1
|
Newman T, Ishihara T, Shaw G, Renfree MB. The structure of the TH/INS locus and the parental allele expressed are not conserved between mammals. Heredity (Edinb) 2024; 133:21-32. [PMID: 38834866 PMCID: PMC11222543 DOI: 10.1038/s41437-024-00689-y] [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: 06/15/2023] [Revised: 05/01/2024] [Accepted: 05/07/2024] [Indexed: 06/06/2024] Open
Abstract
Parent-of-origin-specific expression of imprinted genes is critical for successful mammalian growth and development. Insulin, coded by the INS gene, is an important growth factor expressed from the paternal allele in the yolk sac placenta of therian mammals. The tyrosine hydroxylase gene TH encodes an enzyme involved in dopamine synthesis. TH and INS are closely associated in most vertebrates, but the mouse orthologues, Th and Ins2, are separated by repeated DNA. In mice, Th is expressed from the maternal allele, but the parental origin of expression is not known for any other mammal so it is unclear whether the maternal expression observed in the mouse represents an evolutionary divergence or an ancestral condition. We compared the length of the DNA segment between TH and INS across species and show that separation of these genes occurred in the rodent lineage with an accumulation of repeated DNA. We found that the region containing TH and INS in the tammar wallaby produces at least five distinct RNA transcripts: TH, TH-INS1, TH-INS2, lncINS and INS. Using allele-specific expression analysis, we show that the TH/INS locus is expressed from the paternal allele in pre- and postnatal tammar wallaby tissues. Determining the imprinting pattern of TH/INS in other mammals might clarify if paternal expression is the ancestral condition which has been flipped to maternal expression in rodents by the accumulation of repeat sequences.
Collapse
Affiliation(s)
- Trent Newman
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Teruhito Ishihara
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Geoff Shaw
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Marilyn B Renfree
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia.
| |
Collapse
|
2
|
Moindrot B, Imaizumi Y, Feil R. Differential 3D genome architecture and imprinted gene expression: cause or consequence? Biochem Soc Trans 2024; 52:973-986. [PMID: 38775198 DOI: 10.1042/bst20230143] [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: 02/12/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 06/27/2024]
Abstract
Imprinted genes provide an attractive paradigm to unravel links between transcription and genome architecture. The parental allele-specific expression of these essential genes - which are clustered in chromosomal domains - is mediated by parental methylation imprints at key regulatory DNA sequences. Recent chromatin conformation capture (3C)-based studies show differential organization of topologically associating domains between the parental chromosomes at imprinted domains, in embryonic stem and differentiated cells. At several imprinted domains, differentially methylated regions show allelic binding of the insulator protein CTCF, and linked focal retention of cohesin, at the non-methylated allele only. This generates differential patterns of chromatin looping between the parental chromosomes, already in the early embryo, and thereby facilitates the allelic gene expression. Recent research evokes also the opposite scenario, in which allelic transcription contributes to the differential genome organization, similarly as reported for imprinted X chromosome inactivation. This may occur through epigenetic effects on CTCF binding, through structural effects of RNA Polymerase II, or through imprinted long non-coding RNAs that have chromatin repressive functions. The emerging picture is that epigenetically-controlled differential genome architecture precedes and facilitates imprinted gene expression during development, and that at some domains, conversely, the mono-allelic gene expression also influences genome architecture.
Collapse
Affiliation(s)
- Benoit Moindrot
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Yui Imaizumi
- Institute of Molecular Genetics of Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France
| | - Robert Feil
- Institute of Molecular Genetics of Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France
| |
Collapse
|
3
|
Farhadova S, Ghousein A, Charon F, Surcis C, Gomez-Velazques M, Roidor C, Di Michele F, Borensztein M, De Sario A, Esnault C, Noordermeer D, Moindrot B, Feil R. The long non-coding RNA Meg3 mediates imprinted gene expression during stem cell differentiation. Nucleic Acids Res 2024; 52:6183-6200. [PMID: 38613389 PMCID: PMC11194098 DOI: 10.1093/nar/gkae247] [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: 02/14/2023] [Revised: 03/02/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
The imprinted Dlk1-Dio3 domain comprises the developmental genes Dlk1 and Rtl1, which are silenced on the maternal chromosome in different cell types. On this parental chromosome, the domain's imprinting control region activates a polycistron that produces the lncRNA Meg3 and many miRNAs (Mirg) and C/D-box snoRNAs (Rian). Although Meg3 lncRNA is nuclear and associates with the maternal chromosome, it is unknown whether it controls gene repression in cis. We created mouse embryonic stem cells (mESCs) that carry an ectopic poly(A) signal, reducing RNA levels along the polycistron, and generated Rian-/- mESCs as well. Upon ESC differentiation, we found that Meg3 lncRNA (but not Rian) is required for Dlk1 repression on the maternal chromosome. Biallelic Meg3 expression acquired through CRISPR-mediated demethylation of the paternal Meg3 promoter led to biallelic Dlk1 repression, and to loss of Rtl1 expression. lncRNA expression also correlated with DNA hypomethylation and CTCF binding at the 5'-side of Meg3. Using Capture Hi-C, we found that this creates a Topologically Associating Domain (TAD) organization that brings Meg3 close to Dlk1 on the maternal chromosome. The requirement of Meg3 for gene repression and TAD structure may explain how aberrant MEG3 expression at the human DLK1-DIO3 locus associates with imprinting disorders.
Collapse
Affiliation(s)
- Sabina Farhadova
- Institute of Molecular Genetics of Montpellier (IGMM), Centre National de Recherche Scientifique (CNRS), 34090 Montpellier, France
- University of Montpellier, 34090 Montpellier, France
- Genetic Resources Research Institute, Azerbaijan National Academy of Sciences (ANAS), AZ1106 Baku, Azerbaijan
| | - Amani Ghousein
- Institute of Molecular Genetics of Montpellier (IGMM), Centre National de Recherche Scientifique (CNRS), 34090 Montpellier, France
- University of Montpellier, 34090 Montpellier, France
| | - François Charon
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91190 Gif-sur-Yvette, France
| | - Caroline Surcis
- Institute of Molecular Genetics of Montpellier (IGMM), Centre National de Recherche Scientifique (CNRS), 34090 Montpellier, France
| | - Melisa Gomez-Velazques
- Institute of Molecular Genetics of Montpellier (IGMM), Centre National de Recherche Scientifique (CNRS), 34090 Montpellier, France
- University of Montpellier, 34090 Montpellier, France
| | - Clara Roidor
- Institute of Molecular Genetics of Montpellier (IGMM), Centre National de Recherche Scientifique (CNRS), 34090 Montpellier, France
- University of Montpellier, 34090 Montpellier, France
| | - Flavio Di Michele
- Institute of Molecular Genetics of Montpellier (IGMM), Centre National de Recherche Scientifique (CNRS), 34090 Montpellier, France
- University of Montpellier, 34090 Montpellier, France
| | - Maud Borensztein
- Institute of Molecular Genetics of Montpellier (IGMM), Centre National de Recherche Scientifique (CNRS), 34090 Montpellier, France
- University of Montpellier, 34090 Montpellier, France
| | - Albertina De Sario
- University of Montpellier, 34090 Montpellier, France
- PhyMedExp, Institut National de la Santé et de la Recherche Médicale (INSERM), CNRS, 34295 Montpellier, France
| | - Cyril Esnault
- Institute of Molecular Genetics of Montpellier (IGMM), Centre National de Recherche Scientifique (CNRS), 34090 Montpellier, France
- University of Montpellier, 34090 Montpellier, France
| | - Daan Noordermeer
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91190 Gif-sur-Yvette, France
| | - Benoit Moindrot
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91190 Gif-sur-Yvette, France
| | - Robert Feil
- Institute of Molecular Genetics of Montpellier (IGMM), Centre National de Recherche Scientifique (CNRS), 34090 Montpellier, France
- University of Montpellier, 34090 Montpellier, France
| |
Collapse
|
4
|
Matsuzaki H, Kimura M, Morihashi M, Tanimoto K. Imprinted DNA methylation of the H19 ICR is established and maintained in vivo in the absence of Kaiso. Epigenetics Chromatin 2024; 17:20. [PMID: 38840164 PMCID: PMC11151560 DOI: 10.1186/s13072-024-00544-8] [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: 02/03/2024] [Accepted: 05/23/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND Paternal allele-specific DNA methylation of the imprinting control region (H19 ICR) controls genomic imprinting at the Igf2/H19 locus. We previously demonstrated that the mouse H19 ICR transgene acquires imprinted DNA methylation in preimplantation mouse embryos. This activity is also present in the endogenous H19 ICR and protects it from genome-wide reprogramming after fertilization. We also identified a 118-bp sequence within the H19 ICR that is responsible for post-fertilization imprinted methylation. Two mutations, one in the five RCTG motifs and the other a 36-bp deletion both in the 118-bp segment, caused complete and partial loss, respectively, of methylation following paternal transmission in each transgenic mouse. Interestingly, these mutations overlap with the binding site for the transcription factor Kaiso, which is reportedly involved in maintaining paternal methylation at the human H19 ICR (IC1) in cultured cells. In this study, we investigated if Kaiso regulates imprinted DNA methylation of the H19 ICR in vivo. RESULTS Neither Kaiso deletion nor mutation of Kaiso binding sites in the 118-bp region affected DNA methylation of the mouse H19 ICR transgene. The endogenous mouse H19 ICR was methylated in a wild-type manner in Kaiso-null mutant mice. Additionally, the human IC1 transgene acquired imprinted DNA methylation after fertilization in the absence of Kaiso. CONCLUSIONS Our results indicate that Kaiso is not essential for either post-fertilization imprinted DNA methylation of the transgenic H19 ICR in mouse or for methylation imprinting of the endogenous mouse H19 ICR.
Collapse
Affiliation(s)
- Hitomi Matsuzaki
- Institute of Life and Environmental Sciences, Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tennoudai 1-1-1, Tsukuba, Ibaraki, 305-8577, Japan.
| | - Minami Kimura
- Graduate School of Science and Technology, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Mizuki Morihashi
- Graduate School of Science and Technology, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Keiji Tanimoto
- Institute of Life and Environmental Sciences, Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tennoudai 1-1-1, Tsukuba, Ibaraki, 305-8577, Japan
| |
Collapse
|
5
|
Xu J, Xu X, Huang D, Luo Y, Lin L, Bai X, Zheng Y, Yang Q, Cheng Y, Huang A, Shi J, Bo X, Gu J, Chen H. A comprehensive benchmarking with interpretation and operational guidance for the hierarchy of topologically associating domains. Nat Commun 2024; 15:4376. [PMID: 38782890 PMCID: PMC11116433 DOI: 10.1038/s41467-024-48593-7] [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: 09/18/2023] [Accepted: 05/03/2024] [Indexed: 05/25/2024] Open
Abstract
Topologically associating domains (TADs), megabase-scale features of chromatin spatial architecture, are organized in a domain-within-domain TAD hierarchy. Within TADs, the inner and smaller subTADs not only manifest cell-to-cell variability, but also precisely regulate transcription and differentiation. Although over 20 TAD callers are able to detect TAD, their usability in biomedicine is confined by a disagreement of outputs and a limit in understanding TAD hierarchy. We compare 13 computational tools across various conditions and develop a metric to evaluate the similarity of TAD hierarchy. Although outputs of TAD hierarchy at each level vary among callers, data resolutions, sequencing depths, and matrices normalization, they are more consistent when they have a higher similarity of larger TADs. We present comprehensive benchmarking of TAD hierarchy callers and operational guidance to researchers of life science researchers. Moreover, by simulating the mixing of different types of cells, we confirm that TAD hierarchy is generated not simply from stacking Hi-C heatmaps of heterogeneous cells. Finally, we propose an air conditioner model to decipher the role of TAD hierarchy in transcription.
Collapse
Affiliation(s)
- Jingxuan Xu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Xiang Xu
- Academy of Military Medical Science, Beijing, 100850, China
| | - Dandan Huang
- Department of Oncology, Peking University Shougang Hospital, Beijing, China
- Center for Precision Diagnosis and Treatment of Colorectal Cancer and Inflammatory Diseases, Peking University Health Science Center, Beijing, China
| | - Yawen Luo
- Academy of Military Medical Science, Beijing, 100850, China
| | - Lin Lin
- Academy of Military Medical Science, Beijing, 100850, China
- School of Computer Science and Information Technology& KLAS, Northeast Normal University, Changchun, China
| | - Xuemei Bai
- Academy of Military Medical Science, Beijing, 100850, China
| | - Yang Zheng
- Academy of Military Medical Science, Beijing, 100850, China
| | - Qian Yang
- Academy of Military Medical Science, Beijing, 100850, China
| | - Yu Cheng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - An Huang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Jingyi Shi
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Xiaochen Bo
- Academy of Military Medical Science, Beijing, 100850, China.
| | - Jin Gu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery, Peking University Cancer Hospital & Institute, Beijing, 100142, China.
- Department of Oncology, Peking University Shougang Hospital, Beijing, China.
- Center for Precision Diagnosis and Treatment of Colorectal Cancer and Inflammatory Diseases, Peking University Health Science Center, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
- Peking University International Cancer Institute, Beijing, China.
| | - Hebing Chen
- Academy of Military Medical Science, Beijing, 100850, China.
| |
Collapse
|
6
|
Ordoñez R, Zhang W, Ellis G, Zhu Y, Ashe HJ, Ribeiro-Dos-Santos AM, Brosh R, Huang E, Hogan MS, Boeke JD, Maurano MT. Genomic context sensitizes regulatory elements to genetic disruption. Mol Cell 2024; 84:1842-1854.e7. [PMID: 38759624 PMCID: PMC11104518 DOI: 10.1016/j.molcel.2024.04.013] [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: 10/10/2023] [Revised: 03/11/2024] [Accepted: 04/18/2024] [Indexed: 05/19/2024]
Abstract
Genomic context critically modulates regulatory function but is difficult to manipulate systematically. The murine insulin-like growth factor 2 (Igf2)/H19 locus is a paradigmatic model of enhancer selectivity, whereby CTCF occupancy at an imprinting control region directs downstream enhancers to activate either H19 or Igf2. We used synthetic regulatory genomics to repeatedly replace the native locus with 157-kb payloads, and we systematically dissected its architecture. Enhancer deletion and ectopic delivery revealed previously uncharacterized long-range regulatory dependencies at the native locus. Exchanging the H19 enhancer cluster with the Sox2 locus control region (LCR) showed that the H19 enhancers relied on their native surroundings while the Sox2 LCR functioned autonomously. Analysis of regulatory DNA actuation across cell types revealed that these enhancer clusters typify broader classes of context sensitivity genome wide. These results show that unexpected dependencies influence even well-studied loci, and our approach permits large-scale manipulation of complete loci to investigate the relationship between regulatory architecture and function.
Collapse
Affiliation(s)
- Raquel Ordoñez
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Weimin Zhang
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Gwen Ellis
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Yinan Zhu
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Hannah J Ashe
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | | | - Ran Brosh
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Emily Huang
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Megan S Hogan
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Jef D Boeke
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Biochemistry Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA; Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
| | - Matthew T Maurano
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Pathology, NYU School of Medicine, New York, NY 10016, USA.
| |
Collapse
|
7
|
Irastorza-Azcarate I, Kukalev A, Kempfer R, Thieme CJ, Mastrobuoni G, Markowski J, Loof G, Sparks TM, Brookes E, Natarajan KN, Sauer S, Fisher AG, Nicodemi M, Ren B, Schwarz RF, Kempa S, Pombo A. Extensive folding variability between homologous chromosomes in mammalian cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.08.591087. [PMID: 38766012 PMCID: PMC11100664 DOI: 10.1101/2024.05.08.591087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Genetic variation and 3D chromatin structure have major roles in gene regulation. Due to challenges in mapping chromatin conformation with haplotype-specific resolution, the effects of genetic sequence variation on 3D genome structure and gene expression imbalance remain understudied. Here, we applied Genome Architecture Mapping (GAM) to a hybrid mouse embryonic stem cell (mESC) line with high density of single nucleotide polymorphisms (SNPs). GAM resolved haplotype-specific 3D genome structures with high sensitivity, revealing extensive allelic differences in chromatin compartments, topologically associating domains (TADs), long-range enhancer-promoter contacts, and CTCF loops. Architectural differences often coincide with allele-specific differences in gene expression, mediated by Polycomb repression. We show that histone genes are expressed with allelic imbalance in mESCs, are involved in haplotype-specific chromatin contact marked by H3K27me3, and are targets of Polycomb repression through conditional knockouts of Ezh2 or Ring1b. Our work reveals highly distinct 3D folding structures between homologous chromosomes, and highlights their intricate connections with allelic gene expression.
Collapse
|
8
|
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.
Collapse
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.
| |
Collapse
|
9
|
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.
Collapse
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.
| |
Collapse
|
10
|
Sanceau J, Poupel L, Joubel C, Lagoutte I, Caruso S, Pinto S, Desbois-Mouthon C, Godard C, Hamimi A, Montmory E, Dulary C, Chantalat S, Roehrig A, Muret K, Saint-Pierre B, Deleuze JF, Mouillet-Richard S, Forné T, Grosset CF, Zucman-Rossi J, Colnot S, Gougelet A. DLK1/DIO3 locus upregulation by a β-catenin-dependent enhancer drives cell proliferation and liver tumorigenesis. Mol Ther 2024; 32:1125-1143. [PMID: 38311851 PMCID: PMC11163201 DOI: 10.1016/j.ymthe.2024.01.036] [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: 12/01/2023] [Revised: 01/05/2024] [Accepted: 01/31/2024] [Indexed: 02/06/2024] Open
Abstract
The CTNNB1 gene, encoding β-catenin, is frequently mutated in hepatocellular carcinoma (HCC, ∼30%) and in hepatoblastoma (HB, >80%), in which DLK1/DIO3 locus induction is correlated with CTNNB1 mutations. Here, we aim to decipher how sustained β-catenin activation regulates DLK1/DIO3 locus expression and the role this locus plays in HB and HCC development in mouse models deleted for Apc (ApcΔhep) or Ctnnb1-exon 3 (β-cateninΔExon3) and in human CTNNB1-mutated hepatic cancer cells. We identified an enhancer site bound by TCF-4/β-catenin complexes in an open conformation upon sustained β-catenin activation (DLK1-Wnt responsive element [WRE]) and increasing DLK1/DIO3 locus transcription in β-catenin-mutated human HB and mouse models. DLK1-WRE editing by CRISPR-Cas9 approach impaired DLK1/DIO3 locus expression and slowed tumor growth in subcutaneous CTNNB1-mutated tumor cell grafts, ApcΔhep HB and β-cateninΔExon3 HCC. Tumor growth inhibition resulted either from increased FADD expression and subsequent caspase-3 cleavage in the first case or from decreased expression of cell cycle actors regulated by FoxM1 in the others. Therefore, the DLK1/DIO3 locus is an essential determinant of FoxM1-dependent cell proliferation during β-catenin-driven liver tumorigenesis. Targeting the DLK1-WRE enhancer to silence the DLK1/DIO3 locus might thus represent an interesting therapeutic strategy to restrict tumor growth in primary liver cancers with CTNNB1 mutations.
Collapse
Affiliation(s)
- Julie Sanceau
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université Paris Cité, F-75006 Paris, France; Team « Oncogenic functions of beta-catenin signaling in the liver », Équipe labellisée par la Ligue Nationale contre le Cancer, F-75013 Paris, France; APHP, Institut du Cancer Paris CARPEM, F-75015 Paris, France
| | - Lucie Poupel
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université Paris Cité, F-75006 Paris, France; Team « Oncogenic functions of beta-catenin signaling in the liver », Équipe labellisée par la Ligue Nationale contre le Cancer, F-75013 Paris, France; APHP, Institut du Cancer Paris CARPEM, F-75015 Paris, France; Inovarion, F-75005 Paris, France
| | - Camille Joubel
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université Paris Cité, F-75006 Paris, France; Team « Oncogenic functions of beta-catenin signaling in the liver », Équipe labellisée par la Ligue Nationale contre le Cancer, F-75013 Paris, France; APHP, Institut du Cancer Paris CARPEM, F-75015 Paris, France
| | - Isabelle Lagoutte
- University Paris Cité, Institut Cochin, INSERM, CNRS, F-75014 Paris, France
| | - Stefano Caruso
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université Paris Cité, F-75006 Paris, France; APHP, Institut du Cancer Paris CARPEM, F-75015 Paris, France
| | - Sandra Pinto
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université Paris Cité, F-75006 Paris, France; Team « Oncogenic functions of beta-catenin signaling in the liver », Équipe labellisée par la Ligue Nationale contre le Cancer, F-75013 Paris, France
| | - Christèle Desbois-Mouthon
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université Paris Cité, F-75006 Paris, France; Team « Oncogenic functions of beta-catenin signaling in the liver », Équipe labellisée par la Ligue Nationale contre le Cancer, F-75013 Paris, France; APHP, Institut du Cancer Paris CARPEM, F-75015 Paris, France
| | - Cécile Godard
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université Paris Cité, F-75006 Paris, France; Team « Oncogenic functions of beta-catenin signaling in the liver », Équipe labellisée par la Ligue Nationale contre le Cancer, F-75013 Paris, France; APHP, Institut du Cancer Paris CARPEM, F-75015 Paris, France
| | - Akila Hamimi
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université Paris Cité, F-75006 Paris, France; Team « Oncogenic functions of beta-catenin signaling in the liver », Équipe labellisée par la Ligue Nationale contre le Cancer, F-75013 Paris, France; APHP, Institut du Cancer Paris CARPEM, F-75015 Paris, France
| | - Enzo Montmory
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université Paris Cité, F-75006 Paris, France; Team « Oncogenic functions of beta-catenin signaling in the liver », Équipe labellisée par la Ligue Nationale contre le Cancer, F-75013 Paris, France; APHP, Institut du Cancer Paris CARPEM, F-75015 Paris, France
| | - Cécile Dulary
- Centre National de Génotypage, Institut de Génomique, CEA, F-91057 Evry, France
| | - Sophie Chantalat
- Centre National de Génotypage, Institut de Génomique, CEA, F-91057 Evry, France
| | - Amélie Roehrig
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université Paris Cité, F-75006 Paris, France; APHP, Institut du Cancer Paris CARPEM, F-75015 Paris, France
| | - Kevin Muret
- Centre National de Génotypage, Institut de Génomique, CEA, F-91057 Evry, France
| | | | | | - Sophie Mouillet-Richard
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université Paris Cité, F-75006 Paris, France; APHP, Institut du Cancer Paris CARPEM, F-75015 Paris, France
| | - Thierry Forné
- IGMM, University Montpellier, CNRS, F-34293 Montpellier, France
| | - Christophe F Grosset
- University Bordeaux, INSERM, Biotherapy of Genetic Diseases, Inflammatory Disorders and Cancer, BMGIC, U1035, MIRCADE team, F-33076 Bordeaux, France; University Bordeaux, INSERM, Bordeaux Institute in Oncology, BRIC, U1312, MIRCADE team, F-33076 Bordeaux, France
| | - Jessica Zucman-Rossi
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université Paris Cité, F-75006 Paris, France; APHP, Institut du Cancer Paris CARPEM, F-75015 Paris, France
| | - Sabine Colnot
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université Paris Cité, F-75006 Paris, France; Team « Oncogenic functions of beta-catenin signaling in the liver », Équipe labellisée par la Ligue Nationale contre le Cancer, F-75013 Paris, France; APHP, Institut du Cancer Paris CARPEM, F-75015 Paris, France
| | - Angélique Gougelet
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université Paris Cité, F-75006 Paris, France; Team « Oncogenic functions of beta-catenin signaling in the liver », Équipe labellisée par la Ligue Nationale contre le Cancer, F-75013 Paris, France; APHP, Institut du Cancer Paris CARPEM, F-75015 Paris, France.
| |
Collapse
|
11
|
Ordoñez R, Zhang W, Ellis G, Zhu Y, Ashe HJ, Ribeiro-dos-Santos AM, Brosh R, Huang E, Hogan MS, Boeke JD, Maurano MT. Genomic context sensitizes regulatory elements to genetic disruption. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.02.547201. [PMID: 37781588 PMCID: PMC10541140 DOI: 10.1101/2023.07.02.547201] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Enhancer function is frequently investigated piecemeal using truncated reporter assays or single deletion analysis. Thus it remains unclear to what extent enhancer function at native loci relies on surrounding genomic context. Using the Big-IN technology for targeted integration of large DNAs, we analyzed the regulatory architecture of the murine Igf2/H19 locus, a paradigmatic model of enhancer selectivity. We assembled payloads containing a 157-kb functional Igf2/H19 locus and engineered mutations to genetically direct CTCF occupancy at the imprinting control region (ICR) that switches the target gene of the H19 enhancer cluster. Contrasting activity of payloads delivered at the endogenous Igf2/H19 locus or ectopically at Hprt revealed that the Igf2/H19 locus includes additional, previously unknown long-range regulatory elements. Exchanging components of the Igf2/H19 locus with the well-studied Sox2 locus showed that the H19 enhancer cluster functioned poorly out of context, and required its native surroundings to activate Sox2 expression. Conversely, the Sox2 locus control region (LCR) could activate both Igf2 and H19 outside its native context, but its activity was only partially modulated by CTCF occupancy at the ICR. Analysis of regulatory DNA actuation across different cell types revealed that, while the H19 enhancers are tightly coordinated within their native locus, the Sox2 LCR acts more independently. We show that these enhancer clusters typify broader classes of loci genome-wide. Our results show that unexpected dependencies may influence even the most studied functional elements, and our synthetic regulatory genomics approach permits large-scale manipulation of complete loci to investigate the relationship between locus architecture and function.
Collapse
Affiliation(s)
- Raquel Ordoñez
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
- These authors contributed equally
| | - Weimin Zhang
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
- These authors contributed equally
| | - Gwen Ellis
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
- Present address: Department of Biology, University of Vermont, Burlington, VT 05405, USA
| | - Yinan Zhu
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Hannah J. Ashe
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
- Present address: School of Medicine, University of Maryland, Baltimore, MD 21201, USA
| | | | - Ran Brosh
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Emily Huang
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
- Present address: Highmark Health, Pittsburgh, PA 15222, USA
| | - Megan S. Hogan
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
- Present address: Neochromosome Inc., Long Island City, NY 11101, USA
| | - Jef D. Boeke
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
- Department of Biochemistry Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
| | - Matthew T. Maurano
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA
- Lead contact
| |
Collapse
|
12
|
Monteagudo-Sánchez A, Noordermeer D, Greenberg MVC. The impact of DNA methylation on CTCF-mediated 3D genome organization. Nat Struct Mol Biol 2024; 31:404-412. [PMID: 38499830 DOI: 10.1038/s41594-024-01241-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/05/2024] [Indexed: 03/20/2024]
Abstract
Cytosine DNA methylation is a highly conserved epigenetic mark in eukaryotes. Although the role of DNA methylation at gene promoters and repetitive elements has been extensively studied, the function of DNA methylation in other genomic contexts remains less clear. In the nucleus of mammalian cells, the genome is spatially organized at different levels, and strongly influences myriad genomic processes. There are a number of factors that regulate the three-dimensional (3D) organization of the genome, with the CTCF insulator protein being among the most well-characterized. Pertinently, CTCF binding has been reported as being DNA methylation-sensitive in certain contexts, perhaps most notably in the process of genomic imprinting. Therefore, it stands to reason that DNA methylation may play a broader role in the regulation of chromatin architecture. Here we summarize the current understanding that is relevant to both the mammalian DNA methylation and chromatin architecture fields and attempt to assess the extent to which DNA methylation impacts the folding of the genome. The focus is in early embryonic development and cellular transitions when the epigenome is in flux, but we also describe insights from pathological contexts, such as cancer, in which the epigenome and 3D genome organization are misregulated.
Collapse
Affiliation(s)
| | - Daan Noordermeer
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | | |
Collapse
|
13
|
Albrecht C, Rajaram N, Broche J, Bashtrykov P, Jeltsch A. Locus-Specific and Stable DNA Demethylation at the H19/ IGF2 ICR1 by Epigenome Editing Using a dCas9-SunTag System and the Catalytic Domain of TET1. Genes (Basel) 2024; 15:80. [PMID: 38254969 PMCID: PMC10815749 DOI: 10.3390/genes15010080] [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: 12/19/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
DNA methylation is critically involved in the regulation of chromatin states and cell-type-specific gene expression. The exclusive expression of imprinted genes from either the maternal or the paternal allele is regulated by allele-specific DNA methylation at imprinting control regions (ICRs). Aberrant DNA hyper- or hypomethylation at the ICR1 of the H19/IGF2 imprinting locus is characteristic for the imprinting disorders Beckwith-Wiedemann syndrome (BWS) and Silver-Russell syndrome (SRS), respectively. In this paper, we performed epigenome editing to induce targeted DNA demethylation at ICR1 in HEK293 cells using dCas9-SunTag and the catalytic domain of TET1. 5-methylcytosine (5mC) levels at the target locus were reduced up to 90% and, 27 days after transient transfection, >60% demethylation was still observed. Consistent with the stable demethylation of CTCF-binding sites within the ICR1, the occupancy of the DNA methylation-sensitive insulator CTCF protein increased by >2-fold throughout the 27 days. Additionally, the H19 expression was increased by 2-fold stably, while IGF2 was repressed though only transiently. Our data illustrate the ability of epigenome editing to implement long-term changes in DNA methylation at imprinting control regions after a single transient treatment, potentially paving the way for therapeutic epigenome editing approaches in the treatment of imprinting disorders.
Collapse
Affiliation(s)
| | | | | | | | - Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany; (C.A.)
| |
Collapse
|
14
|
Weinberg-Shukron A, Youngson NA, Ferguson-Smith AC, Edwards CA. Epigenetic control and genomic imprinting dynamics of the Dlk1-Dio3 domain. Front Cell Dev Biol 2023; 11:1328806. [PMID: 38155837 PMCID: PMC10754522 DOI: 10.3389/fcell.2023.1328806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 11/27/2023] [Indexed: 12/30/2023] Open
Abstract
Genomic imprinting is an epigenetic process whereby genes are monoallelically expressed in a parent-of-origin-specific manner. Imprinted genes are frequently found clustered in the genome, likely illustrating their need for both shared regulatory control and functional inter-dependence. The Dlk1-Dio3 domain is one of the largest imprinted clusters. Genes in this region are involved in development, behavior, and postnatal metabolism: failure to correctly regulate the domain leads to Kagami-Ogata or Temple syndromes in humans. The region contains many of the hallmarks of other imprinted domains, such as long non-coding RNAs and parental origin-specific CTCF binding. Recent studies have shown that the Dlk1-Dio3 domain is exquisitely regulated via a bipartite imprinting control region (ICR) which functions differently on the two parental chromosomes to establish monoallelic expression. Furthermore, the Dlk1 gene displays a selective absence of imprinting in the neurogenic niche, illustrating the need for precise dosage modulation of this domain in different tissues. Here, we discuss the following: how differential epigenetic marks laid down in the gametes cause a cascade of events that leads to imprinting in the region, how this mechanism is selectively switched off in the neurogenic niche, and why studying this imprinted region has added a layer of sophistication to how we think about the hierarchical epigenetic control of genome function.
Collapse
Affiliation(s)
| | - Neil A. Youngson
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
| | | | - Carol A. Edwards
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|
15
|
Lawson HA, Liang Y, Wang T. Transposable elements in mammalian chromatin organization. Nat Rev Genet 2023; 24:712-723. [PMID: 37286742 DOI: 10.1038/s41576-023-00609-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2023] [Indexed: 06/09/2023]
Abstract
Transposable elements (TEs) are mobile DNA elements that comprise almost 50% of mammalian genomic sequence. TEs are capable of making additional copies of themselves that integrate into new positions in host genomes. This unique property has had an important impact on mammalian genome evolution and on the regulation of gene expression because TE-derived sequences can function as cis-regulatory elements such as enhancers, promoters and silencers. Now, advances in our ability to identify and characterize TEs have revealed that TE-derived sequences also regulate gene expression by both maintaining and shaping 3D genome architecture. Studies are revealing how TEs contribute raw sequence that can give rise to the structures that shape chromatin organization, and thus gene expression, allowing for species-specific genome innovation and evolutionary novelty.
Collapse
Affiliation(s)
- Heather A Lawson
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA.
| | - Yonghao Liang
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA.
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO, USA.
- McDonnell Genome Institute, Washington University School of Medicine, Saint Louis, MO, USA.
| |
Collapse
|
16
|
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: 4] [Impact Index Per Article: 4.0] [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.
Collapse
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
| |
Collapse
|
17
|
Matsuzaki H, Takahashi T, Kuramochi D, Hirakawa K, Tanimoto K. Five nucleotides found in RCTG motifs are essential for post-fertilization methylation imprinting of the H19 ICR in YAC transgenic mice. Nucleic Acids Res 2023; 51:7236-7253. [PMID: 37334871 PMCID: PMC10415150 DOI: 10.1093/nar/gkad516] [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: 10/18/2022] [Accepted: 06/02/2023] [Indexed: 06/21/2023] Open
Abstract
Genomic imprinting at the mouse Igf2/H19 locus is controlled by the H19 ICR, within which paternal allele-specific DNA methylation originating in sperm is maintained throughout development in offspring. We previously found that a 2.9 kb transgenic H19 ICR fragment in mice can be methylated de novo after fertilization only when paternally inherited, despite its unmethylated state in sperm. When the 118 bp sequence responsible for this methylation in transgenic mice was deleted from the endogenous H19 ICR, the methylation level of its paternal allele was significantly reduced after fertilization, suggesting the activity involving this 118 bp sequence is required for methylation maintenance at the endogenous locus. Here, we determined protein binding to the 118 bp sequence using an in vitro binding assay and inferred the binding motif to be RCTG by using a series of mutant competitors. Furthermore, we generated H19 ICR transgenic mice with a 5-bp substitution mutation that disrupts the RCTG motifs within the 118 bp sequence, and observed loss of methylation from the paternally inherited transgene. These results indicate that imprinted methylation of the H19 ICR established de novo during the post-fertilization period involves binding of specific factors to distinct sequence motifs within the 118 bp sequence.
Collapse
Affiliation(s)
- Hitomi Matsuzaki
- Faculty of Life and Environmental Sciences, Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Takuya Takahashi
- Graduate school of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Daichi Kuramochi
- Graduate school of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Katsuhiko Hirakawa
- Graduate school of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Keiji Tanimoto
- Faculty of Life and Environmental Sciences, Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| |
Collapse
|
18
|
Wang SE, Jiang YH. Novel epigenetic molecular therapies for imprinting disorders. Mol Psychiatry 2023; 28:3182-3193. [PMID: 37626134 PMCID: PMC10618104 DOI: 10.1038/s41380-023-02208-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 07/21/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023]
Abstract
Genomic imprinting disorders are caused by the disruption of genomic imprinting processes leading to a deficit or increase of an active allele. Their unique molecular mechanisms underlying imprinted genes offer an opportunity to investigate epigenetic-based therapy for reactivation of an inactive allele or reduction of an active allele. Current treatments are based on managing symptoms, not targeting the molecular mechanisms underlying imprinting disorders. Here, we highlight molecular approaches of therapeutic candidates in preclinical and clinical studies for individual imprinting disorders. These include the significant progress of discovery and testing of small molecules, antisense oligonucleotides, and CRISPR mediated genome editing approaches as new therapeutic strategies. We discuss the significant challenges of translating these promising therapies from the preclinical stage to the clinic, especially for genome editing based approaches.
Collapse
Affiliation(s)
- Sung Eun Wang
- Department of Genetics, Yale University School of Medicine, 333 Cedar street, New Haven, CT, 06520, USA
| | - Yong-Hui Jiang
- Department of Genetics, Yale University School of Medicine, 333 Cedar street, New Haven, CT, 06520, USA.
- Department of Neuroscience, Yale University School of Medicine, 333 Cedar street, New Haven, CT, 06520, USA.
- Department of Pediatrics, Yale University School of Medicine, 333 Cedar street, New Haven, CT, 06520, USA.
| |
Collapse
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
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: 2] [Impact Index Per Article: 2.0] [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.
Collapse
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
| |
Collapse
|
21
|
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: 7] [Impact Index Per Article: 7.0] [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.
Collapse
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.
| |
Collapse
|
22
|
Liang D, Aygün N, Matoba N, Ideraabdullah FY, Love MI, Stein JL. Inference of putative cell-type-specific imprinted regulatory elements and genes during human neuronal differentiation. Hum Mol Genet 2023; 32:402-416. [PMID: 35994039 PMCID: PMC9851749 DOI: 10.1093/hmg/ddac207] [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: 05/23/2022] [Revised: 08/02/2022] [Accepted: 08/17/2022] [Indexed: 01/24/2023] Open
Abstract
Genomic imprinting results in gene expression bias caused by parental chromosome of origin and occurs in genes with important roles during human brain development. However, the cell-type and temporal specificity of imprinting during human neurogenesis is generally unknown. By detecting within-donor allelic biases in chromatin accessibility and gene expression that are unrelated to cross-donor genotype, we inferred imprinting in both primary human neural progenitor cells and their differentiated neuronal progeny from up to 85 donors. We identified 43/20 putatively imprinted regulatory elements (IREs) in neurons/progenitors, and 133/79 putatively imprinted genes in neurons/progenitors. Although 10 IREs and 42 genes were shared between neurons and progenitors, most putative imprinting was only detected within specific cell types. In addition to well-known imprinted genes and their promoters, we inferred novel putative IREs and imprinted genes. Consistent with both DNA methylation-based and H3K27me3-based regulation of imprinted expression, some putative IREs also overlapped with differentially methylated or histone-marked regions. Finally, we identified a progenitor-specific putatively imprinted gene overlapping with copy number variation that is associated with uniparental disomy-like phenotypes. Our results can therefore be useful in interpreting the function of variants identified in future parent-of-origin association studies.
Collapse
Affiliation(s)
- Dan Liang
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Nil Aygün
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Nana Matoba
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Folami Y Ideraabdullah
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Michael I Love
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jason L Stein
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| |
Collapse
|
23
|
Claxton M, Pulix M, Seah MKY, Bernardo R, Zhou P, Aljuraysi S, Liloglou T, Arnaud P, Kelsey G, Messerschmidt DM, Plagge A. Variable allelic expression of imprinted genes at the Peg13, Trappc9, Ago2 cluster in single neural cells. Front Cell Dev Biol 2022; 10:1022422. [PMID: 36313557 PMCID: PMC9596773 DOI: 10.3389/fcell.2022.1022422] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Genomic imprinting is an epigenetic process through which genes are expressed in a parent-of-origin specific manner resulting in mono-allelic or strongly biased expression of one allele. For some genes, imprinted expression may be tissue-specific and reliant on CTCF-influenced enhancer-promoter interactions. The Peg13 imprinting cluster is associated with neurodevelopmental disorders and comprises canonical imprinted genes, which are conserved between mouse and human, as well as brain-specific imprinted genes in mouse. The latter consist of Trappc9, Chrac1 and Ago2, which have a maternal allelic expression bias of ∼75% in brain. Findings of such allelic expression biases on the tissue level raise the question of how they are reflected in individual cells and whether there is variability and mosaicism in allelic expression between individual cells of the tissue. Here we show that Trappc9 and Ago2 are not imprinted in hippocampus-derived neural stem cells (neurospheres), while Peg13 retains its strong bias of paternal allele expression. Upon analysis of single neural stem cells and in vitro differentiated neurons, we find not uniform, but variable states of allelic expression, especially for Trappc9 and Ago2. These ranged from mono-allelic paternal to equal bi-allelic to mono-allelic maternal, including biased bi-allelic transcriptional states. Even Peg13 expression deviated from its expected paternal allele bias in a small number of cells. Although the cell populations consisted of a mosaic of cells with different allelic expression states, as a whole they reflected bulk tissue data. Furthermore, in an attempt to identify potential brain-specific regulatory elements across the Trappc9 locus, we demonstrate tissue-specific and general silencer activities, which might contribute to the regulation of its imprinted expression bias.
Collapse
Affiliation(s)
- Michael Claxton
- Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Michela Pulix
- Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Michelle K. Y. Seah
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Ralph Bernardo
- Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Peng Zhou
- Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Sultan Aljuraysi
- Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- Department of Physiology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Triantafillos Liloglou
- Faculty of Health, Social Care and Medicine, Edge Hill University, Ormskirk, Lancashire, United Kingdom
| | - Philippe Arnaud
- Université Clermont Auvergne, CNRS, Inserm, GReD, Clermont-Ferrand, France
| | - Gavin Kelsey
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
- Centre for Trophoblast Research, University of Cambridge, Cambridge, United Kingdom
- Wellcome-MRC Institute of Metabolic Science-Metabolic Research Laboratories, Cambridge, United Kingdom
| | - Daniel M. Messerschmidt
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Antonius Plagge
- Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| |
Collapse
|
24
|
Juan AM, Foong YH, Thorvaldsen JL, Lan Y, Leu NA, Rurik JG, Li L, Krapp C, Rosier CL, Epstein JA, Bartolomei MS. Tissue-specific Grb10/Ddc insulator drives allelic architecture for cardiac development. Mol Cell 2022; 82:3613-3631.e7. [PMID: 36108632 PMCID: PMC9547965 DOI: 10.1016/j.molcel.2022.08.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 07/12/2022] [Accepted: 08/18/2022] [Indexed: 11/24/2022]
Abstract
Allele-specific expression of imprinted gene clusters is governed by gametic DNA methylation at master regulators called imprinting control regions (ICRs). Non-gametic or secondary differentially methylated regions (DMRs) at promoters and exonic regions reinforce monoallelic expression but do not control an entire cluster. Here, we unveil an unconventional secondary DMR that is indispensable for tissue-specific imprinting of two previously unlinked genes, Grb10 and Ddc. Using polymorphic mice, we mapped an intronic secondary DMR at Grb10 with paternal-specific CTCF binding (CBR2.3) that forms contacts with Ddc. Deletion of paternal CBR2.3 removed a critical insulator, resulting in substantial shifting of chromatin looping and ectopic enhancer-promoter contacts. Destabilized gene architecture precipitated abnormal Grb10-Ddc expression with developmental consequences in the heart and muscle. Thus, we redefine the Grb10-Ddc imprinting domain by uncovering an unconventional intronic secondary DMR that functions as an insulator to instruct the tissue-specific, monoallelic expression of multiple genes-a feature previously ICR exclusive.
Collapse
Affiliation(s)
- Aimee M Juan
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yee Hoon Foong
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joanne L Thorvaldsen
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, 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
| | - Nicolae A Leu
- Department of Biomedical Sciences, Center for Animal Transgenesis and Germ Cell Research, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA
| | - Joel G Rurik
- Penn Cardiovascular Institute, Department of Medicine, Department Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Li Li
- Penn Cardiovascular Institute, Department of Medicine, Department Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christopher Krapp
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Casey L Rosier
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jonathan A Epstein
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Cardiovascular Institute, Department of Medicine, Department Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marisa S Bartolomei
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
25
|
Gomez RL, Woods LM, Ramachandran R, Abou Tayoun AN, Philpott A, Ali FR. Super-enhancer associated core regulatory circuits mediate susceptibility to retinoic acid in neuroblastoma cells. Front Cell Dev Biol 2022; 10:943924. [PMID: 36147741 PMCID: PMC9485839 DOI: 10.3389/fcell.2022.943924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 08/08/2022] [Indexed: 11/25/2022] Open
Abstract
Neuroblastoma is a pediatric tumour that accounts for more than 15% of cancer-related deaths in children. High-risk tumours are often difficult to treat, and patients' survival chances are less than 50%. Retinoic acid treatment is part of the maintenance therapy given to neuroblastoma patients; however, not all tumours differentiate in response to retinoic acid. Within neuroblastoma tumors, two phenotypically distinct cell types have been identified based on their super-enhancer landscape and transcriptional core regulatory circuitries: adrenergic (ADRN) and mesenchymal (MES). We hypothesized that the distinct super-enhancers in these different tumour cells mediate differential response to retinoic acid. To this end, three different neuroblastoma cell lines, ADRN (MYCN amplified and non-amplified) and MES cells, were treated with retinoic acid, and changes in the super-enhancer landscape upon treatment and after subsequent removal of retinoic acid was studied. Using ChIP-seq for the active histone mark H3K27ac, paired with RNA-seq, we compared the super-enhancer landscape in cells that undergo neuronal differentiation in response to retinoic acid versus those that fail to differentiate and identified unique super-enhancers associated with neuronal differentiation. Among the ADRN cells that respond to treatment, MYCN-amplified cells remain differentiated upon removal of retinoic acid, whereas MYCN non-amplified cells revert to an undifferentiated state, allowing for the identification of super-enhancers responsible for maintaining differentiation. This study identifies key super-enhancers that are crucial for retinoic acid-mediated differentiation.
Collapse
Affiliation(s)
- Roshna Lawrence Gomez
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Laura M. Woods
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Center, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Revathy Ramachandran
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Ahmad N. Abou Tayoun
- Center for Genomic Discovery, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
- Al Jalila Genomics Center, Al Jalila Children’s Hospital, Dubai, United Arab Emirates
| | - Anna Philpott
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Center, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Fahad R. Ali
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
- Center for Genomic Discovery, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| |
Collapse
|
26
|
Han X, He H, Shao L, Cui S, Yu H, Zhang X, Wu Q. Deletion of Meg8-DMR Enhances Migration and Invasion of MLTC-1 Depending on the CTCF Binding Sites. Int J Mol Sci 2022; 23:ijms23158828. [PMID: 35955961 PMCID: PMC9369160 DOI: 10.3390/ijms23158828] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/28/2022] [Accepted: 08/05/2022] [Indexed: 11/30/2022] Open
Abstract
The Dlk1-Dio3 imprinted domain on mouse chromosome 12 contains three well-characterized paternally methylated differentially methylated regions (DMRs): IG-DMR, Gtl2-DMR, and Dlk1-DMR. These DMRs control the expression of many genes involved in embryonic development, inherited diseases, and human cancer in this domain. The first maternal methylation DMR discovered in this domain was the Meg8-DMR, the targets and biological function of which are still unknown. Here, using an enhancer-blocking assay, we first dissected the functional parts of the Meg8-DMR and showed that its insulator activity is dependent on the CCCTC-binding factor (CTCF) in MLTC-1. Results from RNA-seq showed that the deletion of the Meg8-DMR and its compartment CTCF binding sites, but not GGCG repeats, lead to the downregulation of numerous genes on chromosome 12, in particular the drastically reduced expression of Dlk1 and Rtl1 in the Dlk1-Dio3 domain, while differentially expressed genes are enriched in the MAPK pathway. In vitro assays revealed that the deletion of the Meg8-DMR and CTCF binding sites enhances cell migration and invasion by decreasing Dlk1 and activating the Notch1-Rhoc-MAPK/ERK pathway. These findings enhance research into gene regulation in the Dlk1-Dio3 domain by indicating that the Meg8-DMR functions as a long-range regulatory element which is dependent on CTCF binding sites and affects multiple genes in this domain.
Collapse
Affiliation(s)
- Xiao Han
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Hongjuan He
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Lan Shao
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Shuang Cui
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Haoran Yu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Ximeijia Zhang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Qiong Wu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150001, China
- Correspondence: ; Tel./Fax: +86-0451-86416944
| |
Collapse
|
27
|
Ahn J, Lee J, Kim DH, Hwang IS, Park MR, Cho IC, Hwang S, Lee K. Loss of Monoallelic Expression of IGF2 in the Adult Liver Via Alternative Promoter Usage and Chromatin Reorganization. Front Genet 2022; 13:920641. [PMID: 35938007 PMCID: PMC9355166 DOI: 10.3389/fgene.2022.920641] [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: 04/14/2022] [Accepted: 06/21/2022] [Indexed: 11/13/2022] Open
Abstract
In mammals, genomic imprinting operates via gene silencing mechanisms. Although conservation of the imprinting mechanism at the H19/IGF2 locus has been generally described in pigs, tissue-specific imprinting at the transcript level, monoallelic-to-biallelic conversion, and spatio-temporal chromatin reorganization remain largely uninvestigated. Here, we delineate spatially regulated imprinting of IGF2 transcripts, age-dependent hepatic mono- to biallelic conversion, and reorganization of topologically associating domains at the porcine H19/IGF2 locus for better translation to human and animal research. Whole-genome bisulfite sequencing (WGBS) and RNA sequencing (RNA-seq) of normal and parthenogenetic porcine embryos revealed the paternally hypermethylated H19 differentially methylated region and paternal expression of IGF2. Using a polymorphism-based approach and omics datasets from chromatin immunoprecipitation sequencing (ChIP–seq), whole-genome sequencing (WGS), RNA-seq, and Hi-C, regulation of IGF2 during development was analyzed. Regulatory elements in the liver were distinguished from those in the muscle where the porcine IGF2 transcript was monoallelically expressed. The IGF2 transcript from the liver was biallelically expressed at later developmental stages in both pigs and humans. Chromatin interaction was less frequent in the adult liver compared to the fetal liver and skeletal muscle. The duration of genomic imprinting effects within the H19/IGF2 locus might be reduced in the liver with biallelic conversion through alternative promoter usage and chromatin remodeling. Our integrative omics analyses of genome, epigenome, and transcriptome provided a comprehensive view of imprinting status at the H19/IGF2 cluster.
Collapse
Affiliation(s)
- Jinsoo Ahn
- Functional Genomics Laboratory, Department of Animal Sciences, The Ohio State University, Columbus, OH, United States
| | - Joonbum Lee
- Functional Genomics Laboratory, Department of Animal Sciences, The Ohio State University, Columbus, OH, United States
- The Ohio State University Interdisciplinary Human Nutrition Program, The Ohio State University, Columbus, OH, United States
| | - Dong-Hwan Kim
- Functional Genomics Laboratory, Department of Animal Sciences, The Ohio State University, Columbus, OH, United States
| | - In-Sul Hwang
- Animal Biotechnology Division, National Institute of Animal Science, Rural Development Administration, Jeonbuk, South Korea
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, Columbia University, New York, NY, United States
| | - Mi-Ryung Park
- Animal Biotechnology Division, National Institute of Animal Science, Rural Development Administration, Jeonbuk, South Korea
| | - In-Cheol Cho
- National Institute of Animal Science, Rural Development Administration, Jeju, South Korea
| | - Seongsoo Hwang
- Animal Biotechnology Division, National Institute of Animal Science, Rural Development Administration, Jeonbuk, South Korea
| | - Kichoon Lee
- Functional Genomics Laboratory, Department of Animal Sciences, The Ohio State University, Columbus, OH, United States
- The Ohio State University Interdisciplinary Human Nutrition Program, The Ohio State University, Columbus, OH, United States
- *Correspondence: Kichoon Lee,
| |
Collapse
|
28
|
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.
Collapse
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.
| |
Collapse
|
29
|
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.
Collapse
|
30
|
Abstract
One of the most fundamental questions in developmental biology is how one fertilized cell can give rise to a fully mature organism and how gene regulation governs this process. Precise spatiotemporal gene expression is required for development and is believed to be achieved through a complex interplay of sequence-specific information, epigenetic modifications, trans-acting factors, and chromatin folding. Here we review the role of chromatin folding during development, the mechanisms governing 3D genome organization, and how it is established in the embryo. Furthermore, we discuss recent advances and debated questions regarding the contribution of the 3D genome to gene regulation during organogenesis. Finally, we describe the mechanisms that can reshape the 3D genome, including disease-causing structural variations and the emerging view that transposable elements contribute to chromatin organization.
Collapse
Affiliation(s)
- Juliane Glaser
- RG Development and Disease, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Stefan Mundlos
- RG Development and Disease, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
- Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
- Charité - Universitätsmedizin Berlin, BCRT - Berlin Institute of Health Center for Regenerative Therapies, 10178 Berlin, Germany
| |
Collapse
|
31
|
Allele-specific aberration of imprinted domain chromosome architecture associates with large offspring syndrome. iScience 2022; 25:104269. [PMID: 35542046 PMCID: PMC9079005 DOI: 10.1016/j.isci.2022.104269] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 03/12/2022] [Accepted: 04/13/2022] [Indexed: 11/21/2022] Open
Abstract
Large offspring syndrome (LOS) and Beckwith-Wiedemann syndrome are similar epigenetic congenital overgrowth conditions in ruminants and humans, respectively. We have reported global loss-of-imprinting, methylome epimutations, and gene misregulation in LOS. However, less than 4% of gene misregulation can be explained with short range (<20kb) alterations in DNA methylation. Therefore, we hypothesized that methylome epimutations in LOS affect chromosome architecture which results in misregulation of genes located at distances >20kb in cis and in trans (other chromosomes). Our analyses focused on two imprinted domains that frequently reveal misregulation in these syndromes, namely KvDMR1 and IGF2R. Using bovine fetal fibroblasts, we identified CTCF binding at IGF2R imprinting control region but not KvDMR1, and allele-specific chromosome architecture of these domains in controls. In LOS, analyses identified erroneous long-range contacts and clustering tendency in the direction of expression of misregulated genes. In conclusion, altered chromosome architecture is associated with LOS. IGF2R imprinted domain has allele-specific chromosome architecture in bovines In bovines, CTCF binds at IGF2R imprinting control region but not at KvDMR1 Bovine large offspring syndrome (LOS) shows altered chromosome architecture at IGF2R Misregulated genes in LOS exhibit genomic location-based clustering tendency
Collapse
|
32
|
Subnuclear localisation is associated with gene expression more than parental origin at the imprinted Dlk1-Dio3 locus. PLoS Genet 2022; 18:e1010186. [PMID: 35482825 PMCID: PMC9129038 DOI: 10.1371/journal.pgen.1010186] [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: 01/18/2021] [Revised: 05/24/2022] [Accepted: 04/04/2022] [Indexed: 11/30/2022] Open
Abstract
At interphase, de-condensed chromosomes have a non-random three-dimensional architecture within the nucleus, however, little is known about the extent to which nuclear organisation might influence expression or vice versa. Here, using imprinting as a model, we use 3D RNA- and DNA-fluorescence-in-situ-hybridisation in normal and mutant mouse embryonic stem cell lines to assess the relationship between imprinting control, gene expression and allelic distance from the nuclear periphery. We compared the two parentally inherited imprinted domains at the Dlk1-Dio3 domain and find a small but reproducible trend for the maternally inherited domain to be further away from the periphery however we did not observe an enrichment of inactive alleles in the immediate vicinity of the nuclear envelope. Using Zfp57KO ES cells, which harbour a paternal to maternal epigenotype switch, we observe that expressed alleles are significantly further away from the nuclear periphery. However, within individual nuclei, alleles closer to the periphery are equally likely to be expressed as those further away. In other words, absolute position does not predict expression. Taken together, this suggests that whilst stochastic activation can cause subtle shifts in localisation for this locus, there is no dramatic relocation of alleles upon gene activation. Our results suggest that transcriptional activity, rather than the parent-of-origin, defines subnuclear localisation at an endogenous imprinted domain. Genomic imprinting is an epigenetically regulated process that results in the preferential expression of a subset of developmentally regulated genes from either the maternally or the paternally inherited chromosomes. We have used imprinted genes as a model system to investigate the relationship between the parental origin of the chromosomes, the localisation of genes within the cell nucleus and their active expression. By assessing the location of the Dlk1-Dio3 region and the expression of the Gtl2/Meg3 gene within it, we find that there is a small preference for the paternal chromosome to be closer to the periphery but a significant correlation between transcription and distance to the edge of the nucleus for the Gtl2/Meg3 gene. Furthermore, a chromosome nearer the periphery is just as likely to express the gene as the chromosome further away. These findings suggest that the parental origin of the chromosome may not be as important as the transcription of the gene in defining the position of the imprinted region within the nucleus.
Collapse
|
33
|
Hubert JN, Demars J. Genomic Imprinting in the New Omics Era: A Model for Systems-Level Approaches. Front Genet 2022; 13:838534. [PMID: 35368671 PMCID: PMC8965095 DOI: 10.3389/fgene.2022.838534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/28/2022] [Indexed: 11/13/2022] Open
Abstract
Genomic imprinting represents a noteworthy inheritance mechanism leading to allele-specific regulations dependent of the parental origin. Imprinted loci are especially involved in essential mammalian functions related to growth, development and behavior. In this mini-review, we first offer a summary of current representations associated with genomic imprinting through key results of the three last decades. We then outline new perspectives allowed by the spread of new omics technologies tackling various interacting levels of imprinting regulations, including genomics, transcriptomics and epigenomics. We finally discuss the expected contribution of new omics data to unresolved big questions in the field.
Collapse
|
34
|
Chandrasekaran V, Oparina N, Garcia-Bonete MJ, Wasén C, Erlandsson MC, Malmhäll-Bah E, Andersson KME, Jensen M, Silfverswärd ST, Katona G, Bokarewa MI. Cohesin-Mediated Chromatin Interactions and Autoimmunity. Front Immunol 2022; 13:840002. [PMID: 35222432 PMCID: PMC8866859 DOI: 10.3389/fimmu.2022.840002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 01/17/2022] [Indexed: 11/23/2022] Open
Abstract
Proper physiological functioning of any cell type requires ordered chromatin organization. In this context, cohesin complex performs important functions preventing premature separation of sister chromatids after DNA replication. In partnership with CCCTC-binding factor, it ensures insulator activity to organize enhancers and promoters within regulatory chromatin. Homozygous mutations and dysfunction of individual cohesin proteins are embryonically lethal in humans and mice, which limits in vivo research work to embryonic stem cells and progenitors. Conditional alleles of cohesin complex proteins have been generated to investigate their functional roles in greater detail at later developmental stages. Thus, genome regulation enabled by action of cohesin proteins is potentially crucial in lineage cell development, including immune homeostasis. In this review, we provide current knowledge on the role of cohesin complex in leukocyte maturation and adaptive immunity. Conditional knockout and shRNA-mediated inhibition of individual cohesin proteins in mice demonstrated their importance in haematopoiesis, adipogenesis and inflammation. Notably, these effects occur rather through changes in transcriptional gene regulation than through expected cell cycle defects. This positions cohesin at the crossroad of immune pathways including NF-kB, IL-6, and IFNγ signaling. Cohesin proteins emerged as vital regulators at early developmental stages of thymocytes and B cells and after antigen challenge. Human genome-wide association studies are remarkably concordant with these findings and present associations between cohesin and rheumatoid arthritis, multiple sclerosis and HLA-B27 related chronic inflammatory conditions. Furthermore, bioinformatic prediction based on protein-protein interactions reveal a tight connection between the cohesin complex and immune relevant processes supporting the notion that cohesin will unearth new clues in regulation of autoimmunity.
Collapse
Affiliation(s)
- Venkataragavan Chandrasekaran
- Department of Rheumatology and Inflammation Research, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Nina Oparina
- Rheumatology Clinic, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Maria-Jose Garcia-Bonete
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Caroline Wasén
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women’s Hospital, Boston, MA, United States
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Malin C. Erlandsson
- Department of Rheumatology and Inflammation Research, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Eric Malmhäll-Bah
- Department of Rheumatology and Inflammation Research, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Karin M. E. Andersson
- Department of Rheumatology and Inflammation Research, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Maja Jensen
- Department of Chemistry and Molecular Biology, Faculty of Science, University of Gothenburg, Gothenburg, Sweden
| | - Sofia T. Silfverswärd
- Department of Rheumatology and Inflammation Research, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Gergely Katona
- Department of Chemistry and Molecular Biology, Faculty of Science, University of Gothenburg, Gothenburg, Sweden
| | - Maria I. Bokarewa
- Department of Rheumatology and Inflammation Research, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
- Rheumatology Clinic, Sahlgrenska University Hospital, Gothenburg, Sweden
| |
Collapse
|
35
|
Nakamura K, Reid BM, Chen A, Chen Z, Goode EL, Permuth JB, Teer JK, Tyrer J, Yu X, Kanetsky PA, Pharoah PD, Gayther SA, Sellers TA, Lawrenson K, Karreth FA. Functional analysis of the 1p34.3 risk locus implicates GNL2 in high-grade serous ovarian cancer. Am J Hum Genet 2022; 109:116-135. [PMID: 34965383 DOI: 10.1016/j.ajhg.2021.11.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 11/29/2021] [Indexed: 12/20/2022] Open
Abstract
The high-grade serous ovarian cancer (HGSOC) risk locus at chromosome 1p34.3 resides within a frequently amplified genomic region signifying the presence of an oncogene. Here, we integrate in silico variant-to-function analysis with functional studies to characterize the oncogenic potential of candidate genes in the 1p34.3 locus. Fine mapping of genome-wide association statistics identified candidate causal SNPs local to H3K27ac-demarcated enhancer regions that exhibit allele-specific binding for CTCF in HGSOC and normal fallopian tube secretory epithelium cells (FTSECs). SNP risk associations colocalized with eQTL for six genes (DNALI1, GNL2, RSPO1, SNIP1, MEAF6, and LINC01137) that are more highly expressed in carriers of the risk allele, and three (DNALI1, GNL2, and RSPO1) were upregulated in HGSOC compared to normal ovarian surface epithelium cells and/or FTSECs. Increased expression of GNL2 and MEAF6 was associated with shorter survival in HGSOC with 1p34.3 amplifications. Despite its activation of β-catenin signaling, RSPO1 overexpression exerted no effects on proliferation or colony formation in our study of ovarian cancer and FTSECs. Instead, GNL2, MEAF6, and SNIP1 silencing impaired in vitro ovarian cancer cell growth. Additionally, GNL2 silencing diminished xenograft tumor formation, whereas overexpression stimulated proliferation and colony formation in FTSECs. GNL2 influences 60S ribosomal subunit maturation and global protein synthesis in ovarian cancer and FTSECs, providing a potential mechanism of how GNL2 upregulation might promote ovarian cancer development and mediate genetic susceptibility of HGSOC.
Collapse
|
36
|
Miranda M, Noordermeer D, Moindrot B. Detection of Allele-Specific 3D Chromatin Interactions Using High-Resolution In-Nucleus 4C-seq. Methods Mol Biol 2022; 2532:15-33. [PMID: 35867243 DOI: 10.1007/978-1-0716-2497-5_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Chromosome conformation capture techniques are a set of methods used to determine 3D genome organization through the capture and identification of physical contacts between pairs of genomic loci. Among them, 4C-seq (circular chromosome conformation capture coupled to high-throughput sequencing) allows for the identification and quantification of the sequences interacting with a preselected locus of interest. 4C-seq has been widely used in the literature, mainly to study chromatin loops between enhancers and promoters or between CTCF binding sites and to identify chromatin domain boundaries. As 3D-contacts may be established in an allele-specific manner, we describe an up-to-date allele-specific 4C-seq protocol, starting from the selection of allele-specific viewpoints to Illumina sequencing. This protocol has mainly been optimized for cultured mammalian cells, but can be adapted for other cell types with relatively minor changes in initial steps.
Collapse
Affiliation(s)
- Mélanie Miranda
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Daan Noordermeer
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France.
| | - Benoit Moindrot
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France.
| |
Collapse
|
37
|
Matsuzaki H, Miyajima Y, Fukamizu A, Tanimoto K. Orientation of mouse H19 ICR affects imprinted H19 gene expression through promoter methylation-dependent and -independent mechanisms. Commun Biol 2021; 4:1410. [PMID: 34921234 PMCID: PMC8683476 DOI: 10.1038/s42003-021-02939-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 11/30/2021] [Indexed: 11/19/2022] Open
Abstract
The mouse Igf2/H19 locus is regulated by genomic imprinting, in which the paternally methylated H19 imprinting control region (ICR) plays a critical role in mono-allelic expression of the genes in the locus. Although the maternal allele-specific insulator activity of the H19 ICR in regulating imprinted Igf2 expression has been well established, the detailed mechanism by which the H19 ICR controls mono-allelic H19 gene expression has not been fully elucidated. In this study, we evaluated the effect of H19 ICR orientation on imprinting regulation in mutant mice in which the H19 ICR sequence was inverted at the endogenous locus. When the inverted-ICR allele was paternally inherited, the methylation level of the H19 promoter was decreased and the H19 gene was derepressed, suggesting that methylation of the H19 promoter is essential for complete repression of H19 gene expression. Unexpectedly, when the inverted allele was maternally inherited, the expression level of the H19 gene was lower than that of the WT allele, even though the H19 promoter remained fully hypomethylated. These observations suggested that the polarity of the H19 ICR is involved in controlling imprinted H19 gene expression on each parental allele, dependent or independent on DNA methylation of the H19 promoter.
Collapse
Affiliation(s)
- Hitomi Matsuzaki
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki, Japan.
| | - Yu Miyajima
- Graduate school of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Akiyoshi Fukamizu
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Keiji Tanimoto
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki, Japan
| |
Collapse
|
38
|
Aronson BE, Scourzic L, Shah V, Swanzey E, Kloetgen A, Polyzos A, Sinha A, Azziz A, Caspi I, Li J, Pelham-Webb B, Glenn RA, Vierbuchen T, Wichterle H, Tsirigos A, Dawlaty MM, Stadtfeld M, Apostolou E. A bipartite element with allele-specific functions safeguards DNA methylation imprints at the Dlk1-Dio3 locus. Dev Cell 2021; 56:3052-3065.e5. [PMID: 34710357 PMCID: PMC8628258 DOI: 10.1016/j.devcel.2021.10.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 08/06/2021] [Accepted: 10/04/2021] [Indexed: 11/23/2022]
Abstract
Loss of imprinting (LOI) results in severe developmental defects, but the mechanisms preventing LOI remain incompletely understood. Here, we dissect the functional components of the imprinting control region of the essential Dlk1-Dio3 locus (called IG-DMR) in pluripotent stem cells. We demonstrate that the IG-DMR consists of two antagonistic elements: a paternally methylated CpG island that prevents recruitment of TET dioxygenases and a maternally unmethylated non-canonical enhancer that ensures expression of the Gtl2 lncRNA by counteracting de novo DNA methyltransferases. Genetic or epigenetic editing of these elements leads to distinct LOI phenotypes with characteristic alternations of allele-specific gene expression, DNA methylation, and 3D chromatin topology. Although repression of the Gtl2 promoter results in dysregulated imprinting, the stability of LOI phenotypes depends on the IG-DMR, suggesting a functional hierarchy. These findings establish the IG-DMR as a bipartite control element that maintains imprinting by allele-specific restriction of the DNA (de)methylation machinery.
Collapse
Affiliation(s)
- Boaz E Aronson
- Sanford I Weill Department of Medicine, Division of Hematology/Oncology, Sandra and Edward Meyer Cancer Center, New York, NY 10021, USA
| | - Laurianne Scourzic
- Sanford I Weill Department of Medicine, Division of Hematology/Oncology, Sandra and Edward Meyer Cancer Center, New York, NY 10021, USA
| | - Veevek Shah
- Sanford I Weill Department of Medicine, Division of Hematology/Oncology, Sandra and Edward Meyer Cancer Center, New York, NY 10021, USA
| | - Emily Swanzey
- Sanford I Weill Department of Medicine, Division of Regenerative Medicine, Weill Cornell Medicine, New York, NY 10021, USA; The Jackson Laboratory, Bar Harbor, ME, USA
| | - Andreas Kloetgen
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Alexander Polyzos
- Sanford I Weill Department of Medicine, Division of Hematology/Oncology, Sandra and Edward Meyer Cancer Center, New York, NY 10021, USA
| | - Abhishek Sinha
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Annabel Azziz
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY 10065, USA
| | - Inbal Caspi
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jiexi Li
- Sanford I Weill Department of Medicine, Division of Hematology/Oncology, Sandra and Edward Meyer Cancer Center, New York, NY 10021, USA
| | - Bobbie Pelham-Webb
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD program, New York, NY, USA
| | - Rachel A Glenn
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY 10065, USA; Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Stem Cell Biology and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Thomas Vierbuchen
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Stem Cell Biology and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Hynek Wichterle
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Neurology, Neuroscience and Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center, Center for Motor Neuron Biology and Disease and Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Aristotelis Tsirigos
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Institute for Computational Medicine and Applied Bioinformatics Laboratories, New York University School of Medicine, New York, NY 10016, USA
| | - Meelad M Dawlaty
- Ruth L and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Bronx, NY 10461, USA; Department of Genetics, Department of Developmental & Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Matthias Stadtfeld
- Sanford I Weill Department of Medicine, Division of Regenerative Medicine, Weill Cornell Medicine, New York, NY 10021, USA.
| | - Effie Apostolou
- Sanford I Weill Department of Medicine, Division of Hematology/Oncology, Sandra and Edward Meyer Cancer Center, New York, NY 10021, USA.
| |
Collapse
|
39
|
Prasasya R, Grotheer KV, Siracusa LD, Bartolomei MS. Temple syndrome and Kagami-Ogata syndrome: clinical presentations, genotypes, models and mechanisms. Hum Mol Genet 2021; 29:R107-R116. [PMID: 32592473 DOI: 10.1093/hmg/ddaa133] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 06/22/2020] [Accepted: 06/24/2020] [Indexed: 12/13/2022] Open
Abstract
Temple syndrome (TS) and Kagami-Ogata syndrome (KOS) are imprinting disorders caused by absence or overexpression of genes within a single imprinted cluster on human chromosome 14q32. TS most frequently arises from maternal UPD14 or epimutations/deletions on the paternal chromosome, whereas KOS most frequently arises from paternal UPD14 or epimutations/deletions on the maternal chromosome. In this review, we describe the clinical symptoms and genetic/epigenetic features of this imprinted region. The locus encompasses paternally expressed protein-coding genes (DLK1, RTL1 and DIO3) and maternally expressed lncRNAs (MEG3/GTL2, RTL1as and MEG8), as well as numerous miRNAs and snoRNAs. Control of expression is complex, with three differentially methylated regions regulating germline, placental and tissue-specific transcription. The strong conserved synteny between mouse chromosome 12aF1 and human chromosome 14q32 has enabled the use of mouse models to elucidate imprinting mechanisms and decipher the contribution of genes to the symptoms of TS and KOS. In this review, we describe relevant mouse models and highlight their value to better inform treatment options for long-term management of TS and KOS patients.
Collapse
Affiliation(s)
- Rexxi Prasasya
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kristen V Grotheer
- Department of Medical Sciences, Hackensack Meridian School of Medicine at Seton Hall University, 340 Kingsland Street, Building 123, Nutley, NJ 07110, USA
| | - Linda D Siracusa
- Department of Medical Sciences, Hackensack Meridian School of Medicine at Seton Hall University, 340 Kingsland Street, Building 123, Nutley, NJ 07110, USA
| | - Marisa S Bartolomei
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| |
Collapse
|
40
|
Liu N, Low WY, Alinejad-Rokny H, Pederson S, Sadlon T, Barry S, Breen J. Seeing the forest through the trees: prioritising potentially functional interactions from Hi-C. Epigenetics Chromatin 2021; 14:41. [PMID: 34454581 PMCID: PMC8399707 DOI: 10.1186/s13072-021-00417-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/19/2021] [Indexed: 11/30/2022] Open
Abstract
Eukaryotic genomes are highly organised within the nucleus of a cell, allowing widely dispersed regulatory elements such as enhancers to interact with gene promoters through physical contacts in three-dimensional space. Recent chromosome conformation capture methodologies such as Hi-C have enabled the analysis of interacting regions of the genome providing a valuable insight into the three-dimensional organisation of the chromatin in the nucleus, including chromosome compartmentalisation and gene expression. Complicating the analysis of Hi-C data, however, is the massive amount of identified interactions, many of which do not directly drive gene function, thus hindering the identification of potentially biologically functional 3D interactions. In this review, we collate and examine the downstream analysis of Hi-C data with particular focus on methods that prioritise potentially functional interactions. We classify three groups of approaches: structural-based discovery methods, e.g. A/B compartments and topologically associated domains, detection of statistically significant chromatin interactions, and the use of epigenomic data integration to narrow down useful interaction information. Careful use of these three approaches is crucial to successfully identifying potentially functional interactions within the genome.
Collapse
Affiliation(s)
- Ning Liu
- Computational & Systems Biology, Precision Medicine Theme, South Australian Health & Medical Research Institute, SA, 5000, Adelaide, Australia
- Robinson Research Institute, University of Adelaide, SA, 5005, Adelaide, Australia
- Adelaide Medical School, University of Adelaide, SA, 5005, Adelaide, Australia
| | - Wai Yee Low
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, 5371, Australia
| | - Hamid Alinejad-Rokny
- BioMedical Machine Learning Lab, The Graduate School of Biomedical Engineering, The University of New South Wales, NSW, 2052, Sydney, Australia
- Core Member of UNSW Data Science Hub, The University of New South Wales, 2052, Sydney, Australia
| | - Stephen Pederson
- Adelaide Medical School, University of Adelaide, SA, 5005, Adelaide, Australia
- Dame Roma Mitchell Cancer Research Laboratories (DRMCRL), Adelaide Medical School, University of Adelaide, SA, 5005, Adelaide, Australia
| | - Timothy Sadlon
- Robinson Research Institute, University of Adelaide, SA, 5005, Adelaide, Australia
- Women's & Children's Health Network, SA, 5006, North Adelaide, Australia
| | - Simon Barry
- Robinson Research Institute, University of Adelaide, SA, 5005, Adelaide, Australia
- Core Member of UNSW Data Science Hub, The University of New South Wales, 2052, Sydney, Australia
- Women's & Children's Health Network, SA, 5006, North Adelaide, Australia
| | - James Breen
- Computational & Systems Biology, Precision Medicine Theme, South Australian Health & Medical Research Institute, SA, 5000, Adelaide, Australia.
- Robinson Research Institute, University of Adelaide, SA, 5005, Adelaide, Australia.
- Adelaide Medical School, University of Adelaide, SA, 5005, Adelaide, Australia.
- South Australian Genomics Centre (SAGC), South Australian Health & Medical Research Institute (SAHMRI), SA, 5000, Adelaide, Australia.
| |
Collapse
|
41
|
Exploring chromatin structural roles of non-coding RNAs at imprinted domains. Biochem Soc Trans 2021; 49:1867-1879. [PMID: 34338292 PMCID: PMC8421051 DOI: 10.1042/bst20210758] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 12/11/2022]
Abstract
Different classes of non-coding RNA (ncRNA) influence the organization of chromatin. Imprinted gene domains constitute a paradigm for exploring functional long ncRNAs (lncRNAs). Almost all express an lncRNA in a parent-of-origin dependent manner. The mono-allelic expression of these lncRNAs represses close by and distant protein-coding genes, through diverse mechanisms. Some control genes on other chromosomes as well. Interestingly, several imprinted chromosomal domains show a developmentally regulated, chromatin-based mechanism of imprinting with apparent similarities to X-chromosome inactivation. At these domains, the mono-allelic lncRNAs show a relatively stable, focal accumulation in cis. This facilitates the recruitment of Polycomb repressive complexes, lysine methyltranferases and other nuclear proteins — in part through direct RNA–protein interactions. Recent chromosome conformation capture and microscopy studies indicate that the focal aggregation of lncRNA and interacting proteins could play an architectural role as well, and correlates with close positioning of target genes. Higher-order chromatin structure is strongly influenced by CTCF/cohesin complexes, whose allelic association patterns and actions may be influenced by lncRNAs as well. Here, we review the gene-repressive roles of imprinted non-coding RNAs, particularly of lncRNAs, and discuss emerging links with chromatin architecture.
Collapse
|
42
|
Chai P, Yu J, Jia R, Wen X, Ding T, Zhang X, Ni H, Jia R, Ge S, Zhang H, Fan X. Generation of onco-enhancer enhances chromosomal remodeling and accelerates tumorigenesis. Nucleic Acids Res 2020; 48:12135-12150. [PMID: 33196849 PMCID: PMC7708045 DOI: 10.1093/nar/gkaa1051] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 10/16/2020] [Accepted: 10/22/2020] [Indexed: 01/09/2023] Open
Abstract
Chromatin remodeling impacts the structural neighborhoods and regulates gene expression. However, the role of enhancer-guided chromatin remodeling in the gene regulation remains unclear. Here, using RNA-seq and ChIP-seq, we identified for the first time that neurotensin (NTS) serves as a key oncogene in uveal melanoma and that CTCF interacts with the upstream enhancer of NTS and orchestrates an 800 kb chromosomal loop between the promoter and enhancer. Intriguingly, this novel CTCF-guided chromatin loop was ubiquitous in a cohort of tumor patients. In addition, a disruption in this chromosomal interaction prevented the histone acetyltransferase EP300 from embedding in the promoter of NTS and resulted in NTS silencing. Most importantly, in vitro and in vivo experiments showed that the ability of tumor formation was significantly suppressed via deletion of the enhancer by CRISPR-Cas9. These studies delineate a novel onco-enhancer guided epigenetic mechanism and provide a promising therapeutic concept for disease therapy.
Collapse
Affiliation(s)
- Peiwei Chai
- Department of Ophthalmology, Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, P. R. China
| | - Jie Yu
- Department of Ophthalmology, Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, P. R. China
| | - Ruobing Jia
- Department of Ophthalmology, Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, P. R. China
| | - Xuyang Wen
- Department of Ophthalmology, Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, P. R. China
| | - Tianyi Ding
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai, P. R. China.,Frontier Science Research Center for Stem Cells, Tongji University, Shanghai, 200092, P. R. China
| | - Xiaoyu Zhang
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai, P. R. China.,Frontier Science Research Center for Stem Cells, Tongji University, Shanghai, 200092, P. R. China
| | - Hongyan Ni
- Department of Ophthalmology, Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, P. R. China
| | - Renbing Jia
- Department of Ophthalmology, Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, P. R. China
| | - Shengfang Ge
- Department of Ophthalmology, Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, P. R. China
| | - He Zhang
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai, P. R. China.,Frontier Science Research Center for Stem Cells, Tongji University, Shanghai, 200092, P. R. China
| | - Xianqun Fan
- Department of Ophthalmology, Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, P. R. China
| |
Collapse
|
43
|
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.
Collapse
Affiliation(s)
- Tiantian Ye
- Genetics, Genomics and Bioinformatics Program
| | - Wenxiu Ma
- Department of Statistics, University of California Riverside, Riverside, CA 92521, USA
| |
Collapse
|
44
|
Arévalo L, Gardner S, Campbell P. Haldane's rule in the placenta: Sex-biased misregulation of the Kcnq1 imprinting cluster in hybrid mice. Evolution 2020; 75:86-100. [PMID: 33215684 DOI: 10.1111/evo.14132] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 10/08/2020] [Accepted: 10/25/2020] [Indexed: 12/15/2022]
Abstract
Hybrid phenotypes that contribute to postzygotic reproductive isolation often exhibit pronounced asymmetry, both between reciprocal crosses and between the sexes in accordance with Haldane's rule. Inviability in mammalian hybrids is associated with parent-of-origin placental growth abnormalities for which misregulation of imprinted gene (IGs) is the leading candidate mechanism. However, direct evidence for the involvement of IGs in hybrid growth dysplasia is limited. We used transcriptome and reduced representation bisulfite sequencing to conduct the first genome-scale assessment of the contribution of IGs to parent-of-origin placental growth dysplasia in the cross between the house mouse (Mus musculus domesticus) and the Algerian mouse (Mus spretus). IGs with transgressive expression and methylation were concentrated in the Kcnq1 cluster, which contains causal genes for prenatal growth abnormalities in mice and humans. Hypermethylation of the cluster's imprinting control region, and consequent misexpression of the genes Phlda2 and Ascl2, is a strong candidate mechanism for transgressive placental undergrowth. Transgressive placental and gene regulatory phenotypes, including expression and methylation in the Kcnq1 cluster, were more extreme in hybrid males. Although consistent with Haldane's rule, male-biased defects are unexpected in rodent placenta because the X-chromosome is effectively hemizygous in both sexes. In search of an explanation, we found evidence of leaky imprinted (paternal) X-chromosome inactivation in hybrid female placenta, an epigenetic disturbance that may buffer females from the effects of X-linked incompatibilities to which males are fully exposed. Sex differences in chromatin structure on the X and sex-biased maternal effects are nonmutually exclusive alternative explanations for adherence to Haldane's rule in hybrid placenta. The results of this study contribute to understanding the genetic basis of hybrid inviability in mammals, and the role of IGs in speciation.
Collapse
Affiliation(s)
- Lena Arévalo
- Department of Integrative Biology, Oklahoma State University, Stillwater, Oklahoma, 74078.,Current Address: Department of Developmental Pathology, University of Bonn Medical School, Bonn, DE-53127, Germany
| | - Sarah Gardner
- Department of Integrative Biology, Oklahoma State University, Stillwater, Oklahoma, 74078.,Current Address: Department of Evolution, Ecology, and Organismal Biology, University of California Riverside, Riverside, California, 92521
| | - Polly Campbell
- Department of Integrative Biology, Oklahoma State University, Stillwater, Oklahoma, 74078.,Current Address: Department of Evolution, Ecology, and Organismal Biology, University of California Riverside, Riverside, California, 92521
| |
Collapse
|
45
|
Xu L, Pan J, Ding Y, Pan H. Survival-Associated Alternative Splicing Events and Prognostic Signatures in Pancreatic Cancer. Front Genet 2020; 11:522383. [PMID: 33193606 PMCID: PMC7554623 DOI: 10.3389/fgene.2020.522383] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 09/14/2020] [Indexed: 12/27/2022] Open
Abstract
Background Alternative splicing (AS) is reported to be related to the biological process of multiple malignancies. This study is conducted to identify survival-associated AS events and prognostic signatures that may serve as prognostic indicators for pancreatic cancer (PC). Methods Univariate Cox analysis was used to determine the survival-associated AS events in PC. Prognostic signatures were constructed by LASSO Cox analysis based on seven types of survival-associated AS events. The correlation between the expression of splicing factors (SFs) and the percent spliced in values of AS events was analyzed by Pearson correlation analysis. Risk scores were calculated to determine high- or low-risk patients with different types of AS events. Gene functional annotation analysis was performed to reveal pathways in which prognostic AS is enriched. Results A total of 45,313 AS events in 10,624 genes were observed, and there were 1,565 AS events in 1,223 genes significantly correlated with overall survival for PC. Kaplan–Meier analysis, receiver-operator characteristic curve, univariate and multivariate Cox analyses showed that AS prognostic signatures could effectively predict prognosis of patients with PC. Splicing factors–AS regulatory networks were established to demonstrate the interaction between AS events and SFs. Conclusion The survival-associated AS events and prognostic signatures identified in this study can serve as useful tool for predicting prognosis of patients with PC. Moreover, the SF–AS regulatory networks may provide clues for the mechanisms underlying AS in PC.
Collapse
Affiliation(s)
- Lichao Xu
- Department of Interventional Radiology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jingxin Pan
- Department of Internal Medicine, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Yanni Ding
- Department of Surgery, Shaan Xi Provincial Tumor Hospital, Xi'an City, China
| | - Hongda Pan
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| |
Collapse
|
46
|
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.
Collapse
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.
| |
Collapse
|
47
|
Acemel RD, Tena JJ, Gomez-Skarmeta JL, Fibla J, Royo JL. Straightforward protocol for allele-specific chromatin conformation capture. Gene 2020; 767:145185. [PMID: 32998049 DOI: 10.1016/j.gene.2020.145185] [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: 04/29/2020] [Revised: 09/03/2020] [Accepted: 09/23/2020] [Indexed: 11/26/2022]
Abstract
A key advance in our understanding of gene regulation came with the finding that the genome undergoes three-dimensional nuclear folding in a genetically determined process. This 3D conformation directly influences the association between enhancers and their target promoters. This complex interplay has been proven to be essential for gene regulation, and genetic variants affecting this process have been associated to human diseases. The development of new technologies that quantify these DNA interactions represented a revolution in the field. High throughput techniques like HiC provide a general picture of chromatin topology. However, they often lack resolution to evidence subtle effects that single nucleotide polymorphisms exert over the contacts between cis-regulatory regions and target promoters. Here we propose a cost-efficient approach to perform allele-specific chromatin conformation analysis. As a proof of concept, we analyzed the impact of a common deletion mapping between SIRPB1 promoter and one of its downstream enhancers.
Collapse
Affiliation(s)
- R D Acemel
- Andalusian Centre for Developmental Biology, University Pablo de Olavide-CSIC-Junta de Andalucia, Sevilla, Spain
| | - J J Tena
- Andalusian Centre for Developmental Biology, University Pablo de Olavide-CSIC-Junta de Andalucia, Sevilla, Spain
| | - J L Gomez-Skarmeta
- Andalusian Centre for Developmental Biology, University Pablo de Olavide-CSIC-Junta de Andalucia, Sevilla, Spain
| | - J Fibla
- Institute of Biomedical Research of Lleida, University of Lleida, Lleida, Spain
| | - J L Royo
- Department of Surgery, Biochemistry, and Immunology, School of Medicine, University of Malaga, 29071 Malaga, Spain.
| |
Collapse
|
48
|
Klobučar T, Kreibich E, Krueger F, Arez M, Pólvora-Brandão D, von Meyenn F, da Rocha ST, Eckersley-Maslin M. IMPLICON: an ultra-deep sequencing method to uncover DNA methylation at imprinted regions. Nucleic Acids Res 2020; 48:e92. [PMID: 32621604 PMCID: PMC7498334 DOI: 10.1093/nar/gkaa567] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 06/16/2020] [Accepted: 07/02/2020] [Indexed: 12/19/2022] Open
Abstract
Genomic imprinting is an epigenetic phenomenon leading to parental allele-specific expression. Dosage of imprinted genes is crucial for normal development and its dysregulation accounts for several human disorders. This unusual expression pattern is mostly dictated by differences in DNA methylation between parental alleles at specific regulatory elements known as imprinting control regions (ICRs). Although several approaches can be used for methylation inspection, we lack an easy and cost-effective method to simultaneously measure DNA methylation at multiple imprinted regions. Here, we present IMPLICON, a high-throughput method measuring DNA methylation levels at imprinted regions with base-pair resolution and over 1000-fold coverage. We adapted amplicon bisulfite-sequencing protocols to design IMPLICON for ICRs in adult tissues of inbred mice, validating it in hybrid mice from reciprocal crosses for which we could discriminate methylation profiles in the two parental alleles. Lastly, we developed a human version of IMPLICON and detected imprinting errors in embryonic and induced pluripotent stem cells. We also provide rules and guidelines to adapt this method for investigating the DNA methylation landscape of any set of genomic regions. In summary, IMPLICON is a rapid, cost-effective and scalable method, which could become the gold standard in both imprinting research and diagnostics.
Collapse
Affiliation(s)
- Tajda Klobučar
- Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Elisa Kreibich
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Felix Krueger
- Bioinformatics Group, Babraham Institute, Cambridge CB22 3AT, UK
| | - Maria Arez
- Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Duarte Pólvora-Brandão
- Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | | | - Simão Teixeira da Rocha
- Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | | |
Collapse
|
49
|
Varrault A, Dubois E, Le Digarcher A, Bouschet T. Quantifying Genomic Imprinting at Tissue and Cell Resolution in the Brain. EPIGENOMES 2020; 4:21. [PMID: 34968292 PMCID: PMC8594728 DOI: 10.3390/epigenomes4030021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/24/2020] [Accepted: 09/01/2020] [Indexed: 02/06/2023] Open
Abstract
Imprinted genes are a group of ~150 genes that are preferentially expressed from one parental allele owing to epigenetic marks asymmetrically distributed on inherited maternal and paternal chromosomes. Altered imprinted gene expression causes human brain disorders such as Prader-Willi and Angelman syndromes and additional rare brain diseases. Research data principally obtained from the mouse model revealed how imprinted genes act in the normal and pathological brain. However, a better understanding of imprinted gene functions calls for building detailed maps of their parent-of-origin-dependent expression and of associated epigenetic signatures. Here we review current methods for quantifying genomic imprinting at tissue and cell resolutions, with a special emphasis on methods to detect parent-of-origin dependent expression and their applications to the brain. We first focus on bulk RNA-sequencing, the main method to detect parent-of-origin-dependent expression transcriptome-wide. We discuss the benefits and caveats of bulk RNA-sequencing and provide a guideline to use it on F1 hybrid mice. We then review methods for detecting parent-of-origin-dependent expression at cell resolution, including single-cell RNA-seq, genetic reporters, and molecular probes. Finally, we provide an overview of single-cell epigenomics technologies that profile additional features of genomic imprinting, including DNA methylation, histone modifications and chromatin conformation and their combination into sc-multimodal omics approaches, which are expected to yield important insights into genomic imprinting in individual brain cells.
Collapse
Affiliation(s)
- Annie Varrault
- Institut de Génomique Fonctionnelle (IGF), Univ. Montpellier, CNRS, INSERM, 34094 Montpellier, France; (A.V.); (A.L.D.)
| | - Emeric Dubois
- Montpellier GenomiX (MGX), Univ. Montpellier, CNRS, INSERM, 34094 Montpellier, France;
| | - Anne Le Digarcher
- Institut de Génomique Fonctionnelle (IGF), Univ. Montpellier, CNRS, INSERM, 34094 Montpellier, France; (A.V.); (A.L.D.)
| | - Tristan Bouschet
- Institut de Génomique Fonctionnelle (IGF), Univ. Montpellier, CNRS, INSERM, 34094 Montpellier, France; (A.V.); (A.L.D.)
| |
Collapse
|
50
|
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.
Collapse
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:
| |
Collapse
|