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Article ; Online: A Two-Step Mechanism for Creating Stable, Condensed Chromatin with the Polycomb Complex PRC1.

Seif, Elias / Francis, Nicole J

2024 Volume 29, Issue 2

Abstract: ... ...

Abstract	The
MeSH term(s)	Animals ; Nucleosomes ; Heterochromatin ; Chromatin ; Cell Nucleus ; Drosophila Proteins/genetics ; Drosophila
Chemical Substances	Nucleosomes ; Heterochromatin ; Chromatin ; Drosophila Proteins
Language	English
Publishing date	2024-01-09
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules29020323
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Zs.MO 81: Show issues

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Article ; Online: Identification of R-loop-forming Sequences in

Alecki, Célia / Francis, Nicole J

Bio-protocol

2021 Volume 11, Issue 9, Page(s) e4011

Abstract: R-loops are non-canonical nucleic structures composed of an RNA-DNA hybrid and a displaced ssDNA. Originally identified as a source of genomic instability, R-loops have been shown over the last decade to be involved in the targeting of proteins and to be ...

Abstract	R-loops are non-canonical nucleic structures composed of an RNA-DNA hybrid and a displaced ssDNA. Originally identified as a source of genomic instability, R-loops have been shown over the last decade to be involved in the targeting of proteins and to be associated with different histone modifications, suggesting a regulatory function. In addition, R-loops have been demonstrated to form differentially during the development of different tissues in plants and to be associated with diseases in mammals. Here, we provide a single-strand DRIP-seq protocol to identify R-loop-forming sequences in
Language	English
Publishing date	2021-05-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	2833269-6
ISSN	2331-8325 ; 2331-8325
ISSN (online)	2331-8325
ISSN	2331-8325
DOI	10.21769/BioProtoc.4011
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Article ; Online: Regulation of Polyhomeotic Condensates by Intrinsically Disordered Sequences That Affect Chromatin Binding.

Kapur, Ibani / Boulier, Elodie L / Francis, Nicole J

Epigenomes

2022 Volume 6, Issue 4

Abstract: The Polycomb group (PcG) complex PRC1 localizes in the nucleus in condensed structures called Polycomb bodies. The PRC1 subunit Polyhomeotic (Ph) contains an oligomerizing sterile alpha motif (SAM) that is implicated in both PcG body formation and ... ...

Abstract	The Polycomb group (PcG) complex PRC1 localizes in the nucleus in condensed structures called Polycomb bodies. The PRC1 subunit Polyhomeotic (Ph) contains an oligomerizing sterile alpha motif (SAM) that is implicated in both PcG body formation and chromatin organization in
Language	English
Publishing date	2022-11-03
Publishing country	Switzerland
Document type	Journal Article
ISSN	2075-4655
ISSN (online)	2075-4655
DOI	10.3390/epigenomes6040040
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Article: Inheritance of Histone (H3/H4): A Binary Choice?

Francis, Nicole J / Sihou, Djamouna

Trends in biochemical sciences. 2021 Jan., v. 46, no. 1

2021

Abstract: Histones carry information in the form of post-translational modifications (PTMs). For this information to be propagated through cell cycles, parental histones and their PTMs need to be maintained at the same genomic locations. Yet, during DNA ... ...

Abstract	Histones carry information in the form of post-translational modifications (PTMs). For this information to be propagated through cell cycles, parental histones and their PTMs need to be maintained at the same genomic locations. Yet, during DNA replication, every nucleosome in the genome is disrupted to allow passage of the replisome. Recent data have identified histone chaperone activities that are intrinsic components of the replisome and implicate them in maintaining parental histones during DNA replication. We propose that structural and kinetic coordination between DNA replication and replisome-associated histone chaperone activities ensures positional inheritance of histones and their PTMs. When this coordination is perturbed, histones may instead be recycled to random genomic locations by alternative histone chaperones.
Keywords	DNA replication ; genome ; genomics ; histones ; nucleosomes
Language	English
Dates of publication	2021-01
Size	p. 5-14.
Publishing place	Elsevier Ltd
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	194220-7
ISSN	0968-0004 ; 0376-5067
ISSN	0968-0004 ; 0376-5067
DOI	10.1016/j.tibs.2020.08.009
Database	NAL-Catalogue (AGRICOLA)

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Article: Inheritance of Histone (H3/H4): A Binary Choice?

Francis, Nicole J / Sihou, Djamouna

Trends in biochemical sciences

2020 Volume 46, Issue 1, Page(s) 5–14

Abstract	Histones carry information in the form of post-translational modifications (PTMs). For this information to be propagated through cell cycles, parental histones and their PTMs need to be maintained at the same genomic locations. Yet, during DNA replication, every nucleosome in the genome is disrupted to allow passage of the replisome. Recent data have identified histone chaperone activities that are intrinsic components of the replisome and implicate them in maintaining parental histones during DNA replication. We propose that structural and kinetic coordination between DNA replication and replisome-associated histone chaperone activities ensures positional inheritance of histones and their PTMs. When this coordination is perturbed, histones may instead be recycled to random genomic locations by alternative histone chaperones.
MeSH term(s)	DNA Replication ; Histones/metabolism ; Humans ; Protein Processing, Post-Translational
Chemical Substances	Histones
Keywords	covid19
Language	English
Publishing date	2020-09-09
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	194216-5
ISSN	1362-4326 ; 0968-0004 ; 0376-5067
ISSN (online)	1362-4326
ISSN	0968-0004 ; 0376-5067
DOI	10.1016/j.tibs.2020.08.009
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Zs.A 1207: Show issues

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Article ; Online: De novo enhancer deletion of LMX1B produces a mild nail-patella clinical phenotype.

Francis, David / Lall, Paula / Ayres, Samantha / Van Bergen, Nicole J / Christodoulou, John / Brown, Natasha J / Kalitsis, Paul

Clinical genetics

2023 Volume 105, Issue 2, Page(s) 214–219

Abstract: Critical genes involved in embryonic development are often transcription factors, regulating many downstream genes. LMX1B is a homeobox gene that is involved in formation of the limbs, eyes and kidneys, heterozygous loss-of-function sequence variants and ...

Abstract	Critical genes involved in embryonic development are often transcription factors, regulating many downstream genes. LMX1B is a homeobox gene that is involved in formation of the limbs, eyes and kidneys, heterozygous loss-of-function sequence variants and deletions cause Nail-Patella syndrome. Most of the reported variants are localised within the gene's coding sequence, however, approximately 5%-10% of affected individuals do not have a pathogenic variant identified within this region. In this study, we present a family with four affected individuals across two generations with a deletion spanning a conserved upstream LMX1B-binding sequence. This deletion is de novo in the mother of three affected children. Furthermore, in this family, the manifestations appear limited to the nails and limbs, and therefore may reflect an attenuated phenotype of the classic Nail-Patella phenotype that includes ophthalmological and renal manifestations.
MeSH term(s)	Child ; Humans ; Genes, Homeobox ; Homeodomain Proteins/genetics ; Mutation ; Nails ; Patella ; Phenotype ; Transcription Factors/genetics
Chemical Substances	Homeodomain Proteins ; Transcription Factors ; LIM homeobox transcription factor 1 beta
Language	English
Publishing date	2023-10-29
Publishing country	Denmark
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	221209-2
ISSN	1399-0004 ; 0009-9163
ISSN (online)	1399-0004
ISSN	0009-9163
DOI	10.1111/cge.14447
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Zs.A 413: Show issues

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Article ; Online: Regulation of Polyhomeotic Condensates by Intrinsically Disordered Sequences That Affect Chromatin Binding

Kapur, Ibani / Boulier, Elodie L. / Francis, Nicole J.

Epigenomes. 2022 Nov. 03, v. 6, no. 4

2022

Abstract	The Polycomb group (PcG) complex PRC1 localizes in the nucleus in condensed structures called Polycomb bodies. The PRC1 subunit Polyhomeotic (Ph) contains an oligomerizing sterile alpha motif (SAM) that is implicated in both PcG body formation and chromatin organization in Drosophila and mammalian cells. A truncated version of Ph containing the SAM (mini-Ph) forms phase-separated condensates with DNA or chromatin in vitro, suggesting that PcG bodies may form through SAM-driven phase separation. In cells, Ph forms multiple small condensates, while mini-Ph typically forms a single large nuclear condensate. We therefore hypothesized that sequences outside of mini-Ph, which are predicted to be intrinsically disordered, are required for proper condensate formation. We identified three distinct low-complexity regions in Ph based on sequence composition. We systematically tested the role of each of these sequences in Ph condensates using live imaging of transfected Drosophila S2 cells. Each sequence uniquely affected Ph SAM-dependent condensate size, number, and morphology, but the most dramatic effects occurred when the central, glutamine-rich intrinsically disordered region (IDR) was removed, which resulted in large Ph condensates. Like mini-Ph condensates, condensates lacking the glutamine-rich IDR excluded chromatin. Chromatin fractionation experiments indicated that the removal of the glutamine-rich IDR reduced chromatin binding and that the removal of either of the other IDRs increased chromatin binding. Our data suggest that all three IDRs, and functional interactions among them, regulate Ph condensate size and number. Our results can be explained by a model in which tight chromatin binding by Ph IDRs antagonizes Ph SAM-driven phase separation. Our observations highlight the complexity of regulation of biological condensates housed in single proteins.
Keywords	DNA ; Drosophila ; chromatin ; condensates ; fractionation ; mammals ; models ; oligomerization ; separation
Language	English
Dates of publication	2022-1103
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article ; Online
ISSN	2075-4655
DOI	10.3390/epigenomes6040040
Database	NAL-Catalogue (AGRICOLA)

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Article: Inheritance of Histone (H3/H4): A Binary Choice?

Francis, Nicole J / Sihou, Djamouna

Trends biochem. sci

Abstract	Histones carry information in the form of post-translational modifications (PTMs). For this information to be propagated through cell cycles, parental histones and their PTMs need to be maintained at the same genomic locations. Yet, during DNA replication, every nucleosome in the genome is disrupted to allow passage of the replisome. Recent data have identified histone chaperone activities that are intrinsic components of the replisome and implicate them in maintaining parental histones during DNA replication. We propose that structural and kinetic coordination between DNA replication and replisome-associated histone chaperone activities ensures positional inheritance of histones and their PTMs. When this coordination is perturbed, histones may instead be recycled to random genomic locations by alternative histone chaperones.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #32917507
Database	COVID19

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Article ; Online: Feasibility and Implementation of an Oncology Rehabilitation Triage Clinic: Assessing Rehabilitation, Exercise Need, and Triage Pathways within the Alberta Cancer Exercise-Neuro-Oncology Study.

Capozzi, Lauren C / Daun, Julia T / Francis, George J / de Guzman Wilding, Marie / Urgoiti, Gloria Roldan / Langelier, David / Culos-Reed, Nicole

Current oncology (Toronto, Ont.)

2023 Volume 30, Issue 7, Page(s) 6220–6245

Abstract: Individuals living with and beyond cancer face physical impairment and inactivity in survivorship. Neuro-oncology populations have especially high rates of sedentary behaviour and functional deficits, including impaired balance, motor skills, and ... ...

Abstract	Individuals living with and beyond cancer face physical impairment and inactivity in survivorship. Neuro-oncology populations have especially high rates of sedentary behaviour and functional deficits, including impaired balance, motor skills, and cognition. Our purpose was to assess the rehabilitation and exercise needs of patients with brain tumours while examining the feasibility of a rehabilitation triage clinic as a part of the Alberta Cancer Exercise-Neuro-Oncology study, where patients were referred to a triage clinic, where health, neurologic, and functional status was assessed, followed by a referral to one or multiple resources, including exercise, physiotherapy, occupational therapy, or physiatry. Qualitative perception of the triage clinic was collected. Overall, the triage clinic was feasible and safe for participants, facilitating referral into rehabilitation and exercise resources. Pre-determined enrollment and attendance rates were met, but referral rates to the triage clinic were not met. Oncology clinic staff reported forgetting to refer patients or uncertainty of who was appropriate for rehabilitation as barriers. Oncology clinic-based screening may improve the identification of patients who are sedentary or have a physical impairment. A proposed screening tool, the Cancer Rehabilitation and Exercise Screening Tool (CREST), is presented within our Cancer Rehabilitation and Exercise Pathways Model. The CREST can identify patients who are sedentary or have a functional impairment, facilitating referral to appropriate rehabilitation resources and ultimately improving patient recovery and functioning.
MeSH term(s)	Humans ; Triage ; Alberta ; Feasibility Studies ; Medical Oncology ; Brain Neoplasms
Language	English
Publishing date	2023-06-28
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1236972-x
ISSN	1718-7729 ; 1198-0052
ISSN (online)	1718-7729
ISSN	1198-0052
DOI	10.3390/curroncol30070461
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Article: How a disordered linker in the Polycomb protein Polyhomeotic tunes phase separation and oligomerization.

Gemeinhardt, Tim M / Regy, Roshan M / Mendiola, Andrea J / Ledterman, Heather J / Henrickson, Amy / Phan, Tien M / Kim, Young C / Demeler, Borries / Kim, Chongwoo A / Mittal, Jeetain / Francis, Nicole J

bioRxiv : the preprint server for biology

2023

Abstract: The Polycomb Group (PcG) complex PRC1 represses transcription, forms condensates in cells, and modifies chromatin architecture. These processes are connected through the essential, polymerizing Sterile Alpha Motif (SAM) present in the PRC1 subunit ... ...

Abstract	The Polycomb Group (PcG) complex PRC1 represses transcription, forms condensates in cells, and modifies chromatin architecture. These processes are connected through the essential, polymerizing Sterile Alpha Motif (SAM) present in the PRC1 subunit Polyhomeotic (Ph).
Language	English
Publishing date	2023-10-27
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.10.26.564264
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