A bioinformatics screen reveals hox and chromatin remodeling factors at the Drosophila histone locus

• Published in: BMC genetics Vol. 24; no. 1; p. 54
• Main Authors: Hodkinson, Lauren J, Smith, Connor, Comstra, H Skye, Ajani, Bukola A, Albanese, Eric H, Arsalan, Kawsar, Daisson, Alvaro Perez, Forrest, Katherine B, Fox, Elijah H, Guerette, Matthew R, Khan, Samia, Koenig, Madeleine P, Lam, Shivani, Lewandowski, Ava S, Mahoney, Lauren J, Manai, Nasserallah, Miglay, JonCarlo, Miller, Blake A, Milloway, Olivia, Ngo, Nhi, Ngo, Vu D, Oey, Nicole F, Punjani, Tanya A, SiMa, HaoMin, Zeng, Hollis, Schmidt, Casey A, Rieder, Leila E
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 21.09.2023; BioMed Central; BMC
• Subjects: Analysis; Animals; Arrays; Bioinformatics; Biosynthesis; Candidates; Cell cycle; Cell division; ChIP-seq; Chromatin; Chromatin Assembly and Disassembly - genetics; Chromatin remodeling; Computational Biology; Course-based Undergraduate Research Experience; Datasets; DNA binding proteins; DNA microarrays; Drosophila; Drosophila melanogaster - genetics; Drosophila Proteins - genetics; Evaluation; Female; Galaxy; Gene expression; Genes; Genetic aspects; Genetic transcription; Genomes; Histone locus; Histones; Histones - genetics; Homeodomain Proteins - genetics; Hox factors; Infertility; Insects; Localization; Morphogenesis; Properties; Protein Serine-Threonine Kinases; Proteins; Transcription factors; Transcription Factors - genetics; Transcription initiation factor TFIIB; United States; Galaxy; Drosophila; ChIP-seq; Hox factors; Histone locus body; Course-based Undergraduate Research Experience; Histone locus
• ISSN: 2730-6844; 2730-6844; 1471-2156
• DOI: 10.1186/s12863-023-01147-0

Cells orchestrate histone biogenesis with strict temporal and quantitative control. To efficiently regulate histone biogenesis, the repetitive Drosophila melanogaster replication-dependent histone genes are arrayed and clustered at a single locus. Regulatory factors concentrate in a nuclear body known as the histone locus body (HLB), which forms around the locus. Historically, HLB factors are largely discovered by chance, and few are known to interact directly with DNA. It is therefore unclear how the histone genes are specifically targeted for unique and coordinated regulation. To expand the list of known HLB factors, we performed a candidate-based screen by mapping 30 publicly available ChIP datasets of 27 unique factors to the Drosophila histone gene array. We identified novel transcription factor candidates, including the Drosophila Hox proteins Ultrabithorax (Ubx), Abdominal-A (Abd-A), and Abdominal-B (Abd-B), suggesting a new pathway for these factors in influencing body plan morphogenesis. Additionally, we identified six other factors that target the histone gene array: JIL-1, hormone-like receptor 78 (Hr78), the long isoform of female sterile homeotic (1) (fs(1)h) as well as the general transcription factors TBP associated factor 1 (TAF-1), Transcription Factor IIB (TFIIB), and Transcription Factor IIF (TFIIF). Our foundational screen provides several candidates for future studies into factors that may influence histone biogenesis. Further, our study emphasizes the powerful reservoir of publicly available datasets, which can be mined as a primary screening technique.