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

Content Provider	Springer Nature : BioMed Central
Author	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.
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.
Related Links	https://bmcgenomdata.biomedcentral.com/counter/pdf/10.1186/s12863-023-01147-0.pdf
Ending Page	18
Page Count	18
Starting Page	1
File Format	HTM / HTML
ISSN	27306844
DOI	10.1186/s12863-023-01147-0
Journal	BMC Genomic Data
Issue Number	1
Volume Number	24
Language	English
Publisher	BioMed Central
Publisher Date	2023-09-21
Access Restriction	Open
Subject Keyword	Life Sciences Animal Genetics and Genomics Microbial Genetics and Genomics Plant Genetics and Genomics Genetics and Population Dynamics Drosophila ChIP-seq Galaxy Course-based Undergraduate Research Experience Hox factors Histone locus Histone locus body
Content Type	Text
Resource Type	Article
Subject	Health Informatics Genetics
Journal Impact Factor	1.9/2023
5-Year Journal Impact Factor	1.9/2023

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