EXPERIMENT_TITLE: GSM7105854: HiC_NC_rep1; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: The in situ Hi-C libraries was performed as previously described (Rao et al., 2014). Briefly, cells were grown to about 70%-80 % confluence, washed with PBS, fixed in 1% formaldehyde were suspended in Hi-C lysis buffer, to which 100 U MobI restriction enzyme (NEB, R0147) was added for overnight chromatin digestion. Free ends were labeled with biotin and then ligated together in situ. Crosslinks were reversed, the DNA was sheared to 300-500 bp and then biotinylated ligation junctions were recovered with streptavidin beads. Hi-C libraries were amplified using PCR and constructed according to the NEBnext library preparation protocol (NEB, E7335) and sequenced on the Illumina HiSeq X Ten platform.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Nucleoskeleton is generally considered to be the grid structure involved in regulation of genome expression and maintenance in the eukaryotic nucleus. However, its actual biological functions and mechanisms remain controversial. Here, we show the nuclear mitotic apparatus protein (NuMA), an essential regulator of the spindle, serve as one of the components of nucleoskeleton to regulates genome high-order architecture. In the interphase, fast depletion of NuMA leads to changes in chromatin organization, including increased accessibility of the genome, remodeling of nucleosome fibers and changes of transcription levels in certain heterochromatin regions. These effects are probably due to NuMA and linker histone H1's interplay. We prove that NuMA interacts with linker histone H1 and linker DNA through its C-terminal domain. Such interaction facilitates H1's binding to DNA and promotes nucleosome stacking, and might be part of the reason that NuMA maintains the local condensed state of heterochromatin. Collectively, our results reveal new biological functions of NuMA in the interphase, and also associates nucleoskeleton with genome organization at the mono-nucleosome level for the first time. This in-depth study on the mechanism of NuMA's regulation on H1 and nucleosomes shed new light on how nucleoskeleton regulates genome architecture and gene expression. Overall design: Hi-C analysis of 3D genome architecture in wildtype and NuMA depleted HCT116 cell lines.
SAMPLE_TITLE: HiC_NC_rep1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "colon cancer"}, {"TAG": "tissue", "VALUE": "colon cancer"}, {"TAG": "cell line", "VALUE": "HCT116"}, {"TAG": "cell type", "VALUE": "human colon cancer cell line"}, {"TAG": "genotype", "VALUE": "wild type"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: HiC_NC_rep1
RUN_SET_RUN_Pool_Member_@attributes_sample_title: HiC_NC_rep1
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "NC-1_combined_R1.fastq.gz", "size": "5996595847", "date": "2023-03-20 13:33:10", "md5": "c1ca82c399b57e5c58135905d1399148", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "NC-1_combined_R2.fastq.gz", "size": "6690951859", "date": "2023-03-20 13:34:23", "md5": "e684304a2333cd9bdbcfcc9c94cd3a7b", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR23918683", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR23918683/SRR23918683", "size": "8660860916", "date": "2023-03-20 13:38:27", "md5": "8842fea2c03114a7c2a6cc9aa8b8ff21", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR23918683.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-zq-20/SRR023/23918/SRR23918683/SRR23918683.lite.1", "size": "5098552152", "date": "2023-04-06 00:03:34", "md5": "325da50f8c92404cbd4ca2e4d183d469", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]