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Epigenome analysis of HELLS in liver cancer [methylation]

ABSTRACT: Epigenome analysis of HELLS in liver cancer [methylation]

PROVIDER: PRJNA875945 | ENA |

REPOSITORIES: ENA

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Epigenome analysis of HELLS in liver cancer

Project description:Epigenome analysis of HELLS in liver cancer

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Epigenome analysis of HELLS in liver cancer [methylation]

Project description:Genome wide DNA methylation profiling of shControl and shHELLS in HepG2. The Illumina Infinium MethylationEPIC BeadChip kits was used to obtain DNA methylation profiles.

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HELLS knockdown or overexpression in liver cancer cells

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HELLS is required for DNA methylation at human satellite repeats [RNA-seq]

Project description:HELLS is a known chromatin remodeler, but its specific genomic targets have not been sufficiently described. Here, we report the generation of HELLS knockout human pluripotent cells and through telomere-to-telomere mapping of whole genome bisulfite sequencing data combined with ATAC-sequencing, we discovered a striking loss of DNA methylation over inaccessible, satellite repeats. Our study further clarifies the role of HELLS and provides insights into functional consequences through its deregulation in diseases.

2025-06-23 | GSE296398 | GEO

Impact of Hells loss-of-function on DNA methylation in B cells during humoral immune responses: kinetic comparison of Mb1-Hells knockout and control mice by enzymatic-methyl sequencing

Project description:We are interested in deciphering the mechanism by which DNA methylation in late B cell differentiation affects humoral immune response. We were using enzymatic-methyl sequencing (EM-seq) and chose to study a very rare immunodeficiency called ICF type 4, where a point mutation in a gene encoding the protein HELLS causes a lack of both circulating antibodies and memory B cells in human. HELLS is a chromatin remodeler, that allows for DNA methylation to occur.

2023-07-27 | E-MTAB-12609 | biostudies-arrayexpress

Impact of Hells loss-of-function on DNA methylation in B cells during humoral immune responses: kinetic comparison of Mb1-Hells knockout and control mice by single-cell RNA sequencing

Project description:We are interested in deciphering the mechanism by which DNA methylation in late B cell differentiation affects humoral immune response. We chose to study a very rare immunodeficiency called ICF type 4, where a point mutation in a gene encoding the protein HELLS causes a lack of both circulating antibodies and memory B cells in human. HELLS is a chromatin remodeler, that allows for DNA methylation to occur. Using a Hells conditional knock-out in B cells, we measured the kinetics of the immune B cell response, following immunization with NP-CGG, and show a lack of memory and plasma cells accompanied by a defect in germinal center maintenance, but not by its formation. Single cell RNAseq of cell sorted naive, germinal center B cells and memory B cells at day 7 and day 14 post NP-immunization helped us better characterize the phenotype.

2023-07-25 | E-MTAB-12499 | biostudies-arrayexpress

The role of HELLS in human induced pluripotent stem cells

Project description:DNA methylation is essential for genome integrity and involves multi-layered chromatin interac-tions that require remodeling proteins like the Helicase, Lymphoid-specific (HELLS). Here, we generate HELLS and de novo DNA methyltransferase 3 A and B (DNMT3A/B) knockout human pluripotent stem cells and assemble telomere-to-telomere maps of whole genome bisulfite se-quencing data combined with ATAC-sequencing. Disrupting HELLS induces a global loss of DNA methylation that is distinct from the de novo DNMTs, in particular over peri/centromeric satellite repeats as defined in the telomere-to-telomere genome assembly. However, HELLS is dispen-sable for local enhancer remodeling and the potential to differentiate into the three germ layers. Taken together, these findings further clarify the genomic targets and role of HELLS in human cells.

2025-06-23 | GSE241688 | GEO

Epigenome analysis of HELLS in liver cancer

Project description:Genome wide H3K9me3 profiling of shControl and shHELLS in HepG2 Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3K9me3 in HepG2

2025-04-09 | GSE212429 | GEO

The role of HELLS in human induced pluripotent stem cells II

Project description:interactions that require remodeling proteins like the Helicase, Lymphoid-specific (HELLS). Here, we generate HELLS and de novo DNA methyltransferase 3 A and B (DNMT3A/B) knockout hu-man pluripotent stem cells and assemble telomere-to-telomere maps of whole genome bisulfite sequencing data combined with ATAC-sequencing. Disrupting HELLS induces a global loss of DNA methylation that is distinct from the de novo DNMTs, in particular over peri/centromeric satellite repeats as defined in the telomere-to-telomere genome assembly. However, HELLS is dispensable for local enhancer remodeling and the potential to differentiate into the three germ layers. Taken together, these findings further clarify the genomic targets and role of HELLS in human cells.

2025-06-23 | GSE250465 | GEO

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