Evidence map›Paper›PMID 37094694›Full record

ArticleGene2023

Spatiotemporal higher-order chromatin landscape of human histone gene clusters at histone locus bodies during the cell cycle in breast cancer progression.

Prachi N Ghule, Joseph R Boyd, Fleur Kabala, Andrew J Fritz, Nicole A Bouffard, Cong Gao, Kathleen Bright, Jill Macfarlane, David J Seward, Gianluca Pegoraro and 6 more

Erratum issuedOpen access · hybridAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Gene, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
0.6field-weighted citation impact, top 31% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

4 citing papers in PubMed, 4 citations in OpenAlex.

  1. Article
  2. Article
  3. bioRxiv : the preprint server for biology · 2024
    Article
  4. Review
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

16 authors at 2 institutions in 1 country.

Prachi N GhuleDepartment of Biochemistry and University of Vermont Cancer Center, Larner College of Medicine at the University of Vermont, 89 Beaumont Avenue, Burlington, VT 05405, USA. Electronic address: prachi.ghule@med.uvm.edu.
Joseph R BoydDepartment of Biomedical and Health Sciences and University of Vermont Cancer Center, College of Nursing and Health Sciences, University of Vermont, 89 Beaumont Avenue, Burlington, VT 05405, USA. Electronic address: joseph.boyd@med.uvm.edu.
Fleur KabalaDepartment 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 FritzDepartment of Biochemistry and University of Vermont Cancer Center, Larner College of Medicine at the University of Vermont, 89 Beaumont Avenue, Burlington, VT 05405, USA. Electronic address: andrew.fritz@med.uvm.edu.
Nicole A BouffardMicroscopy Imaging Center, Center for Biomedical Shared Resources at the University of Vermont, 150 Firestone Building, 149 Beaumont Ave, Burlington, VT 05405, USA.
Cong GaoDepartment of Biomedical and Health Sciences and University of Vermont Cancer Center, College of Nursing and Health Sciences, University of Vermont, 89 Beaumont Avenue, Burlington, VT 05405, USA.
Kathleen BrightDepartment of Biomedical and Health Sciences and University of Vermont Cancer Center, College of Nursing and Health Sciences, University of Vermont, 89 Beaumont Avenue, Burlington, VT 05405, USA.
Jill MacfarlaneDepartment 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 SewardDepartment of Pathology and University of Vermont Cancer Center, Larner College of Medicine at the University of Vermont, 89 Beaumont Avenue, Burlington, VT 05405, USA. Electronic address: david.seward@uvmhealth.org.
Gianluca PegoraroHigh-Throughput Imaging Facility (HiTIF), Center for Cancer Research (CCR), National Cancer Institute, NIH, Bethesda, MD 20892, USA.
Tom MisteliCell Biology of Genomes, Center for Cancer Research (CCR), National Cancer Institute, NIH, Bethesda, MD 20892, USA.
Jane B LianDepartment of Biochemistry and University of Vermont Cancer Center, Larner College of Medicine at the University of Vermont, 89 Beaumont Avenue, Burlington, VT 05405, USA. Electronic address: jane.lian@med.uvm.edu.
Seth FrietzeDepartment of Biomedical and Health Sciences and University of Vermont Cancer Center, College of Nursing and Health Sciences, University of Vermont, 89 Beaumont Avenue, Burlington, VT 05405, USA. Electronic address: seth.frietze@med.uvm.edu.
Janet L SteinDepartment of Biochemistry and University of Vermont Cancer Center, Larner College of Medicine at the University of Vermont, 89 Beaumont Avenue, Burlington, VT 05405, USA. Electronic address: janet.stein@med.uvm.edu.
Andre J van WijnenDepartment of Biochemistry and University of Vermont Cancer Center, Larner College of Medicine at the University of Vermont, 89 Beaumont Avenue, Burlington, VT 05405, USA. Electronic address: andre.vanwijnen@uvm.edu.
Gary S SteinDepartment of Biochemistry and University of Vermont Cancer Center, Larner College of Medicine at the University of Vermont, 89 Beaumont Avenue, Burlington, VT 05405, USA. Electronic address: gary.stein@uvm.edu.
University of Vermont · USNational Cancer Institute · US

Funding

Understanding Factors Influencing COVID-19 Testing and Vaccination in Immigrant Low-income and Homeless Populations and Testing Targeted InterventionsU54GM115516 · NIGMS · MAINEHEALTH · PI Robert A Koza · 2017 to 2026
$51.6M
Nuclear Architecture and DiseaseZIABC010309 · NCI · DIVISION OF BASIC SCIENCES - NCI · PI MISTELI, THOMAS A · 2009 to 2025
$39.8M
HiTIF Microscopy Core FacilityZICBC011567 · NCI · DIVISION OF BASIC SCIENCES - NCI · PI PEGORARO, GIANLUCA · 2014 to 2025
$15.8M
Project 3: MANCR Mediates Epigenetic Mechanisms for Survival of Advanced Breast CancerP01CA240685 · NCI · UNIVERSITY OF VERMONT & ST AGRIC COLLEGE · PI STEIN, JANET L · 2021 to 2025
$8.7M
Deciphering the molecular mechanisms of histone code recognition by ATAD2/BR01GM129338 · NIGMS · UNIVERSITY OF VERMONT & ST AGRIC COLLEGE · PI FRIETZE, SETH E, GLASS, KAREN CHAMPAGNE · 2018 to 2022
$2.1M
Understanding Ikaros molecular functions for targeted therapies of pre-B ALLR01CA230618 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI FRIETZE, SETH E, SCHJERVEN, HILDE · 2018 to 2022
$1.8M
Cell Cycle Regulation of Histone Gene ExpressionR01CA139322 · NCI · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI STEIN, GARY S. · 2009 to 2013
$1.6M
INVERTED LASER-SCANNING CONFOCAL MICROSCOPE: LUNG RESEARCHS10RR019246 · NCRR · UNIVERSITY OF VERMONT &ST AGRIC COLLEGE · PI TAATJES, DOUGLAS J. · 2004 to 2004
$473k
NCI NIH HHS P01 CA240685NCI NIH HHS R01 CA139322NCI NIH HHS R01 CA230618NCRR NIH HHS S10 RR019246NIGMS NIH HHS R01 GM129338NIGMS NIH HHS U54 GM115516
6 · The paper itself

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 ∼ 2 MB 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.

Indexed as

Breast NeoplasmsHistonesCell CycleCell Cycle ProteinsChromatinFemaleHumansMultigene FamilyNuclear BodiesCell Cycle ProteinsChromatinHistonesHiCHINFPHistone genesHistone locus body (HLB)NPAT

Identifiers

PMID37094694
PMCPMC10370284
OpenAlexW4366748121

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.