EXPERIMENT_TITLE: GSM6433364: DELTA-5 HIC 24h rep1; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Cells were harvested after 24 or 48 hours of α-amanitin treatment to perform western-blot analysis. Since Δ5 is unstable after 48 hours of α-amanitin treatment, cells were harvest after 24 hours to perform ChIP using specific antibodies (HA, H3K4me1, H3K4me3 and CTCF) or extraction of Total RNA, PolyA-RNA and chromatin-associated RNA (ChrRNA) using corresponding protocols as described in manuscript. ChIP-seq libraries were prepared with Illumina's ChIP Sample Prep Kit according to standard protocol. RNA-seq libraries were prepared with Illumina's Small RNA Library Prep Kit by using a modified protocol described in manuscript. HiC libraries were prepared by proceeding to end-repair, A-tailing followed by the ligation of Illumina adaptaters and amplification.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: The largest subunit of RNA polymerase (Pol) II harbors a evolutionary conserved C-Terminal-Domain (CTD), composed of a repetition of heptapeptides, central in the transcriptional process. Here, we have analysed the transcriptional phenotypes of a CTD-?5 mutant that carries a large CTD truncation. Unexpectedly, our results indicate that this mutant can widely transcribe genes in living cells but displays an extreme pervasive phenotype with severely impaired termination, similar to but more severely impaired than previously characterized mutations of CTD tyrosine residues. The CTD-?5 mutant has also lost its interactions with the Mediator and Integrator complexes involved in activation of transcription and maturation of RNAs. Examination of long-distance interactions and CTCF binding pattern in CTD-?5 did not indicate major changes in TAD domains or borders. Our data demonstrate that the CTD is largely dispensable for the act of transcription per se in living cells. We propose a model in which CTD-depleted Pol II has a lower entry rate into DNA but becomes extremely pervasive once engaged in transcription, resulting in a global loss of termination. Overall design: This study was performed in a human Raji cell line. It contains ChIP-seq data for HA-tagged RNA Pol II, H3K4me1, H3K4me3 and CTCF as well as RNA-seq data for PolyA-RNA and chromatin-associated RNA (ChrRNA) and HiC data. All sequencing were performed in paired-end sequencing runs.
SAMPLE_TITLE: DELTA-5 HIC 24h rep1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Raji B cells"}, {"TAG": "cell type", "VALUE": "B lymphocyte"}, {"TAG": "strain", "VALUE": "Burkitt's lymphoma"}, {"TAG": "cell line", "VALUE": "Raji"}, {"TAG": "genotype", "VALUE": "DELTA-5"}, {"TAG": "time", "VALUE": "24h"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: DELTA-5 HIC 24h rep1
RUN_SET_RUN_Pool_Member_@attributes_sample_title: DELTA-5 HIC 24h rep1
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR20854725.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-zq-38/SRR020/20854/SRR20854725/SRR20854725.lite.1", "size": "7053038934", "date": "2022-10-20 22:27:37", "md5": "3a5abfa8a944e2980712463b14d49e07", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR20854725", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR20854725/SRR20854725", "size": "13638021446", "date": "2022-08-05 15:13:10", "md5": "e86a18ed3bb17f39fa4ad5414896d25c", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "DELTA-5_HIC_24h_rep1_2.fastq.gz", "size": "10616893855", "date": "2022-08-05 15:05:13", "md5": "a2986f71f9b63fa1017458d7edf7c7e9", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "DELTA-5_HIC_24h_rep1_1.fastq.gz", "size": "10279383905", "date": "2022-08-05 15:07:10", "md5": "2b1d3458d9654db169d3ecf8001a0833", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]