis of liver diseases. This comprehensive review is aimed to provide useful perspectives and translational applications of H19 as a potential therapeutic target of liver diseases.
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Affiliation(s)
- Zhihong Yang
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana.
| | - Ting Zhang
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Sen Han
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Praveen Kusumanchi
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Nazmul Huda
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Yanchao Jiang
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Suthat Liangpunsakul
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana; Roudebush Veterans Administration Medical Center, Indianapolis, Indiana; Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
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CTCF-binding element regulates ESC differentiation via orchestrating long-range chromatin interaction between enhancers and HoxA. J Biol Chem 2021; 296:100413. [PMID: 33581110 PMCID: PMC7960549 DOI: 10.1016/j.jbc.2021.100413] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/19/2021] [Accepted: 02/09/2021] [Indexed: 12/20/2022] Open
Abstract
Proper expression of Homeobox A cluster genes (HoxA) is essential for embryonic stem cell (ESC) differentiation and individual development. However, mechanisms controlling precise spatiotemporal expression of HoxA during early ESC differentiation remain poorly understood. Herein, we identified a functional CTCF-binding element (CBE+47) closest to the 3'-end of HoxA within the same topologically associated domain (TAD) in ESC. CRISPR-Cas9-mediated deletion of CBE+47 significantly upregulated HoxA expression and enhanced early ESC differentiation induced by retinoic acid (RA) relative to wild-type cells. Mechanistic analysis by chromosome conformation capture assay (Capture-C) revealed that CBE+47 deletion decreased interactions between adjacent enhancers, enabling formation of a relatively loose enhancer-enhancer interaction complex (EEIC), which overall increased interactions between that EEIC and central regions of HoxA chromatin. These findings indicate that CBE+47 organizes chromatin interactions between its adjacent enhancers and HoxA. Furthermore, deletion of those adjacent enhancers synergistically inhibited HoxA activation, suggesting that these enhancers serve as an EEIC required for RA-induced HoxA activation. Collectively, these results provide new insight into RA-induced HoxA expression during early ESC differentiation, also highlight precise regulatory roles of the CTCF-binding element in orchestrating high-order chromatin structure.
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Heidari R, Akbariqomi M, Asgari Y, Ebrahimi D, Alinejad-Rokny H. A systematic review of long non-coding RNAs with a potential role in breast cancer. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2021; 787:108375. [PMID: 34083033 DOI: 10.1016/j.mrrev.2021.108375] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 04/07/2021] [Accepted: 04/12/2021] [Indexed: 12/13/2022]
Abstract
The human transcriptome contains many non-coding RNAs (ncRNAs), which play important roles in gene regulation. Long noncoding RNAs (lncRNAs) are an important class of ncRNAs with lengths between 200 and 200,000 bases. Unlike mRNA, lncRNA lacks protein-coding features, specifically, open-reading frames, and start and stop codons. LncRNAs have been reported to play a role in the pathogenesis and progression of many cancers, including breast cancer (BC), acting as tumor suppressors or oncogenes. In this review, we systematically mined the literature to identify 65 BC-related lncRNAs. We then perform an integrative bioinformatics analysis to identify 14 lncRNAs with a potential regulatory role in BC. The biological function of these 14 lncRNAs, their regulatory mechanisms, and roles in the initiation and progression of BC are discussed in this review. Additionally, we elaborate on the current and future applications of lncRNAs as diagnostic and/or therapeutic biomarkers in BC.
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Affiliation(s)
- Reza Heidari
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran; Department of Molecular Medicine, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mostafa Akbariqomi
- Department of Molecular Medicine, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Yazdan Asgari
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Diako Ebrahimi
- Biomedical Informatics Lab, Texas Biomedical Research Institute, San Antonio, TX, 78227, United States
| | - Hamid Alinejad-Rokny
- BioMedical Machine Learning Lab (BML), The Graduate School of Biomedical Engineering, UNSW Sydney, Sydney, NSW, 2052, Australia; Core Member of UNSW Data Science Hub, The University of New South Wales (UNSW Sydney), Sydney, NSW, 2052, Australia; Health Data Analytics Program Leader, AI-enabled Processes (AIP) Research Centre, Macquarie University, Sydney, 2109, Australia.
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38
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Ye T, Ma W. ASHIC: hierarchical Bayesian modeling of diploid chromatin contacts and structures. Nucleic Acids Res 2020; 48:e123. [PMID: 33074315 PMCID: PMC7708071 DOI: 10.1093/nar/gkaa872] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 09/15/2020] [Accepted: 09/24/2020] [Indexed: 12/29/2022] Open
Abstract
The recently developed Hi-C technique has been widely applied to map genome-wide chromatin interactions. However, current methods for analyzing diploid Hi-C data cannot fully distinguish between homologous chromosomes. Consequently, the existing diploid Hi-C analyses are based on sparse and inaccurate allele-specific contact matrices, which might lead to incorrect modeling of diploid genome architecture. Here we present ASHIC, a hierarchical Bayesian framework to model allele-specific chromatin organizations in diploid genomes. We developed two models under the Bayesian framework: the Poisson-multinomial (ASHIC-PM) model and the zero-inflated Poisson-multinomial (ASHIC-ZIPM) model. The proposed ASHIC methods impute allele-specific contact maps from diploid Hi-C data and simultaneously infer allelic 3D structures. Through simulation studies, we demonstrated that ASHIC methods outperformed existing approaches, especially under low coverage and low SNP density conditions. Additionally, in the analyses of diploid Hi-C datasets in mouse and human, our ASHIC-ZIPM method produced fine-resolution diploid chromatin maps and 3D structures and provided insights into the allelic chromatin organizations and functions. To summarize, our work provides a statistically rigorous framework for investigating fine-scale allele-specific chromatin conformations. The ASHIC software is publicly available at https://github.com/wmalab/ASHIC.
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Affiliation(s)
- Tiantian Ye
- Genetics, Genomics and Bioinformatics Program
| | - Wenxiu Ma
- Department of Statistics, University of California Riverside, Riverside, CA 92521, USA
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Chandradoss KR, Chawla B, Dhuppar S, Nayak R, Ramachandran R, Kurukuti S, Mazumder A, Sandhu KS. CTCF-Mediated Genome Architecture Regulates the Dosage of Mitotically Stable Mono-allelic Expression of Autosomal Genes. Cell Rep 2020; 33:108302. [PMID: 33113374 DOI: 10.1016/j.celrep.2020.108302] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 07/31/2020] [Accepted: 09/30/2020] [Indexed: 11/30/2022] Open
Abstract
The mechanisms that guide the clonally stable random mono-allelic expression of autosomal genes remain enigmatic. We show that (1) mono-allelically expressed (MAE) genes are assorted and insulated from bi-allelically expressed (BAE) genes through CTCF-mediated chromatin loops; (2) the cell-type-specific dynamics of mono-allelic expression coincides with the gain and loss of chromatin insulator sites; (3) dosage of MAE genes is more sensitive to the loss of chromatin insulation than that of BAE genes; and (4) inactive alleles of MAE genes are significantly more insulated than active alleles and are de-repressed upon CTCF depletion. This alludes to a topology wherein the inactive alleles of MAE genes are insulated from the spatial interference of transcriptional states from the neighboring bi-allelic domains via CTCF-mediated loops. We propose that CTCF functions as a typical insulator on inactive alleles, but facilitates transcription through enhancer-linking on active allele of MAE genes, indicating widespread allele-specific regulatory roles of CTCF.
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Affiliation(s)
- Keerthivasan Raanin Chandradoss
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER)-Mohali, Knowledge City, Sector 81, SAS Nagar 140306, India
| | - Bindia Chawla
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER)-Mohali, Knowledge City, Sector 81, SAS Nagar 140306, India
| | - Shivnarayan Dhuppar
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research (TIFR) Hyderabad, 36/P, Gopanpally Village, Serilingampally Mandal, Hyderabad 500046, India
| | - Rakhee Nayak
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Gachibowli, Hyderabad 500046, India
| | - Rajesh Ramachandran
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER)-Mohali, Knowledge City, Sector 81, SAS Nagar 140306, India
| | - Sreenivasulu Kurukuti
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Gachibowli, Hyderabad 500046, India
| | - Aprotim Mazumder
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research (TIFR) Hyderabad, 36/P, Gopanpally Village, Serilingampally Mandal, Hyderabad 500046, India
| | - Kuljeet Singh Sandhu
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER)-Mohali, Knowledge City, Sector 81, SAS Nagar 140306, India.
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40
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Melnikova LS, Georgiev PG, Golovnin AK. The Functions and Mechanisms of Action of Insulators in the Genomes of Higher Eukaryotes. Acta Naturae 2020; 12:15-33. [PMID: 33456975 PMCID: PMC7800606 DOI: 10.32607/actanaturae.11144] [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: 08/07/2020] [Accepted: 10/12/2020] [Indexed: 12/22/2022] Open
Abstract
The mechanisms underlying long-range interactions between chromatin regions and the principles of chromosomal architecture formation are currently under extensive scrutiny. A special class of regulatory elements known as insulators is believed to be involved in the regulation of specific long-range interactions between enhancers and promoters. This review focuses on the insulators of Drosophila and mammals, and it also briefly characterizes the proteins responsible for their functional activity. It was initially believed that the main properties of insulators are blocking of enhancers and the formation of independent transcription domains. We present experimental data proving that the chromatin loops formed by insulators play only an auxiliary role in enhancer blocking. The review also discusses the mechanisms involved in the formation of topologically associating domains and their role in the formation of the chromosomal architecture and regulation of gene transcription.
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Affiliation(s)
- L. S. Melnikova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
| | - P. G. Georgiev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
| | - A. K. Golovnin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
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Abstract
Genomic imprinting is a parent-of-origin dependent phenomenon that restricts transcription to predominantly one parental allele. Since the discovery of the first long noncoding RNA (lncRNA), which notably was an imprinted lncRNA, a body of knowledge has demonstrated pivotal roles for imprinted lncRNAs in regulating parental-specific expression of neighboring imprinted genes. In this Review, we will discuss the multiple functionalities attributed to lncRNAs and how they regulate imprinted gene expression. We also raise unresolved questions about imprinted lncRNA function, which may lead to new avenues of investigation. This Review is dedicated to the memory of Denise Barlow, a giant in the field of genomic imprinting and functional lncRNAs. With her passion for understanding the inner workings of science, her indominable spirit and her consummate curiosity, Denise blazed a path of scientific investigation that made many seminal contributions to genomic imprinting and the wider field of epigenetic regulation, in addition to inspiring future generations of scientists.
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Affiliation(s)
- William A. MacDonald
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Rangos Research Center, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Mellissa R. W. Mann
- Department of Obstetrics, Gynaecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Magee-Womens Research Institute, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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Wu Q, Liu P, Wang L. Many facades of CTCF unified by its coding for three-dimensional genome architecture. J Genet Genomics 2020; 47:407-424. [PMID: 33187878 DOI: 10.1016/j.jgg.2020.06.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 04/15/2020] [Accepted: 06/01/2020] [Indexed: 02/06/2023]
Abstract
CCCTC-binding factor (CTCF) is a multifunctional zinc finger protein that is conserved in metazoan species. CTCF is consistently found to play an important role in many diverse biological processes. CTCF/cohesin-mediated active chromatin 'loop extrusion' architects three-dimensional (3D) genome folding. The 3D architectural role of CTCF underlies its multifarious functions, including developmental regulation of gene expression, protocadherin (Pcdh) promoter choice in the nervous system, immunoglobulin (Ig) and T-cell receptor (Tcr) V(D)J recombination in the immune system, homeobox (Hox) gene control during limb development, as well as many other aspects of biology. Here, we review the pleiotropic functions of CTCF from the perspective of its essential role in 3D genome architecture and topological promoter/enhancer selection. We envision the 3D genome as an enormous complex architecture, with tens of thousands of CTCF sites as connecting nodes and CTCF proteins as mysterious bonds that glue together genomic building parts with distinct articulation joints. In particular, we focus on the internal mechanisms by which CTCF controls higher order chromatin structures that manifest its many façades of physiological and pathological functions. We also discuss the dichotomic role of CTCF sites as intriguing 3D genome nodes for seemingly contradictory 'looping bridges' and 'topological insulators' to frame a beautiful magnificent house for a cell's nuclear home.
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Affiliation(s)
- Qiang Wu
- MOE Key Lab of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Center for Comparative Biomedicine, Institute of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University (SJTU), Shanghai, 200240, China.
| | - Peifeng Liu
- MOE Key Lab of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Center for Comparative Biomedicine, Institute of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University (SJTU), Shanghai, 200240, China
| | - Leyang Wang
- MOE Key Lab of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Center for Comparative Biomedicine, Institute of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University (SJTU), Shanghai, 200240, China
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43
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The influence of DNA methylation on monoallelic expression. Essays Biochem 2020; 63:663-676. [PMID: 31782494 PMCID: PMC6923323 DOI: 10.1042/ebc20190034] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/10/2019] [Accepted: 11/11/2019] [Indexed: 01/02/2023]
Abstract
Monoallelic gene expression occurs in diploid cells when only one of the two alleles of a gene is active. There are three main classes of genes that display monoallelic expression in mammalian genomes: (1) imprinted genes that are monoallelically expressed in a parent-of-origin dependent manner; (2) X-linked genes that undergo random X-chromosome inactivation in female cells; (3) random monoallelically expressed single and clustered genes located on autosomes. The heritability of monoallelic expression patterns during cell divisions implies that epigenetic mechanisms are involved in the cellular memory of these expression states. Among these, methylation of CpG sites on DNA is one of the best described modification to explain somatic inheritance. Here, we discuss the relevance of DNA methylation for the establishment and maintenance of monoallelic expression patterns among these three groups of genes, and how this is intrinsically linked to development and cellular states.
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44
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Diehl AG, Ouyang N, Boyle AP. Transposable elements contribute to cell and species-specific chromatin looping and gene regulation in mammalian genomes. Nat Commun 2020; 11:1796. [PMID: 32286261 PMCID: PMC7156512 DOI: 10.1038/s41467-020-15520-5] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 03/14/2020] [Indexed: 01/12/2023] Open
Abstract
Chromatin looping is important for gene regulation, and studies of 3D chromatin structure across species and cell types have improved our understanding of the principles governing chromatin looping. However, 3D genome evolution and its relationship with natural selection remains largely unexplored. In mammals, the CTCF protein defines the boundaries of most chromatin loops, and variations in CTCF occupancy are associated with looping divergence. While many CTCF binding sites fall within transposable elements (TEs), their contribution to 3D chromatin structural evolution is unknown. Here we report the relative contributions of TE-driven CTCF binding site expansions to conserved and divergent chromatin looping in human and mouse. We demonstrate that TE-derived CTCF binding divergence may explain a large fraction of variable loops. These variable loops contribute significantly to corresponding gene expression variability across cells and species, possibly by refining sub-TAD-scale loop contacts responsible for cell-type-specific enhancer-promoter interactions.
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Affiliation(s)
- Adam G Diehl
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Ningxin Ouyang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Alan P Boyle
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
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Maternal Folic Acid Supplementation Mediates Offspring Health via DNA Methylation. Reprod Sci 2020; 27:963-976. [PMID: 32124397 DOI: 10.1007/s43032-020-00161-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 09/09/2019] [Indexed: 10/24/2022]
Abstract
The clinical significance of periconceptional folic acid supplementation (FAS) in the prevention of neonatal neural tube defects (NTDs) has been recognized for decades. Epidemiological data and experimental findings have consistently been indicating an association between folate deficiency in the first trimester of pregnancy and poor fetal development as well as offspring health (i.e., NTDs, isolated orofacial clefts, neurodevelopmental disorders). Moreover, compelling evidence has suggested adverse effects of folate overload during perinatal period on offspring health (i.e., immune diseases, autism, lipid disorders). In addition to several single-nucleotide polymorphisms (SNPs) in genes related to folate one-carbon metabolism (FOCM), folate concentrations in maternal serum/plasma/red blood cells must be considered when counseling FAS. Epigenetic information encoded by 5-methylcytosines (5mC) plays a critical role in fetal development and offspring health. S-adenosylmethionine (SAM), a methyl donor for 5mC, could be derived from FOCM. As such, folic acid plays a double-edged sword role in offspring health via mediating DNA methylation. However, the underlying epigenetic mechanism is still largely unclear. In this review, we summarized the link across DNA methylation, maternal FAS, and offspring health to provide more evidence for clinical guidance in terms of precise FAS dosage and time point. Future studies are, therefore, required to set up the reference intervals of folate concentrations at different trimesters of pregnancy for different populations and to clarify the epigenetic mechanism for specific offspring diseases.
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Choudhary MN, Friedman RZ, Wang JT, Jang HS, Zhuo X, Wang T. Co-opted transposons help perpetuate conserved higher-order chromosomal structures. Genome Biol 2020; 21:16. [PMID: 31973766 PMCID: PMC6979391 DOI: 10.1186/s13059-019-1916-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 12/08/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Transposable elements (TEs) make up half of mammalian genomes and shape genome regulation by harboring binding sites for regulatory factors. These include binding sites for architectural proteins, such as CTCF, RAD21, and SMC3, that are involved in tethering chromatin loops and marking domain boundaries. The 3D organization of the mammalian genome is intimately linked to its function and is remarkably conserved. However, the mechanisms by which these structural intricacies emerge and evolve have not been thoroughly probed. RESULTS Here, we show that TEs contribute extensively to both the formation of species-specific loops in humans and mice through deposition of novel anchoring motifs, as well as to the maintenance of conserved loops across both species through CTCF binding site turnover. The latter function demonstrates the ability of TEs to contribute to genome plasticity and reinforce conserved genome architecture as redundant loop anchors. Deleting such candidate TEs in human cells leads to the collapse of conserved loop and domain structures. These TEs are also marked by reduced DNA methylation and bear mutational signatures of hypomethylation through evolutionary time. CONCLUSIONS TEs have long been considered a source of genetic innovation. By examining their contribution to genome topology, we show that TEs can contribute to regulatory plasticity by inducing redundancy and potentiating genetic drift locally while conserving genome architecture globally, revealing a paradigm for defining regulatory conservation in the noncoding genome beyond classic sequence-level conservation.
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Affiliation(s)
- Mayank Nk Choudhary
- The Edison Family Center for Genome Sciences & Systems Biology, Department of Genetics, Washington University, 4515 McKinley Avenue, Campus Box 8510, St. Louis, MO, 63110, USA
| | - Ryan Z Friedman
- The Edison Family Center for Genome Sciences & Systems Biology, Department of Genetics, Washington University, 4515 McKinley Avenue, Campus Box 8510, St. Louis, MO, 63110, USA
| | - Julia T Wang
- The Edison Family Center for Genome Sciences & Systems Biology, Department of Genetics, Washington University, 4515 McKinley Avenue, Campus Box 8510, St. Louis, MO, 63110, USA
| | - Hyo Sik Jang
- The Edison Family Center for Genome Sciences & Systems Biology, Department of Genetics, Washington University, 4515 McKinley Avenue, Campus Box 8510, St. Louis, MO, 63110, USA
| | - Xiaoyu Zhuo
- The Edison Family Center for Genome Sciences & Systems Biology, Department of Genetics, Washington University, 4515 McKinley Avenue, Campus Box 8510, St. Louis, MO, 63110, USA
| | - Ting Wang
- The Edison Family Center for Genome Sciences & Systems Biology, Department of Genetics, Washington University, 4515 McKinley Avenue, Campus Box 8510, St. Louis, MO, 63110, USA.
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47
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Finn EH, Misteli T. Molecular basis and biological function of variability in spatial genome organization. Science 2019; 365:365/6457/eaaw9498. [PMID: 31488662 DOI: 10.1126/science.aaw9498] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 07/22/2019] [Indexed: 12/14/2022]
Abstract
The complex three-dimensional organization of genomes in the cell nucleus arises from a wide range of architectural features including DNA loops, chromatin domains, and higher-order compartments. Although these features are universally present in most cell types and tissues, recent single-cell biochemistry and imaging approaches have demonstrated stochasticity in transcription and high variability of chromatin architecture in individual cells. We review the occurrence, mechanistic basis, and functional implications of stochasticity in genome organization. We summarize recent observations on cell- and allele-specific variability of genome architecture, discuss the nature of extrinsic and intrinsic sources of variability in genome organization, and highlight potential implications of structural heterogeneity for genome function.
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Affiliation(s)
| | - Tom Misteli
- National Cancer Institute, Bethesda, MD 20892, USA.
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48
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Llères D, Moindrot B, Pathak R, Piras V, Matelot M, Pignard B, Marchand A, Poncelet M, Perrin A, Tellier V, Feil R, Noordermeer D. CTCF modulates allele-specific sub-TAD organization and imprinted gene activity at the mouse Dlk1-Dio3 and Igf2-H19 domains. Genome Biol 2019; 20:272. [PMID: 31831055 PMCID: PMC6909504 DOI: 10.1186/s13059-019-1896-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 11/22/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Genomic imprinting is essential for mammalian development and provides a unique paradigm to explore intra-cellular differences in chromatin configuration. So far, the detailed allele-specific chromatin organization of imprinted gene domains has mostly been lacking. Here, we explored the chromatin structure of the two conserved imprinted domains controlled by paternal DNA methylation imprints-the Igf2-H19 and Dlk1-Dio3 domains-and assessed the involvement of the insulator protein CTCF in mouse cells. RESULTS Both imprinted domains are located within overarching topologically associating domains (TADs) that are similar on both parental chromosomes. At each domain, a single differentially methylated region is bound by CTCF on the maternal chromosome only, in addition to multiple instances of bi-allelic CTCF binding. Combinations of allelic 4C-seq and DNA-FISH revealed that bi-allelic CTCF binding alone, on the paternal chromosome, correlates with a first level of sub-TAD structure. On the maternal chromosome, additional CTCF binding at the differentially methylated region adds a further layer of sub-TAD organization, which essentially hijacks the existing paternal-specific sub-TAD organization. Perturbation of maternal-specific CTCF binding site at the Dlk1-Dio3 locus, using genome editing, results in perturbed sub-TAD organization and bi-allelic Dlk1 activation during differentiation. CONCLUSIONS Maternal allele-specific CTCF binding at the imprinted Igf2-H19 and the Dlk1-Dio3 domains adds an additional layer of sub-TAD organization, on top of an existing three-dimensional configuration and prior to imprinted activation of protein-coding genes. We speculate that this allele-specific sub-TAD organization provides an instructive or permissive context for imprinted gene activation during development.
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Affiliation(s)
- David Llères
- Institute of Molecular Genetics of Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France
| | - Benoît Moindrot
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-sud and University Paris-Saclay, Gif-sur-Yvette, France
| | - Rakesh Pathak
- Institute of Molecular Genetics of Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France
| | - Vincent Piras
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-sud and University Paris-Saclay, Gif-sur-Yvette, France
| | - Mélody Matelot
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-sud and University Paris-Saclay, Gif-sur-Yvette, France
| | - Benoît Pignard
- Institute of Molecular Genetics of Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France
| | - Alice Marchand
- Institute of Molecular Genetics of Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France
| | - Mallory Poncelet
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-sud and University Paris-Saclay, Gif-sur-Yvette, France
| | - Aurélien Perrin
- Institute of Molecular Genetics of Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France
| | - Virgile Tellier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-sud and University Paris-Saclay, Gif-sur-Yvette, France
| | - Robert Feil
- Institute of Molecular Genetics of Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France.
| | - Daan Noordermeer
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-sud and University Paris-Saclay, Gif-sur-Yvette, France.
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49
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Greenstein RA, Barrales RR, Sanchez NA, Bisanz JE, Braun S, Al-Sady B. Set1/COMPASS repels heterochromatin invasion at euchromatic sites by disrupting Suv39/Clr4 activity and nucleosome stability. Genes Dev 2019; 34:99-117. [PMID: 31805521 PMCID: PMC6938669 DOI: 10.1101/gad.328468.119] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 10/30/2019] [Indexed: 12/27/2022]
Abstract
In this study, Greenstein et al. set out to define the spatial encoding signals within euchromatin that act to limit heterochromatin spreading. Using molecular and cell-based assays in fission yeast, the authors report that heterochromatin repulsion is locally encoded by Set1/COMPASS on certain actively transcribed genes and that this protective role is most prominent at heterochromatin islands, small domains interspersed in euchromatin that regulate cell fate specifiers. Protection of euchromatin from invasion by gene-repressive heterochromatin is critical for cellular health and viability. In addition to constitutive loci such as pericentromeres and subtelomeres, heterochromatin can be found interspersed in gene-rich euchromatin, where it regulates gene expression pertinent to cell fate. While heterochromatin and euchromatin are globally poised for mutual antagonism, the mechanisms underlying precise spatial encoding of heterochromatin containment within euchromatic sites remain opaque. We investigated ectopic heterochromatin invasion by manipulating the fission yeast mating type locus boundary using a single-cell spreading reporter system. We found that heterochromatin repulsion is locally encoded by Set1/COMPASS on certain actively transcribed genes and that this protective role is most prominent at heterochromatin islands, small domains interspersed in euchromatin that regulate cell fate specifiers. Sensitivity to invasion by heterochromatin, surprisingly, is not dependent on Set1 altering overall gene expression levels. Rather, the gene-protective effect is strictly dependent on Set1's catalytic activity. H3K4 methylation, the Set1 product, antagonizes spreading in two ways: directly inhibiting catalysis by Suv39/Clr4 and locally disrupting nucleosome stability. Taken together, these results describe a mechanism for spatial encoding of euchromatic signals that repel heterochromatin invasion.
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Affiliation(s)
- R A Greenstein
- Department of Microbiology and Immunology, George Williams Hooper Foundation, University of California at San Francisco, San Francisco, California 94143, USA.,TETRAD Graduate Program, University of California at San Francisco, San Francisco, California 94143, USA
| | - Ramon R Barrales
- Department of Physiological Chemistry, Biomedical Center (BMC), Ludwig Maximilians University of Munich, 82152 Martinsried, Germany.,International Max Planck Research School for Molecular and Cellular Life Sciences, 82152 Martinsried, Germany
| | - Nicholas A Sanchez
- Department of Microbiology and Immunology, George Williams Hooper Foundation, University of California at San Francisco, San Francisco, California 94143, USA.,TETRAD Graduate Program, University of California at San Francisco, San Francisco, California 94143, USA
| | - Jordan E Bisanz
- Department of Microbiology and Immunology, George Williams Hooper Foundation, University of California at San Francisco, San Francisco, California 94143, USA
| | - Sigurd Braun
- Department of Physiological Chemistry, Biomedical Center (BMC), Ludwig Maximilians University of Munich, 82152 Martinsried, Germany.,International Max Planck Research School for Molecular and Cellular Life Sciences, 82152 Martinsried, Germany
| | - Bassem Al-Sady
- Department of Microbiology and Immunology, George Williams Hooper Foundation, University of California at San Francisco, San Francisco, California 94143, USA
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50
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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]
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