Altered chromatin landscape and 3D interactions associated with primary constitutional MLH1 epimutations
Abstract Background Lynch syndrome (LS), characterised by an increased risk for cancer, is mainly caused by germline pathogenic variants affecting a mismatch repair gene (MLH1, MSH2, MSH6, PMS2). Occasionally, LS may be caused by constitutional MLH1 epimutation (CME) characterised by soma-wide methy...
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BMC
2024-12-01
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| Online Access: | https://doi.org/10.1186/s13148-024-01770-3 |
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| author | Paula Climent-Cantó Marc Subirana-Granés Mireia Ramos-Rodríguez Estela Dámaso Fátima Marín Covadonga Vara Beatriz Pérez-González Helena Raurell Elisabet Munté José Luis Soto Ángel Alonso GiWon Shin Hanlee Ji Megan Hitchins Gabriel Capellá Lorenzo Pasquali Marta Pineda |
| author_facet | Paula Climent-Cantó Marc Subirana-Granés Mireia Ramos-Rodríguez Estela Dámaso Fátima Marín Covadonga Vara Beatriz Pérez-González Helena Raurell Elisabet Munté José Luis Soto Ángel Alonso GiWon Shin Hanlee Ji Megan Hitchins Gabriel Capellá Lorenzo Pasquali Marta Pineda |
| author_sort | Paula Climent-Cantó |
| collection | DOAJ |
| description | Abstract Background Lynch syndrome (LS), characterised by an increased risk for cancer, is mainly caused by germline pathogenic variants affecting a mismatch repair gene (MLH1, MSH2, MSH6, PMS2). Occasionally, LS may be caused by constitutional MLH1 epimutation (CME) characterised by soma-wide methylation of one allele of the MLH1 promoter. Most of these are “primary” epimutations, arising de novo without any apparent underlying cis-genetic cause, and are reversible between generations. We aimed to characterise genetic and gene regulatory changes associated with primary CME to elucidate possible underlying molecular mechanisms. Methods Four carriers of a primary CME and three non-methylated relatives carrying the same genetic haplotype were included. Genetic alterations were sought using linked-read WGS in blood DNA. Transcriptome (RNA-seq), chromatin landscape (ATAC-seq, H3K27ac CUT&Tag) and 3D chromatin interactions (UMI-4C) were studied in lymphoblastoid cell lines. The MLH1 promoter SNP (c.-93G > A, rs1800734) was used as a reporter in heterozygotes to assess allele-specific chromatin conformation states. Results MLH1 epimutant alleles presented a closed chromatin conformation and decreased levels of H3K27ac, as compared to the unmethylated allele. Moreover, the epimutant MLH1 promoter exhibited differential 3D chromatin contacts, including lost and gained interactions with distal regulatory elements. Of note, rare genetic alterations potentially affecting transcription factor binding sites were found in the promoter-contacting region of CME carriers. Conclusions Primary CMEs present allele-specific differential interaction patterns with neighbouring genes and regulatory elements. The role of the identified cis-regulatory regions in the molecular mechanism underlying the origin and maintenance of CME requires further investigation. |
| format | Article |
| id | doaj-art-b0709bf94557455ab1ed3d02b07cc5b7 |
| institution | Kabale University |
| issn | 1868-7083 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | BMC |
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| series | Clinical Epigenetics |
| spelling | doaj-art-b0709bf94557455ab1ed3d02b07cc5b72025-01-05T12:33:57ZengBMCClinical Epigenetics1868-70832024-12-0116111510.1186/s13148-024-01770-3Altered chromatin landscape and 3D interactions associated with primary constitutional MLH1 epimutationsPaula Climent-Cantó0Marc Subirana-Granés1Mireia Ramos-Rodríguez2Estela Dámaso3Fátima Marín4Covadonga Vara5Beatriz Pérez-González6Helena Raurell7Elisabet Munté8José Luis Soto9Ángel Alonso10GiWon Shin11Hanlee Ji12Megan Hitchins13Gabriel Capellá14Lorenzo Pasquali15Marta Pineda16Hereditary Cancer Group, ONCOBELL Program, Institut d’Investigació Biomèdica de Bellvitge (IDIBELL)Department of Medicine and Life Sciences, Universitat Pompeu FabraDepartment of Medicine and Life Sciences, Universitat Pompeu FabraHereditary Cancer Group, ONCOBELL Program, Institut d’Investigació Biomèdica de Bellvitge (IDIBELL)Hereditary Cancer Group, ONCOBELL Program, Institut d’Investigació Biomèdica de Bellvitge (IDIBELL)Hereditary Cancer Group, ONCOBELL Program, Institut d’Investigació Biomèdica de Bellvitge (IDIBELL)Department of Medicine and Life Sciences, Universitat Pompeu FabraDepartment of Medicine and Life Sciences, Universitat Pompeu FabraHereditary Cancer Group, ONCOBELL Program, Institut d’Investigació Biomèdica de Bellvitge (IDIBELL)Molecular Genetics Laboratory, Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO), University Hospital of ElcheGenomics Medicine Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNADepartment of Medicine (Oncology), Stanford Cancer Institute, Stanford UniversityDepartment of Medicine (Oncology), Stanford Cancer Institute, Stanford UniversityDepartment of Biomedical Sciences, Cedars-Sinai Medical CenterHereditary Cancer Group, ONCOBELL Program, Institut d’Investigació Biomèdica de Bellvitge (IDIBELL)Department of Medicine and Life Sciences, Universitat Pompeu FabraHereditary Cancer Group, ONCOBELL Program, Institut d’Investigació Biomèdica de Bellvitge (IDIBELL)Abstract Background Lynch syndrome (LS), characterised by an increased risk for cancer, is mainly caused by germline pathogenic variants affecting a mismatch repair gene (MLH1, MSH2, MSH6, PMS2). Occasionally, LS may be caused by constitutional MLH1 epimutation (CME) characterised by soma-wide methylation of one allele of the MLH1 promoter. Most of these are “primary” epimutations, arising de novo without any apparent underlying cis-genetic cause, and are reversible between generations. We aimed to characterise genetic and gene regulatory changes associated with primary CME to elucidate possible underlying molecular mechanisms. Methods Four carriers of a primary CME and three non-methylated relatives carrying the same genetic haplotype were included. Genetic alterations were sought using linked-read WGS in blood DNA. Transcriptome (RNA-seq), chromatin landscape (ATAC-seq, H3K27ac CUT&Tag) and 3D chromatin interactions (UMI-4C) were studied in lymphoblastoid cell lines. The MLH1 promoter SNP (c.-93G > A, rs1800734) was used as a reporter in heterozygotes to assess allele-specific chromatin conformation states. Results MLH1 epimutant alleles presented a closed chromatin conformation and decreased levels of H3K27ac, as compared to the unmethylated allele. Moreover, the epimutant MLH1 promoter exhibited differential 3D chromatin contacts, including lost and gained interactions with distal regulatory elements. Of note, rare genetic alterations potentially affecting transcription factor binding sites were found in the promoter-contacting region of CME carriers. Conclusions Primary CMEs present allele-specific differential interaction patterns with neighbouring genes and regulatory elements. The role of the identified cis-regulatory regions in the molecular mechanism underlying the origin and maintenance of CME requires further investigation.https://doi.org/10.1186/s13148-024-01770-3Lynch syndromeConstitutional MLH1 epimutationMLH1 promoter methylation3D interactionsChromatin structureCis-regulatory regions |
| spellingShingle | Paula Climent-Cantó Marc Subirana-Granés Mireia Ramos-Rodríguez Estela Dámaso Fátima Marín Covadonga Vara Beatriz Pérez-González Helena Raurell Elisabet Munté José Luis Soto Ángel Alonso GiWon Shin Hanlee Ji Megan Hitchins Gabriel Capellá Lorenzo Pasquali Marta Pineda Altered chromatin landscape and 3D interactions associated with primary constitutional MLH1 epimutations Clinical Epigenetics Lynch syndrome Constitutional MLH1 epimutation MLH1 promoter methylation 3D interactions Chromatin structure Cis-regulatory regions |
| title | Altered chromatin landscape and 3D interactions associated with primary constitutional MLH1 epimutations |
| title_full | Altered chromatin landscape and 3D interactions associated with primary constitutional MLH1 epimutations |
| title_fullStr | Altered chromatin landscape and 3D interactions associated with primary constitutional MLH1 epimutations |
| title_full_unstemmed | Altered chromatin landscape and 3D interactions associated with primary constitutional MLH1 epimutations |
| title_short | Altered chromatin landscape and 3D interactions associated with primary constitutional MLH1 epimutations |
| title_sort | altered chromatin landscape and 3d interactions associated with primary constitutional mlh1 epimutations |
| topic | Lynch syndrome Constitutional MLH1 epimutation MLH1 promoter methylation 3D interactions Chromatin structure Cis-regulatory regions |
| url | https://doi.org/10.1186/s13148-024-01770-3 |
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