Genome-Wide Mapping of the Distribution of CarD, RNAP σA, and RNAP β on the Mycobacterium smegmatis Chromosome using Chromatin Immunoprecipitation Sequencing.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:25089258", "kind": "science-record", "revision": 7, "content_hash": "sha256:8170cc88a8b1e4ae077d28624935cc1f6414132f769ce7c6dbabfbb5501e33a4", "created_at": "2026-11-01T15:40:05Z", "updated_at": "2026-11-01T21:58:20Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Genome-Wide Mapping of the Distribution of CarD, RNAP σA, and RNAP β on the Mycobacterium smegmatis Chromosome using Chromatin Immunoprecipitation Sequencing.", "doi": "10.1016/j.gdata.2014.05.012", "pmid": "25089258", "authors": ["Robert Landick", "Azra Krek", "Michael S Glickman", "Nicholas D Socci", "Christina L Stallings"], "journal": "Genomics data", "year": 2014, "abstract": "CarD is an essential mycobacterial protein that binds the RNA polymerase (RNAP) and affects the transcriptional profile of Mycobacterium smegmatis and Mycobacterium tuberculosis (6). We predicted that CarD was directly regulating RNAP function but our prior experiments had not determined at what stage of transcription CarD was functioning and at which genes CarD interacted with the RNAP. To begin to address these open questions, we performed Chromatin Immunoprecipitation sequencing (ChIP-seq) to survey the distribution of CarD throughout the M. smegmatis chromosome. The distribution of RNAP subunits β and σA were also profiled. We expected that RNAP β would be present throughout transcribed regions and RNAP σA would be predominantly enriched at promoters based on work in Escherichia coli (3), however this had yet to be determined in mycobacteria. The ChIP-seq analyses revealed that CarD was never present on the genome in the absence of RNAP, was primarily associated with promoter regions, and was highly correlated with the distribution of RNAP σA. The colocalization of σA and CarD led us to propose that in vivo, CarD associates with RNAP initiation complexes at most promoters and is therefore a global regulator of transcription initiation. Here we describe in detail the data from the ChIP-seq experiments associated with the study published by Srivastava and colleagues in the Proceedings of the National Academy of Science in 2013 (5) as well as discuss the findings from this dataset in relation to both CarD and mycobacterial transcription as a whole. The ChIP-seq data have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. GSE48164).", "claims": [{"id": "claim-method", "statement": "Using the Wilcoxon–Mann–Whitney ranksum test for nonsimilarity of distributions [3], [4], RNAP σA peaks in the 1.1–1.2 peak-height bins and CarD-HA peaks in the 0.5–0.6 peak-height bins were statistically significant (P values for similarity of the distributions < 0.0001).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25089258", "locator": "sections[8] \"Data analysis\" paragraph 5", "quote": "Using the Wilcoxon–Mann–Whitney ranksum test for nonsimilarity of distributions [3], [4], RNAP σA peaks in the 1.1–1.2 peak-height bins and CarD-HA peaks in the 0.5–0.6 peak-height bins were statistically significant (P values for similarity of the distributions < 0.0001)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The ChIP-seq data have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. GSE48164).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25089258", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "The ChIP-seq data have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. GSE48164)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper used DESeq normalization and the Wilcoxon–Mann–Whitney ranksum test to analyze ChIP-seq data deposited in GEO under accession GSE48164, and found that “CarD was never present on the genome in the absence of RNAP, was primarily associated with promoter regions, and was highly correlated with the distribution of RNAP σA.”", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:25089258", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The ChIP-seq analyses revealed that CarD was never present on the genome in the absence of RNAP, was primarily associated with promoter regions, and was highly correlated with the distribution of RNAP σA."}, {"asset": "source:pmid:25089258", "locator": "sections[7] \"Normalization\" paragraph 2", "quote": "The DESeq method [1] was used to normalize the raw data sequence reads."}, {"asset": "source:pmid:25089258", "locator": "sections[8] \"Data analysis\" paragraph 5", "quote": "Using the Wilcoxon–Mann–Whitney ranksum test for nonsimilarity of distributions [3], [4], RNAP σA peaks in the 1.1–1.2 peak-height bins and CarD-HA peaks in the 0.5–0.6 peak-height bins were statistically significant (P values for similarity of the distributions < 0.0001)."}, {"asset": "source:pmid:25089258", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "The ChIP-seq data have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. GSE48164)."}, {"asset": "source:pmid:25089258", "locator": "sections[2] \"Direct link to deposited data\" paragraph 2", "quote": "The direct link for the ChIP-seq data is: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE48164."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The paper used DESeq normalization and the Wilcoxon–Mann–Whitney ranksum test to analyze ChIP-seq data deposited in GEO under accession GSE48164, and found that “CarD was never present on the genome in the absence of RNAP, was primarily associated with promoter regions, and was highly correlated with the distribution of RNAP σA.”", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:25089258"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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The ChIP-seq analyses revealed that CarD was never presen", "Here we describe in detail the data from the ChIP-seq experiments associated with the study publis", "mycobacterial transcription as a whole. The ChIP-seq data have been deposited in the Gene Express"], "order_basis": "paper_text_order:602", "id": "assay:1"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["zation of σA and CarD led us to propose that in vivo, CarD associates with RNAP initiation comple"], "order_basis": "paper_text_order:1235", "id": "assay:2"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Using the Wilcoxon–Mann–Whitney ranksum test for nonsimilarity of distributions [3], [4], RNAP σA peaks in the 1.1–1.2 peak-height bins and CarD-HA peaks in the 0.5–0.6 peak-height bins were statistically significant (P values for similarity of the distributions < 0.0001)."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}