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Simultaneous identification of DNA variation and methylation at HLA class II locus and immune gene promoters using targeted SureSelect Methyl-Sequencing

ABSTRACT: Simultaneous identification of DNA variation and methylation at HLA class II locus and immune gene promoters using targeted SureSelect Methyl-Sequencing

PROVIDER: PRJNA997991 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR25403306_1.fastq.gz	Fastqsanger.gz
	SRR25403306_2.fastq.gz	Fastqsanger.gz
	SRR25403307_1.fastq.gz	Fastqsanger.gz
	SRR25403307_2.fastq.gz	Fastqsanger.gz
	SRR25403308_1.fastq.gz	Fastqsanger.gz

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Simultaneous identification of DNA variation and methylation at HLA class II locus and immune gene promoters using targeted SureSelect Methyl-Sequencing

Project description:The Human Leukocyte Antigen (HLA) locus associates with a variety of complex diseases, particularly autoimmune and inflammatory conditions. The HLA-DR15 haplotype, for example, confers the major risk for developing Multiple Sclerosis in Caucasians, pinpointing important role in the etiology of this chronic inflammatory disease of the central nervous system. In addition to the protein-coding variants that shape the functional HLA-antigen-T cell interaction, recent studies suggest that the levels of HLA molecule expression, that are epigenetically controlled, also play a role in disease development. However, deciphering the exact molecular mechanisms of the HLA association has been hampered by the tremendous genetic complexity of the locus and a lack of robust approaches to investigate it. Here we developed a method to specifically enrich the genomic DNA from the HLA class II locus (chr6:32,426,802-34,167,129) and proximal promoters of 2,157 immune-relevant genes, utilizing the Agilent RNA-based SureSelect Methyl-Seq Capture method, followed by sequencing to detect genetic and epigenetic variation. We demonstrated successful simultaneous detection of the genetic variation and quantification of DNA methylation levels in the HLA locus. Moreover, by utilizing differentially methylated positions in promoters of immune-related genes, we detected relevant pathways following stimulation of cells. Taken together, we present a method that can be utilized to study the impact of the interplay of genetic and epigenetic regulation in HLA class II region on cellular states in a wide context of HLA haplotypes and diseases.

2023-08-15 | GSE238121 | GEO

Simultaneous detection of DNA variation and methylation at HLA class II locus and immune gene promoters using targeted SureSelect Methyl-Sequencing.

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Identification of epigenetic recovery factor from medicinal-herb (Descurainia sophia) treated asthma based on multi-omics approach [Methyl-Seq]

Project description:Sequencing of bisulfite-converted mouse genomic DNA captured on SureSelect Methyl-Seq

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Methyl-Micro-C

Project description:Simultaneous measurement of epigenetic signatures from the same cell and tissue provides significant benefits for research, especially when resources are limited, and precise analysis is essential. Here, we report a technique called Methyl-Micro-C to simultaneously map chromatin accessibility, interaction, and DNA methylation in the same sample. Methyl-Micro-C enhances the resolution of chromatin interaction and the coverage of CpGs by combining MNase-mediated fragmentation with enzymatic conversion. This technique is relatively straightforward, making it easy for researchers to apply. It also allows for the profiling of three-dimensional epigenomes with consistent chromatin accessibility, interaction, and DNA methylation signals in a cost-efficient manner.

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