The mismatch-repair proteins MSH2 and MSH6 interact with the imprinting control regions through the ZFP57-KAP1 complex
Abstract Background Imprinting Control Regions (ICRs) are CpG-rich sequences acquiring differential methylation in the female and male germline and maintaining it in a parental origin-specific manner in somatic cells. Despite their expected high mutation rate due to spontaneous deamination of methyl...
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| Format: | Article |
| Language: | English |
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BMC
2022-08-01
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| Series: | Epigenetics & Chromatin |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13072-022-00462-7 |
| _version_ | 1828293637368184832 |
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| author | Basilia Acurzio Francesco Cecere Carlo Giaccari Ankit Verma Rosita Russo Mariangela Valletta Bruno Hay Mele Claudia Angelini Angela Chambery Andrea Riccio |
| author_facet | Basilia Acurzio Francesco Cecere Carlo Giaccari Ankit Verma Rosita Russo Mariangela Valletta Bruno Hay Mele Claudia Angelini Angela Chambery Andrea Riccio |
| author_sort | Basilia Acurzio |
| collection | DOAJ |
| description | Abstract Background Imprinting Control Regions (ICRs) are CpG-rich sequences acquiring differential methylation in the female and male germline and maintaining it in a parental origin-specific manner in somatic cells. Despite their expected high mutation rate due to spontaneous deamination of methylated cytosines, ICRs show conservation of CpG-richness and CpG-containing transcription factor binding sites in mammalian species. However, little is known about the mechanisms contributing to the maintenance of a high density of methyl CpGs at these loci. Results To gain functional insights into the mechanisms for maintaining CpG methylation, we sought to identify the proteins binding the methylated allele of the ICRs by determining the interactors of ZFP57 that recognizes a methylated hexanucleotide motif of these DNA regions in mouse ESCs. By using a tagged approach coupled to LC–MS/MS analysis, we identified several proteins, including factors involved in mRNA processing/splicing, chromosome organization, transcription and DNA repair processes. The presence of the post-replicative mismatch-repair (MMR) complex components MSH2 and MSH6 among the identified ZFP57 interactors prompted us to investigate their DNA binding profile by chromatin immunoprecipitation and sequencing. We demonstrated that MSH2 was enriched at gene promoters overlapping unmethylated CpG islands and at repeats. We also found that both MSH2 and MSH6 interacted with the methylated allele of the ICRs, where their binding to DNA was mediated by the ZFP57/KAP1 complex. Conclusions Our findings show that the MMR complex is concentrated on gene promoters and repeats in mouse ESCs, suggesting that maintaining the integrity of these regions is a primary function of highly proliferating cells. Furthermore, the demonstration that MSH2/MSH6 are recruited to the methylated allele of the ICRs through interaction with ZFP57/KAP1 suggests a role of the MMR complex in the maintenance of the integrity of these regulatory regions and evolution of genomic imprinting in mammalian species. |
| first_indexed | 2024-04-13T11:23:59Z |
| format | Article |
| id | doaj.art-2085eb33bc934ff1a983e8a3a6b76346 |
| institution | Directory Open Access Journal |
| issn | 1756-8935 |
| language | English |
| last_indexed | 2024-04-13T11:23:59Z |
| publishDate | 2022-08-01 |
| publisher | BMC |
| record_format | Article |
| series | Epigenetics & Chromatin |
| spelling | doaj.art-2085eb33bc934ff1a983e8a3a6b763462022-12-22T02:48:44ZengBMCEpigenetics & Chromatin1756-89352022-08-0115111310.1186/s13072-022-00462-7The mismatch-repair proteins MSH2 and MSH6 interact with the imprinting control regions through the ZFP57-KAP1 complexBasilia Acurzio0Francesco Cecere1Carlo Giaccari2Ankit Verma3Rosita Russo4Mariangela Valletta5Bruno Hay Mele6Claudia Angelini7Angela Chambery8Andrea Riccio9Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania “Luigi Vanvitelli”Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania “Luigi Vanvitelli”Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania “Luigi Vanvitelli”Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania “Luigi Vanvitelli”Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania “Luigi Vanvitelli”Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania “Luigi Vanvitelli”Department of Biology, Università Degli Studi Di Napoli “Federico II”Istituto Per Le Applicazioni del Calcolo “Mauro Picone” (IAC), CNRDepartment of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania “Luigi Vanvitelli”Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania “Luigi Vanvitelli”Abstract Background Imprinting Control Regions (ICRs) are CpG-rich sequences acquiring differential methylation in the female and male germline and maintaining it in a parental origin-specific manner in somatic cells. Despite their expected high mutation rate due to spontaneous deamination of methylated cytosines, ICRs show conservation of CpG-richness and CpG-containing transcription factor binding sites in mammalian species. However, little is known about the mechanisms contributing to the maintenance of a high density of methyl CpGs at these loci. Results To gain functional insights into the mechanisms for maintaining CpG methylation, we sought to identify the proteins binding the methylated allele of the ICRs by determining the interactors of ZFP57 that recognizes a methylated hexanucleotide motif of these DNA regions in mouse ESCs. By using a tagged approach coupled to LC–MS/MS analysis, we identified several proteins, including factors involved in mRNA processing/splicing, chromosome organization, transcription and DNA repair processes. The presence of the post-replicative mismatch-repair (MMR) complex components MSH2 and MSH6 among the identified ZFP57 interactors prompted us to investigate their DNA binding profile by chromatin immunoprecipitation and sequencing. We demonstrated that MSH2 was enriched at gene promoters overlapping unmethylated CpG islands and at repeats. We also found that both MSH2 and MSH6 interacted with the methylated allele of the ICRs, where their binding to DNA was mediated by the ZFP57/KAP1 complex. Conclusions Our findings show that the MMR complex is concentrated on gene promoters and repeats in mouse ESCs, suggesting that maintaining the integrity of these regions is a primary function of highly proliferating cells. Furthermore, the demonstration that MSH2/MSH6 are recruited to the methylated allele of the ICRs through interaction with ZFP57/KAP1 suggests a role of the MMR complex in the maintenance of the integrity of these regulatory regions and evolution of genomic imprinting in mammalian species.https://doi.org/10.1186/s13072-022-00462-7LC–MS/MSChip-seqAllele-specific analysisCpG islandsMethyl CpGGenomic imprinting |
| spellingShingle | Basilia Acurzio Francesco Cecere Carlo Giaccari Ankit Verma Rosita Russo Mariangela Valletta Bruno Hay Mele Claudia Angelini Angela Chambery Andrea Riccio The mismatch-repair proteins MSH2 and MSH6 interact with the imprinting control regions through the ZFP57-KAP1 complex Epigenetics & Chromatin LC–MS/MS Chip-seq Allele-specific analysis CpG islands Methyl CpG Genomic imprinting |
| title | The mismatch-repair proteins MSH2 and MSH6 interact with the imprinting control regions through the ZFP57-KAP1 complex |
| title_full | The mismatch-repair proteins MSH2 and MSH6 interact with the imprinting control regions through the ZFP57-KAP1 complex |
| title_fullStr | The mismatch-repair proteins MSH2 and MSH6 interact with the imprinting control regions through the ZFP57-KAP1 complex |
| title_full_unstemmed | The mismatch-repair proteins MSH2 and MSH6 interact with the imprinting control regions through the ZFP57-KAP1 complex |
| title_short | The mismatch-repair proteins MSH2 and MSH6 interact with the imprinting control regions through the ZFP57-KAP1 complex |
| title_sort | mismatch repair proteins msh2 and msh6 interact with the imprinting control regions through the zfp57 kap1 complex |
| topic | LC–MS/MS Chip-seq Allele-specific analysis CpG islands Methyl CpG Genomic imprinting |
| url | https://doi.org/10.1186/s13072-022-00462-7 |
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