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Article ; Online: Identification of epigenetic modulators as determinants of nuclear size and shape.

Schibler, Andria C / Jevtic, Predrag / Pegoraro, Gianluca / Levy, Daniel L / Misteli, Tom

2023 Volume 12

Abstract: The shape and size of the human cell nucleus is highly variable among cell types and tissues. Changes in nuclear morphology are associated with disease, including cancer, as well as with premature and normal aging. Despite the very fundamental nature of ... ...

Abstract	The shape and size of the human cell nucleus is highly variable among cell types and tissues. Changes in nuclear morphology are associated with disease, including cancer, as well as with premature and normal aging. Despite the very fundamental nature of nuclear morphology, the cellular factors that determine nuclear shape and size are not well understood. To identify regulators of nuclear architecture in a systematic and unbiased fashion, we performed a high-throughput imaging-based siRNA screen targeting 867 nuclear proteins including chromatin-associated proteins, epigenetic regulators, and nuclear envelope components. Using multiple morphometric parameters, and eliminating cell cycle effectors, we identified a set of novel determinants of nuclear size and shape. Interestingly, most identified factors altered nuclear morphology without affecting the levels of lamin proteins, which are known prominent regulators of nuclear shape. In contrast, a major group of nuclear shape regulators were modifiers of repressive heterochromatin. Biochemical and molecular analysis uncovered a direct physical interaction of histone H3 with lamin A mediated via combinatorial histone modifications. Furthermore, disease-causing lamin A mutations that result in disruption of nuclear shape inhibited lamin A-histone H3 interactions. Oncogenic histone H3.3 mutants defective for H3K27 methylation resulted in nuclear morphology abnormalities. Altogether, our results represent a systematic exploration of cellular factors involved in determining nuclear morphology and they identify the interaction of lamin A with histone H3 as an important contributor to nuclear morphology in human cells.
MeSH term(s)	Humans ; Histones/metabolism ; Lamin Type A/genetics ; Lamin Type A/metabolism ; Cell Nucleus/metabolism ; Nuclear Proteins/metabolism ; Nuclear Envelope/metabolism ; Epigenesis, Genetic
Chemical Substances	Histones ; Lamin Type A ; Nuclear Proteins
Language	English
Publishing date	2023-05-23
Publishing country	England
Document type	Journal Article
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.80653
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Article ; Online: Identification of epigenetic modulators as determinants of nuclear size and shape

Andria C Schibler / Predrag Jevtic / Gianluca Pegoraro / Daniel L Levy / Tom Misteli

eLife, Vol

2023 Volume 12

Abstract	The shape and size of the human cell nucleus is highly variable among cell types and tissues. Changes in nuclear morphology are associated with disease, including cancer, as well as with premature and normal aging. Despite the very fundamental nature of nuclear morphology, the cellular factors that determine nuclear shape and size are not well understood. To identify regulators of nuclear architecture in a systematic and unbiased fashion, we performed a high-throughput imaging-based siRNA screen targeting 867 nuclear proteins including chromatin-associated proteins, epigenetic regulators, and nuclear envelope components. Using multiple morphometric parameters, and eliminating cell cycle effectors, we identified a set of novel determinants of nuclear size and shape. Interestingly, most identified factors altered nuclear morphology without affecting the levels of lamin proteins, which are known prominent regulators of nuclear shape. In contrast, a major group of nuclear shape regulators were modifiers of repressive heterochromatin. Biochemical and molecular analysis uncovered a direct physical interaction of histone H3 with lamin A mediated via combinatorial histone modifications. Furthermore, disease-causing lamin A mutations that result in disruption of nuclear shape inhibited lamin A-histone H3 interactions. Oncogenic histone H3.3 mutants defective for H3K27 methylation resulted in nuclear morphology abnormalities. Altogether, our results represent a systematic exploration of cellular factors involved in determining nuclear morphology and they identify the interaction of lamin A with histone H3 as an important contributor to nuclear morphology in human cells.
Keywords	nucleus ; lamins ; histones ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
Subject code	570
Language	English
Publishing date	2023-05-01T00:00:00Z
Publisher	eLife Sciences Publications Ltd
Document type	Article ; Online
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Article ; Online: The nucleoporin ELYS regulates nuclear size by controlling NPC number and nuclear import capacity.

Jevtić, Predrag / Schibler, Andria C / Wesley, Chase C / Pegoraro, Gianluca / Misteli, Tom / Levy, Daniel L

EMBO reports

2019 Volume 20, Issue 6

Abstract: How intracellular organelles acquire their characteristic sizes is a fundamental question in cell biology. Given stereotypical changes in nuclear size in cancer, it is important to understand the mechanisms that control nuclear size in human cells. Using ...

Abstract	How intracellular organelles acquire their characteristic sizes is a fundamental question in cell biology. Given stereotypical changes in nuclear size in cancer, it is important to understand the mechanisms that control nuclear size in human cells. Using a high-throughput imaging RNAi screen, we identify and mechanistically characterize ELYS, a nucleoporin required for post-mitotic nuclear pore complex (NPC) assembly, as a determinant of nuclear size in mammalian cells. ELYS knockdown results in small nuclei, reduced nuclear lamin B2 localization, lower NPC density, and decreased nuclear import. Increasing nuclear import by importin α overexpression rescues nuclear size and lamin B2 import, while inhibiting importin α/β-mediated nuclear import decreases nuclear size. Conversely, ELYS overexpression increases nuclear size, enriches nuclear lamin B2 at the nuclear periphery, and elevates NPC density and nuclear import. Consistent with these observations, knockdown or inhibition of exportin 1 increases nuclear size. Thus, we identify ELYS as a novel positive effector of mammalian nuclear size and propose that nuclear size is sensitive to NPC density and nuclear import capacity.
MeSH term(s)	Active Transport, Cell Nucleus ; Biomarkers ; Cell Line, Tumor ; Cell Nucleus/genetics ; Cell Nucleus/metabolism ; Cell Nucleus/pathology ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/metabolism ; Gene Expression Profiling ; Gene Knockdown Techniques ; Humans ; Molecular Imaging ; Nuclear Pore ; Nuclear Pore Complex Proteins/genetics ; Nuclear Pore Complex Proteins/metabolism ; Protein Binding ; RNA Interference ; RNA, Small Interfering/genetics ; Transcription Factors/genetics ; Transcription Factors/metabolism
Chemical Substances	AHCTF1 protein, human ; Biomarkers ; DNA-Binding Proteins ; Nuclear Pore Complex Proteins ; RNA, Small Interfering ; Transcription Factors
Language	English
Publishing date	2019-05-13
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural
ZDB-ID	2020896-0
ISSN	1469-3178 ; 1469-221X
ISSN (online)	1469-3178
ISSN	1469-221X
DOI	10.15252/embr.201847283
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Zs.A 5433: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article: A screen for genetic defects of the zebrafish ear.

Schibler, Andria / Malicki, Jarema

Mechanisms of development

2007 Volume 124, Issue 7-8, Page(s) 592–604

Abstract: To advance the understanding of genetic mechanisms involved in the patterning and the differentiation of the vertebrate auditory system, we screened for mutations affecting ear development in the zebrafish larva. Fifteen recessive mutant alleles have ... ...

Abstract	To advance the understanding of genetic mechanisms involved in the patterning and the differentiation of the vertebrate auditory system, we screened for mutations affecting ear development in the zebrafish larva. Fifteen recessive mutant alleles have been isolated and analyzed. The phenotypes of these mutants involve abnormalities in ear morphology, otolith formation, or both processes in parallel. Among morphological defects, we found mutations affecting early patterning of the otic vesicle, the morphogenesis of semicircular canals, and the expansion of the ear lumen. The two most severe mutant phenotypes involve the absence of anterior and posterior cristae, as well as a severely misshapen morphology of the ear. In the category of otolith mutants, we found defects in otolith formation, growth, and shape. As it proved to be the case in past screening efforts of this type, these mutant lines represent an asset in the studies of molecular mechanisms that regulate vertebrate ear development.
MeSH term(s)	Animals ; Body Patterning ; Ear/abnormalities ; Ear/growth & development ; Ear/physiology ; Larva ; Mutation ; Zebrafish/growth & development ; Zebrafish/metabolism ; Zebrafish Proteins/genetics ; Zebrafish Proteins/metabolism
Chemical Substances	Zebrafish Proteins
Language	English
Publishing date	2007-08
Publishing country	Ireland
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1055986-3
ISSN	1872-6356 ; 0925-4773
ISSN (online)	1872-6356
ISSN	0925-4773
DOI	10.1016/j.mod.2007.04.005
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Zs.A 1152: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MG 35: Show issues

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Article ; Online: Histone-modifying enzymes: regulators of developmental decisions and drivers of human disease.

Butler, Jill S / Koutelou, Evangelia / Schibler, Andria C / Dent, Sharon Y R

Epigenomics

2012 Volume 4, Issue 2, Page(s) 163–177

Abstract: Precise transcriptional networks drive the orchestration and execution of complex developmental processes. Transcription factors possessing sequence-specific DNA binding properties activate or repress target genes in a step-wise manner to control most ... ...

Abstract	Precise transcriptional networks drive the orchestration and execution of complex developmental processes. Transcription factors possessing sequence-specific DNA binding properties activate or repress target genes in a step-wise manner to control most cell lineage decisions. This regulation often requires the interaction between transcription factors and subunits of massive protein complexes that bear enzymatic activities towards histones. The functional coupling of transcription proteins and histone modifiers underscores the importance of transcriptional regulation through chromatin modification in developmental cell fate decisions and in disease pathogenesis.
MeSH term(s)	Chromatin/metabolism ; DNA Methylation ; Enzyme Inhibitors/therapeutic use ; Histone Deacetylases/chemistry ; Histone Deacetylases/genetics ; Histone Deacetylases/metabolism ; Histone Demethylases/antagonists & inhibitors ; Histone Demethylases/genetics ; Histone Demethylases/metabolism ; Histones/genetics ; Histones/metabolism ; Humans ; Jumonji Domain-Containing Histone Demethylases/antagonists & inhibitors ; Jumonji Domain-Containing Histone Demethylases/genetics ; Jumonji Domain-Containing Histone Demethylases/metabolism ; Mutation ; Neoplasms/drug therapy ; Neoplasms/enzymology ; Neoplasms/pathology
Chemical Substances	Chromatin ; Enzyme Inhibitors ; Histones ; Histone Demethylases (EC 1.14.11.-) ; Jumonji Domain-Containing Histone Demethylases (EC 1.14.11.-) ; Histone Deacetylases (EC 3.5.1.98) ; histone deacetylase 3 (EC 3.5.1.98)
Language	English
Publishing date	2012-03-26
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ISSN	1750-192X
ISSN (online)	1750-192X
DOI	10.2217/epi.12.3
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Article ; Online: Blank spots on the map: some current questions on nuclear organization and genome architecture.

Adriaens, Carmen / Serebryannyy, Leonid A / Feric, Marina / Schibler, Andria / Meaburn, Karen J / Kubben, Nard / Trzaskoma, Pawel / Shachar, Sigal / Vidak, Sandra / Finn, Elizabeth H / Sood, Varun / Pegoraro, Gianluca / Misteli, Tom

Histochemistry and cell biology

2018 Volume 150, Issue 6, Page(s) 579–592

Abstract: The past decades have provided remarkable insights into how the eukaryotic cell nucleus and the genome within it are organized. The combined use of imaging, biochemistry and molecular biology approaches has revealed several basic principles of nuclear ... ...

Abstract	The past decades have provided remarkable insights into how the eukaryotic cell nucleus and the genome within it are organized. The combined use of imaging, biochemistry and molecular biology approaches has revealed several basic principles of nuclear architecture and function, including the existence of chromatin domains of various sizes, the presence of a large number of non-membranous intranuclear bodies, non-random positioning of genes and chromosomes in 3D space, and a prominent role of the nuclear lamina in organizing genomes. Despite this tremendous progress in elucidating the biological properties of the cell nucleus, many questions remain. Here, we highlight some of the key open areas of investigation in the field of nuclear organization and genome architecture with a particular focus on the mechanisms and principles of higher-order genome organization, the emerging role of liquid phase separation in cellular organization, and the functional role of the nuclear lamina in physiological processes.
MeSH term(s)	Animals ; Cell Nucleus/genetics ; Cell Nucleus/metabolism ; Humans ; Nuclear Lamina/genetics ; Nuclear Lamina/metabolism
Language	English
Publishing date	2018-09-20
Publishing country	Germany
Document type	Journal Article ; Review
ZDB-ID	1222930-1
ISSN	1432-119X ; 0301-5564 ; 0948-6143
ISSN (online)	1432-119X
ISSN	0301-5564 ; 0948-6143
DOI	10.1007/s00418-018-1726-1
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Article ; Online: USP22 controls multiple signaling pathways that are essential for vasculature formation in the mouse placenta.

Koutelou, Evangelia / Wang, Li / Schibler, Andria C / Chao, Hsueh-Ping / Kuang, Xianghong / Lin, Kevin / Lu, Yue / Shen, Jianjun / Jeter, Collene R / Salinger, Andrew / Wilson, Marenda / Chen, Yi Chun / Atanassov, Boyko S / Tang, Dean G / Dent, Sharon Y R

Development (Cambridge, England)

2019 Volume 146, Issue 4

Abstract: USP22, a component of the SAGA complex, is overexpressed in highly aggressive cancers, but the normal functions of this deubiquitinase are not well defined. We determined that loss of USP22 in mice results in embryonic lethality due to defects in extra- ... ...

Abstract	USP22, a component of the SAGA complex, is overexpressed in highly aggressive cancers, but the normal functions of this deubiquitinase are not well defined. We determined that loss of USP22 in mice results in embryonic lethality due to defects in extra-embryonic placental tissues and failure to establish proper vascular interactions with the maternal circulatory system. These phenotypes arise from abnormal gene expression patterns that reflect defective kinase signaling, including TGFβ and several receptor tyrosine kinase pathways. USP22 deletion in endothelial cells and pericytes that are induced from embryonic stem cells also hinders these signaling cascades, with detrimental effects on cell survival and differentiation as well as on the ability to form vessels. Our findings provide new insights into the functions of USP22 during development that may offer clues to its role in disease states.
MeSH term(s)	Animals ; Cardiovascular System/metabolism ; Cell Differentiation ; Cell Survival ; Chorioallantoic Membrane/metabolism ; Ear, Inner/embryology ; Embryonic Stem Cells/metabolism ; Endopeptidases/metabolism ; Endothelial Cells/metabolism ; Female ; Gene Expression ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Mice ; Phenotype ; Placenta/metabolism ; Pregnancy ; Protein Processing, Post-Translational ; Signal Transduction ; Time Factors ; Transforming Growth Factor beta/metabolism ; Transforming Growth Factor beta1/metabolism
Chemical Substances	Tgfb1 protein, mouse ; Transforming Growth Factor beta ; Transforming Growth Factor beta1 ; Endopeptidases (EC 3.4.-) ; USP22 protein, mouse (EC 3.4.19.12)
Language	English
Publishing date	2019-02-22
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	90607-4
ISSN	1477-9129 ; 0950-1991
ISSN (online)	1477-9129
ISSN	0950-1991
DOI	10.1242/dev.174037
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Ub I Zs.183: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Poly(Q) Expansions in ATXN7 Affect Solubility but Not Activity of the SAGA Deubiquitinating Module.

Lan, Xianjiang / Koutelou, Evangelia / Schibler, Andria C / Chen, Yi Chun / Grant, Patrick A / Dent, Sharon Y R

Molecular and cellular biology

2015 Volume 35, Issue 10, Page(s) 1777–1787

Abstract: Spinocerebellar ataxia type 7 (SCA7) is a debilitating neurodegenerative disease caused by expansion of a polyglutamine [poly(Q)] tract in ATXN7, a subunit of the deubiquitinase (DUB) module (DUBm) in the SAGA complex. The effects of ATXN7-poly(Q) on DUB ...

Abstract	Spinocerebellar ataxia type 7 (SCA7) is a debilitating neurodegenerative disease caused by expansion of a polyglutamine [poly(Q)] tract in ATXN7, a subunit of the deubiquitinase (DUB) module (DUBm) in the SAGA complex. The effects of ATXN7-poly(Q) on DUB activity are not known. To address this important question, we reconstituted the DUBm in vitro with either wild-type ATXN7 or a pathogenic form, ATXN7-92Q NT, with 92 Q residues at the N terminus (NT). We found that both forms of ATXN7 greatly enhance DUB activity but that ATXN7-92Q NT is largely insoluble unless it is incorporated into the DUBm. Cooverexpression of DUBm components in human astrocytes also promoted the solubility of ATXN7-92Q, inhibiting its aggregation into nuclear inclusions that sequester DUBm components, leading to global increases in ubiquitinated H2B (H2Bub) levels. Global H2Bub levels were also increased in the cerebellums of mice in a SCA7 mouse model. Our findings indicate that although ATXN7 poly(Q) expansions do not change the enzymatic activity of the DUBm, they likely contribute to SCA7 by initiating aggregates that sequester the DUBm away from its substrates.
MeSH term(s)	Animals ; Astrocytes/metabolism ; Ataxin-7 ; Cerebellum/metabolism ; Disease Models, Animal ; HEK293 Cells ; Humans ; In Vitro Techniques ; Mice ; Nerve Tissue Proteins/genetics ; Nerve Tissue Proteins/metabolism ; Peptides/metabolism ; Sf9 Cells ; Solubility ; Spinocerebellar Ataxias/metabolism ; Spinocerebellar Ataxias/pathology ; Spodoptera ; Ubiquitin-Specific Proteases/metabolism
Chemical Substances	ATXN7 protein, human ; Ataxin-7 ; Atxn7 protein, mouse ; Nerve Tissue Proteins ; Peptides ; polyglutamine (26700-71-0) ; Ubiquitin-Specific Proteases (EC 3.4.19.12)
Language	English
Publishing date	2015-03-09
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	779397-2
ISSN	1098-5549 ; 0270-7306
ISSN (online)	1098-5549
ISSN	0270-7306
DOI	10.1128/MCB.01454-14
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Article ; Online: REV7 is essential for DNA damage tolerance via two REV3L binding sites in mammalian DNA polymerase ζ.

Tomida, Junya / Takata, Kei-ichi / Lange, Sabine S / Schibler, Andria C / Yousefzadeh, Matthew J / Bhetawal, Sarita / Dent, Sharon Y R / Wood, Richard D

Nucleic acids research

2015 Volume 43, Issue 2, Page(s) 1000–1011

Abstract: DNA polymerase zeta (pol ζ) is exceptionally important for controlling mutagenesis and genetic instability. REV3L comprises the catalytic subunit, while REV7 (MAD2L2) is considered an accessory subunit. However, it has not been established that the role ... ...

Abstract	DNA polymerase zeta (pol ζ) is exceptionally important for controlling mutagenesis and genetic instability. REV3L comprises the catalytic subunit, while REV7 (MAD2L2) is considered an accessory subunit. However, it has not been established that the role of REV7 in DNA damage tolerance is necessarily connected with mammalian pol ζ, and there is accumulating evidence that REV7 and REV3L have independent functions. Analysis of pol ζ has been hampered by difficulties in expression of REV3L in mammalian cells, and lack of a functional complementation system. Here, we report that REV7 interacts with full-length REV3L in vivo and we identify a new conserved REV7 interaction site in human REV3L (residues 1993-2003), distinct from the known binding site (residues 1877-1887). Mutation of both REV7-binding sites eliminates the REV3L-REV7 interaction. In vivo complementation shows that both REV7-binding sites in REV3L are necessary for preventing spontaneous chromosome breaks and conferring resistance to UV radiation and cisplatin. This demonstrates a damage-specific function of REV7 in pol ζ, in contrast to the distinct roles of REV3L and REV7 in primary cell viability and embryogenesis.
MeSH term(s)	Binding Sites ; Cell Line ; DNA Damage ; DNA-Binding Proteins/chemistry ; DNA-Binding Proteins/metabolism ; DNA-Directed DNA Polymerase/chemistry ; DNA-Directed DNA Polymerase/metabolism ; HeLa Cells ; Humans ; Mad2 Proteins/metabolism
Chemical Substances	DNA-Binding Proteins ; MAD2L2 protein, human ; Mad2 Proteins ; DNA-Directed DNA Polymerase (EC 2.7.7.7) ; REV3L protein, human (EC 2.7.7.7)
Language	English
Publishing date	2015-01-07
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gku1385
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Article ; Online: GCN5 Regulates FGF Signaling and Activates Selective MYC Target Genes during Early Embryoid Body Differentiation

Li Wang / Evangelia Koutelou / Calley Hirsch / Ryan McCarthy / Andria Schibler / Kevin Lin / Yue Lu / Collene Jeter / Jianjun Shen / Michelle C. Barton / Sharon Y.R. Dent

Stem Cell Reports, Vol 10, Iss 1, Pp 287-

2018 Volume 299

Abstract: Summary: Precise control of gene expression during development is orchestrated by transcription factors and co-regulators including chromatin modifiers. How particular chromatin-modifying enzymes affect specific developmental processes is not well ... ...

Abstract	Summary: Precise control of gene expression during development is orchestrated by transcription factors and co-regulators including chromatin modifiers. How particular chromatin-modifying enzymes affect specific developmental processes is not well defined. Here, we report that GCN5, a histone acetyltransferase essential for embryonic development, is required for proper expression of multiple genes encoding components of the fibroblast growth factor (FGF) signaling pathway in early embryoid bodies (EBs). Gcn5−/− EBs display deficient activation of ERK and p38, mislocalization of cytoskeletal components, and compromised capacity to differentiate toward mesodermal lineage. Genomic analyses identified seven genes as putative direct targets of GCN5 during early differentiation, four of which are cMYC targets. These findings established a link between GCN5 and the FGF signaling pathway and highlighted specific GCN5-MYC partnerships in gene regulation during early differentiation.
Keywords	GCN5 ; MYC ; FGF signaling ; embryoid body ; chromatin ; histone H3 ; Medicine (General) ; R5-920 ; Biology (General) ; QH301-705.5
Subject code	572
Language	English
Publishing date	2018-01-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
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