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

• Type of Material: Article
• Authors: Lauren Hodkinson, Emory University; Connor Smith, Emory University; Skye Comstra, Emory University; Bukola A. Ajani, Emory University; Eric Albanese, Emory University; Kawsar Arsalan, Emory University; Alvarao Perez Daisson, Emory University; Katherine Forrest, Emory University; Elijah H. Fox, Emory University; Matthew R. Guerette, Emory University; Samia Khan, Emory University; Madeleine Koenig, Emory University; Shivani Lam, Emory University; Ava S. Lewandowski, Emory University; Lauren J. Mahoney, Emory University; Nasserallah Manai, Emory University; JonCarlo Miglay, Emory University; Blake Miller, Emory University; Olivia Milloway, Emory University; Nhi Ngo, Emory University; Vu D. Ngo, Emory University; Nicole Oey, Emory University; Tanya Punjani, Emory University; HaoMin SiMa, Emory University; Hollis Zeng, Emory University; Casey A. Schmidt, Emory University; Leila Rieder, Emory University
• Language: English
• Date: 2023-09-21
• Publisher: BMC
• Publication Version: Final Published Version
• Copyright Statement: © The Author(s) 2023
• License: Creative Commons Attribution 4.0 International
• Final Published Version (URL): https://doi.org/10.1186%2Fs12863-023-01147-0
• Title of Journal or Parent Work: BMC Genomic Data
• Volume: 24
• Start Page: 54
• Grant/Funding Information: This work was supported by T32GM00008490 and F31HD105452 to LJH, 3R35GM142724-01S2 to CS, K12GM00068 to CAS and HSC; F32GM140778 to CAS; and R00HD092625 and R35GM142724 to LER.
• Keywords: ChIP-seq; Histone locus body; Histone locus; Drosophila; Galaxy; Hox factors; Course-based Undergraduate Research Experience
• Research Categories: Biology, Genetics; Biology, Bioinformatics

Abstract

Background 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. Results 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). Conclusions 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.