1
|
Ghule PN, Boyd JR, Kabala F, Fritz AJ, Bouffard NA, Gao C, Bright K, Macfarlane J, Seward DJ, Pegoraro G, Misteli T, Lian JB, Frietze S, Stein JL, van Wijnen AJ, Stein GS. Spatiotemporal higher-order chromatin landscape of human histone gene clusters at Histone Locus Bodies during the cell cycle in breast cancer progression. Gene 2023; 872:147441. [PMID: 37094694 PMCID: PMC10370284 DOI: 10.1016/j.gene.2023.147441] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 04/26/2023]
Abstract
Human Histone Locus Bodies (HLBs) are nuclear subdomains comprised of clustered histone genes that are coordinately regulated throughout the cell cycle. We addressed temporal-spatial higher-order genome organization for time-dependent chromatin remodeling at HLBs that supports control of cell proliferation. Proximity distances of specific genomic contacts within histone gene clusters exhibit subtle changes during the G1 phase in MCF10 breast cancer progression model cell lines. This approach directly demonstrates that the two principal histone gene regulatory proteins, HINFP (H4 gene regulator) and NPAT, localize at chromatin loop anchor-points, denoted by CTCF binding, supporting the stringent requirement for histone biosynthesis to package newly replicated DNA as chromatin. We identified a novel enhancer region located ∼2MB distal to histone gene sub-clusters on chromosome 6 that consistently makes genomic contacts with HLB chromatin and is bound by NPAT. During G1 progression the first DNA loops form between one of three histone gene sub-clusters bound by HINFP and the distal enhancer region. Our findings are consistent with a model that the HINFP/NPAT complex controls the formation and dynamic remodeling of higher-order genomic organization of histone gene clusters at HLBs in early to late G1 phase to support transcription of histone mRNAs in S phase.
Collapse
Affiliation(s)
- Prachi N Ghule
- Department of Biochemistry and University of Vermont Cancer Center, Larner College of Medicine at the University of Vermont, 89 Beaumont Avenue, Burlington, VT, 05405, USA.
| | - Joseph R Boyd
- Department of Biomedical and Health Sciences and University of Vermont Cancer Center, Larner College of Medicine at the University of Vermont, 89 Beaumont Avenue, Burlington, VT, 05405, USA.
| | - Fleur Kabala
- Department of Biochemistry and University of Vermont Cancer Center, Larner College of Medicine at the University of Vermont, 89 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Andrew J Fritz
- Department of Biochemistry and University of Vermont Cancer Center, Larner College of Medicine at the University of Vermont, 89 Beaumont Avenue, Burlington, VT, 05405, USA.
| | - Nicole A Bouffard
- Microscopy Imaging Core, Center for Biomedical Shared Resources at the University of Vermont, 150 Firestone Building, 149 Beaumont Ave, Burlington, VT, 05405, USA
| | - Cong Gao
- Department of Biomedical and Health Sciences and University of Vermont Cancer Center, Larner College of Medicine at the University of Vermont, 89 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Kathleen Bright
- Department of Biomedical and Health Sciences and University of Vermont Cancer Center, Larner College of Medicine at the University of Vermont, 89 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Jill Macfarlane
- Department of Biochemistry and University of Vermont Cancer Center, Larner College of Medicine at the University of Vermont, 89 Beaumont Avenue, Burlington, VT, 05405, USA
| | - David J Seward
- Department of Pathology and University of Vermont Cancer Center, Larner College of Medicine at the University of Vermont, 89 Beaumont Avenue, Burlington, VT, 05405, USA.
| | - Gianluca Pegoraro
- High-Throughput Imaging Facility (HiTIF), Center for Cancer Research (CCR), National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Tom Misteli
- Cell Biology of Genomes, Center for Cancer Research (CCR), National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Jane B Lian
- Department of Biochemistry and University of Vermont Cancer Center, Larner College of Medicine at the University of Vermont, 89 Beaumont Avenue, Burlington, VT, 05405, USA.
| | - Seth Frietze
- Department of Biomedical and Health Sciences and University of Vermont Cancer Center, Larner College of Medicine at the University of Vermont, 89 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Janet L Stein
- Department of Biochemistry and University of Vermont Cancer Center, Larner College of Medicine at the University of Vermont, 89 Beaumont Avenue, Burlington, VT, 05405, USA.
| | - Andre J van Wijnen
- Department of Biochemistry and University of Vermont Cancer Center, Larner College of Medicine at the University of Vermont, 89 Beaumont Avenue, Burlington, VT, 05405, USA.
| | - Gary S Stein
- Department of Biochemistry and University of Vermont Cancer Center, Larner College of Medicine at the University of Vermont, 89 Beaumont Avenue, Burlington, VT, 05405, USA.
| |
Collapse
|