Dynamic regulation of alternative splicing and chromatin structure in Drosophila gonads revealed by RNA-seq.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:20440302", "kind": "science-record", "revision": 6, "content_hash": "sha256:1a0efe44db8cfd3ecae37a2da78c71d1f17acb2fb5223ed24313fe4c2711287a", "created_at": "2026-11-01T15:14:34Z", "updated_at": "2026-11-01T18:46:46Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Dynamic regulation of alternative splicing and chromatin structure in Drosophila gonads revealed by RNA-seq.", "doi": "10.1038/cr.2010.64", "pmid": "20440302", "authors": ["Qiang Gan", "Iouri Chepelev", "Gang Wei", "Lama Tarayrah", "Kairong Cui", "Keji Zhao", "Xin Chen"], "journal": "Cell research", "year": 2010, "abstract": "Both transcription and post-transcriptional processes, such as alternative splicing, play crucial roles in controlling developmental programs in metazoans. Recently emerged RNA-seq method has brought our understanding of eukaryotic transcriptomes to a new level, because it can resolve both gene expression level and alternative splicing events simultaneously. To gain a better understanding of cellular differentiation in gonads, we analyzed mRNA profiles from Drosophila testes and ovaries using RNA-seq. We identified a set of genes that have sex-specific isoforms in wild-type (WT) gonads, including several transcription factors. We found that differentiation of sperms from undifferentiated germ cells induced a dramatic downregulation of RNA splicing factors. Our data confirmed that RNA splicing events are significantly more frequent in the undifferentiated cell-enriched bag of marbles (bam) mutant testis, but downregulated upon differentiation in WT testis. Consistent with this, we showed that genes required for meiosis and terminal differentiation in WT testis were mainly regulated at the transcriptional level, but not by alternative splicing. Unexpectedly, we observed an increase in expression of all families of chromatin remodeling factors and histone modifying enzymes in the undifferentiated cell-enriched bam testis. More interestingly, chromatin regulators and histone modifying enzymes with opposite enzymatic activities are coenriched in undifferentiated cells in testis, suggesting that these cells may possess dynamic chromatin architecture. Finally, our data revealed many new features of the Drosophila gonadal transcriptomes, and will lead to a more comprehensive understanding of how differential gene expression and splicing regulate gametogenesis in Drosophila. Our data provided a foundation for the systematic study of gene expression and alternative splicing in many interesting areas of germ cell biology in Drosophila, such as the molecular basis for sexual dimorphism and the regulation of the proliferation vs terminal differentiation programs in germline stem cell lineages. The GEO accession number for the raw and analyzed RNA-seq data is GSE16960.", "claims": [{"id": "claim-target-result", "statement": "The paper identified sex-specific isoforms in wild-type Drosophila gonads and compared its RNA-seq data with published microarray data using RMA normalization in limma and P≤0.05 plus ≥2-fold-change cutoffs; the microarray CEL files were obtained from NCBI GEO.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:20440302", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "We identified a set of genes that have sex-specific isoforms in wild-type (wt) gonads, including several transcription factors."}, {"asset": "source:pmid:20440302", "locator": "sections[26] \"Comparison of RNA-seq data with published microarray data\" paragraph 2", "quote": "We first downloaded the CEL files generated by Parisi et al 22 and Chintapalli et al 96 from NCBI GEO database."}, {"asset": "source:pmid:20440302", "locator": "sections[26] \"Comparison of RNA-seq data with published microarray data\" paragraph 2", "quote": "We then extracted and normalized microarray signals with RMA function embedded in the limma package [downloaded from Bioconductor R packages (http://www.bioconductor.org)]."}, {"asset": "source:pmid:20440302", "locator": "sections[26] \"Comparison of RNA-seq data with published microarray data\" paragraph 2", "quote": "Differentially expressed genes were identified using the combination of P-value (P≤0.05) and fold change (≥2) cutoffs, followed by comparison with their expression level using the RNA-seq data."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The paper identified sex-specific isoforms in wild-type Drosophila gonads and compared its RNA-seq data with published microarray data using RMA normalization in limma and P≤0.05 plus ≥2-fold-change cutoffs; the microarray CEL files were obtained from NCBI GEO.", "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:20440302"], "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": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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For each chromatin regulator, the fold change in bam/wt gonads is listed, as well as the RPKM values in bam and wt gonads, respectively. Red numbers indicate enrichment in bam gonads, and blue numbers indicate enrichment in wt gonads. Most of the chromatin regulators have high expression in bam testis (RPKM> 10), therefore the down-regulation in wt testis is significant.", "structure": {"pmcid": "PMC2919574", "section_index": 39, "section_title": "Figures and Tables", "row_count": 22, "column_count": 16}, "table": {"label": "Table 2", "caption": "Chromatin regulators are enriched in bam testis compared to wt testisThe chromatin remodeling factors were retrieved from http://web.wi.mit.edu/young/pub/chromatin_remodeling.html; the histone modifying enzymes were from 99–107 (All chromatin remodeling factors and histone modifying enzymes listed here are supported by published research papers.). For each chromatin regulator, the fold change in bam/wt gonads is listed, as well as the RPKM values in bam and wt gonads, respectively. Red numbers indicate enrichment in bam gonads, and blue numbers indicate enrichment in wt gonads. Most of the chromatin regulators have high expression in bam testis (RPKM> 10), therefore the down-regulation in wt testis is significant.", "rows": [["Gene Name", "bam/wt testis", "bam testis (RPKM)", "wt testis (RPKM)", "Gene Name", "bam/wt testis", "bam testis (RPKM)", "wt testis (RPKM)", "Gene Name", "bam/wt testis", "bam testis (RPKM)", "wt testis (RPKM)", "Gene Name", "bam/wt ovary", "bam ovary (RPKM)", "wt ovary (RPKM)"], ["Rpd3", "15.35", "158.02", "10.29", "CG11033", "4.70", "43.67", "9.30", "trr", "3.05", "26.58", "8.72", "tna", "2.81", "48.70", "17.31"], ["ph-p", "13.46", "17.27", "1.28", "Suv4-20", "4.56", "78.75", "17.25", "mof", "2.90", "34.20", "11.80", "Iswi", "2.29", "122.00", "53.20"], ["Art4", "11.92", "43.10", "3.62", "kis", "4.45", "120.73", "27.16", "tlk", "2.89", "80.46", "27.86", "SuUR", "0.29", "8.37", "28.63"], ["CG3654", "8.45", "48.74", "5.77", "Mi-2", "4.30", "138.92", "32.32", "Snr1", "2.82", "59.58", "21.12", "Art4", "0.36", "26.46", "73.45"], ["tara", "8.38", "17.31", "2.07", "osa", "4.20", "174.52", "41.54", "Su(var)3-9", "2.74", "85.46", "31.20", "Ada2b", "0.37", "28.12", "75.50"], ["mod", "8.24", "127.82", "15.52", "CG13902", "4.19", "22.48", "5.36", "Su(var)2-HP2", "2.58", "37.82", "14.65", "Sgf11", "0.48", "14.46", "30.38"], ["egg", "6.77", "76.40", "11.29", "ial", "4.11", "56.06", "13.62", "CG2982", "2.52", "72.24", "28.65", "borr", "0.48", "28.40", "59.37"], ["MED21", "6.53", "14.72", "2.25", "E(z)", "4.06", "51.80", "12.75", "wda", "2.48", "18.39", "7.42", "z", "0.50", "22.94", "46.21"], ["Psc", "6.31", "15.90", "2.52", "not", "4.02", "66.83", "16.62", "Hcf", "2.32", "43.82", "18.91", "Scm", "0.49", "23.64", "48.50"], ["Rpb4", "6.19", "20.81", "3.36", "Bre1", "3.96", "52.01", "13.13", "Su(var)3-3", "2.27", "28.13", "12.39", "Set2", "0.50", "29.84", "60.13"], ["BAP60", "6.12", "69.93", "11.43", "CG12879", "3.90", "15.40", "3.95", "Sce", "2.17", "47.07", "21.73", "", "", "", ""], ["esc", "6.03", "51.57", "8.55", "CG8165", "3.87", "10.56", "2.73", "Invadolysin", "2.14", "50.45", "23.56", "", "", "", ""], ["BAP55", "5.77", "87.57", "15.17", "phol", "3.77", "68.00", "18.03", "Su(var)205", "2.14", "101.00", "47.23", "", "", "", ""], ["lid", "5.56", "149.49", "26.87", "pr-set7", "3.52", "44.45", "12.64", "Taf1", "2.05", "46.89", "22.86", "", "", "", ""], ["Hdac3", "5.56", "68.80", "12.38", "Nurf-38", "3.39", "191.34", "56.43", "ash1", "0.49", "18.95", "38.48", "", "", "", ""], ["Art1", "5.53", "140.78", "25.47", "Sir2", "3.37", "39.03", "11.58", "Mst35Ba", "0.49", "0.00", "84.60", "", "", "", ""], ["mor", "5.39", "103.02", "19.12", "trx", "3.28", "29.73", "9.07", "Kdm4B", "0.49", "54.43", "111.24", "", "", "", ""], ["Dp1", "5.37", "157.07", "29.24", "Pc", "3.28", "12.13", "3.70", "tna", "0.21", "42.48", "205.15", "", "", "", ""], ["Elp3", "5.30", "57.39", "10.83", "Nurf55", "3.21", "123.73", "38.50", "Mst35Bb", "0.01", "0.00", "135.32", "", "", "", ""], ["Acf1", "4.97", "55.55", "11.17", "HDAC4", "3.16", "31.95", "10.12", "CG31281", "0.00", "0.00", "282.35", "", "", "", ""], ["Pcaf", "4.86", "50.72", "10.44", "Su(z)12", "3.10", "75.43", "24.30", "", "", "", "", "", "", "", ""]], "row_count": 22, "column_count": 16, "numeric_cells": 238, "header_rows": 1, "locator": "section[39]/table-wrap[2]#T2"}}, {"id": "asset:table:pmid:20440302:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:ab9e479c77ea1cf546a0b3ba2b7f8fef0743ebe9999eb2e9eae623af04dbda1f", "bytes": 2884, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[39]/table-wrap[3]#T3", "version": null, "note": "Genes that exhibit sex-specific or sex-biased isoforms in bam and wt gonadsGenes that encode transcription factors or putative transcription factors were highlighted in red. Genes that encode splicing factors or putative splicing factors were highlighted in yellow.", "structure": {"pmcid": "PMC2919574", "section_index": 39, "section_title": "Figures and Tables", "row_count": 25, "column_count": 3}, "table": {"label": "Table 3", "caption": "Genes that exhibit sex-specific or sex-biased isoforms in bam and wt gonadsGenes that encode transcription factors or putative transcription factors were highlighted in red. 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