EXPERIMENT_TITLE: GSM7731443: HiC Primary Astrocyte, Replicate 1; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Cells were fixed with formaldehyde, then chromatin was digested with multiple restriction enzymes, and DNA was sheared and then size-selected for 200-600 bp fragments Libraries were prepared using the Arima-HiC, Swift Accel-NGS 2S Plus DNA, and Swift 2S Indexing kit, according to manufacturer's instructions.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: The ch12q13 obesity locus is among the most significant childhood obesity loci identified in genome-wide association studies. This locus resides in a non-coding region within FAIM2; thus, the underlying causal variant(s) presumably influence disease susceptibility via an influence on cis-regulation within the genomic region. We implicated rs7132908 as a putative causal variant at this locus leveraging a combination of our inhouse 3D genomic data, public domain datasets, and several computational approaches. Using a luciferase reporter assay in human primary astrocytes, we observed allele-specific cis-regulatory activity of the immediate region harboring rs7132908. Motivated by this finding, we went on to generate isogenic human embryonic stem cell lines homozygous for either rs7132908 allele with CRISPR-Cas9 homology-directed repair to assess changes in gene expression due to genotype and chromatin accessibility throughout a differentiation to hypothalamic neurons, a key cell type known to regulate feeding behavior. We observed that the rs7132908 obesity risk allele influenced the expression of FAIM2 along with other genes, decreased the proportion of neurons produced during differentiation, up-regulated cell death gene sets, and conversely down-regulated neuron differentiation gene sets. We have therefore functionally validated rs7132908 as a causal obesity variant which temporally regulates nearby effector genes at the ch12q13 locus and influences neurodevelopment and survival. Overall design: To identify putative cis-regulatory elements harboring childhood obesity GWAS variants and implicate their effector genes, we performed Hi-C using a human primary astrocyte cell line. During downstream analyses, this data was used in combination with ATAC-seq and RNA-seq in the same cell type, following our established 'variant-to-gene' mapping approach.
SAMPLE_TITLE: HiC Primary Astrocyte, Replicate 1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Lonza NHA"}, {"TAG": "cell line", "VALUE": "Lonza NHA"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null], "@attributes": {"cluster": "public", "filename": "Astrocyte_HiC_A1_S3_R2_001.fastq.gz", "url": "https://sra-pub-src-2.s3.amazonaws.com/SRR25752923/Astrocyte_HiC_A1_S3_R2_001.fastq.gz.1", "size": "164753724968", "date": "2023-08-24 04:27:23", "md5": "c559fa189b656569d26cfefbc378f308", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": [null, null], "@attributes": {"cluster": "public", "filename": "Astrocyte_HiC_A1_S3_R1_001.fastq.gz", "url": "https://sra-pub-src-2.s3.amazonaws.com/SRR25752923/Astrocyte_HiC_A1_S3_R1_001.fastq.gz.1", "size": "158797252227", "date": "2023-08-24 04:15:26", "md5": "06ff7e079ebc648a310730cc69ede7ec", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]