Glucose-Responsive Regulators of Gene Expression inSaccharomyces cerevisiaeFunction at the Nuclear Periphery via a Reverse Recruitment Mechanism

Genomic regions preferentially associate with regions of similar transcriptional activity, partitioning genomes into active and inactive compartments within the nucleus. Here we explore mechanisms controlling genome compartment organization inCaenorhabditis elegansand investigate roles for compartments in regulating gene expression. Distal arms ofC. eleganschromosomes, which are enriched for heterochromatic histone modifications H3K9me1/me2/me3, interact with each other bothin cisandin trans,while interacting less frequently with central regions, leading to genome compartmentalization. Arms are anchored to the nuclear periphery via the nuclear envelope protein CEC-4, which binds to H3K9me. By performing genome-wide chromosome conformation capture experiments (Hi-C), we showed that eliminating H3K9me1/me2/me3 through mutations in the methyltransferase genesmet-2andset-25significantly impaired formation of inactive Arm and active Center compartments.cec-4mutations also impaired compartmentalization, but to a lesser extent. We found that H3K9me promotes compartmentalization through two distinct mechanisms: Perinuclear anchoring of chromosome arms via CEC-4 to promote theircisassociation, and an anchoring-independent mechanism that compacts individual chromosome arms. In bothmet-2 set-25andcec-4mutants, no dramatic changes in gene expression were found for genes that switched compartments or for genes that remained in their original compartment, suggesting that compartment strength does not dictate gene-expression levels. Furthermore, H3K9me, but not perinuclear anchoring, also contributes to formation of another prominent feature of chromosome organization, megabase-scale topologically associating domains on X established by the dosage compensation condensin complex. Our results demonstrate that H3K9me plays crucial roles in regulating genome organization at multiple levels.

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Actin-based motility drives baculovirus transit to the nucleus and cell surface

The Journal of Cell Biology ◽

10.1083/jcb.201001162 ◽

2010 ◽

Vol 190 (2) ◽

pp. 187-195 ◽

Cited By ~ 143

Author(s):

Taro Ohkawa ◽

Loy E. Volkman ◽

Matthew D. Welch

Keyword(s):

Gene Expression ◽

Actin Polymerization ◽

Nuclear Periphery ◽

Viral Gene Expression ◽

Early Gene ◽

Evolutionary Strategy ◽

Viral Gene ◽

Nuclear Pore ◽

Nuclear Pore Complexes ◽

Nuclear Entry

Most viruses move intracellularly to and from their sites of replication using microtubule-based mechanisms. In this study, we show that nucleocapsids of the baculovirus Autographa californica multiple nucleopolyhedrovirus undergo intracellular motility driven by actin polymerization. Motility requires the viral P78/83 capsid protein and the host Arp2/3 complex. Surprisingly, the virus directs two sequential and coordinated phases of actin-based motility. Immediately after cell entry, motility enables exploration of the cytoplasm and collision with the nuclear periphery, speeding nuclear entry and the initiation of viral gene expression. Nuclear entry itself requires transit through nuclear pore complexes. Later, after the onset of early gene expression, motility is required for accumulation of a subpopulation of nucleocapsids in the tips of actin-rich surface spikes. Temporal coordination of actin-based nuclear and surface translocation likely enables rapid transmission to neighboring cells during infection in insects and represents a distinctive evolutionary strategy for overcoming host defenses.

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Transposition of DNase hypersensitive chromatin to the nuclear periphery coincides temporally with nerve growth factor-induced up-regulation of gene expression in PC12 cells.

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.93.21.11646 ◽

1996 ◽

Vol 93 (21) ◽

pp. 11646-11651 ◽

Cited By ~ 11

Author(s):

P. C. Park ◽

U. De Boni

Keyword(s):

Gene Expression ◽

Nerve Growth Factor ◽

Growth Factor ◽

Pc12 Cells ◽

Regulation Of Gene Expression ◽

Nuclear Periphery ◽

Nerve Growth

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Impact of Chromosome Fusions on 3D Genome Organization and Gene Expression in Budding Yeast

Genetics ◽

10.1534/genetics.119.302978 ◽

2020 ◽

Vol 214 (3) ◽

pp. 651-667 ◽

Cited By ~ 2

Author(s):

Marco Di Stefano ◽

Francesca Di Giovanni ◽

Vasilisa Pozharskaia ◽

Mercè Gomar-Alba ◽

Davide Baù ◽

...

Keyword(s):

Gene Expression ◽

Budding Yeast ◽

Nuclear Organization ◽

Nuclear Periphery ◽

Three Dimensional ◽

Global Gene Expression ◽

3D Genome ◽

Expression Of Genes ◽

Genome Wide ◽

Chromosome Fusions

The three-dimensional (3D) organization of chromosomes can influence transcription. However, the frequency and magnitude of these effects remain debated. To determine how changes in chromosome positioning affect transcription across thousands of genes with minimal perturbation, we characterized nuclear organization and global gene expression in budding yeast containing chromosome fusions. We used computational modeling and single-cell imaging to determine chromosome positions, and integrated these data with genome-wide transcriptional profiles from RNA sequencing. We find that chromosome fusions dramatically alter 3D nuclear organization without leading to strong genome-wide changes in transcription. However, we observe a mild but significant and reproducible increase in the expression of genes displaced away from the periphery. The increase in transcription is inversely proportional to the propensity of a given locus to be at the nuclear periphery; for example, a 10% decrease in the propensity of a gene to reside at the nuclear envelope is accompanied by a 10% increase in gene expression. Modeling suggests that this is due to both deletion of telomeres and to displacement of genes relative to the nuclear periphery. These data suggest that basal transcriptional activity is sensitive to radial changes in gene position, and provide insight into the functional relevance of budding yeast chromosome-level 3D organization in gene expression.

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Multiple facets of nuclear periphery in gene expression control

Current Opinion in Cell Biology ◽

10.1016/j.ceb.2010.12.005 ◽

2011 ◽

Vol 23 (3) ◽

pp. 346-353 ◽

Cited By ~ 41

Author(s):

Ghislaine Arib ◽

Asifa Akhtar

Keyword(s):

Gene Expression ◽

Nuclear Periphery ◽

Expression Control ◽

Gene Expression Control

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Nuclear organization of splicing snRNPs during differentiation of murine erythroleukemia cells in vitro.

The Journal of Cell Biology ◽

10.1083/jcb.123.5.1055 ◽

1993 ◽

Vol 123 (5) ◽

pp. 1055-1068 ◽

Cited By ~ 31

Author(s):

M Antoniou ◽

M Carmo-Fonseca ◽

J Ferreira ◽

A I Lamond

Keyword(s):

Gene Expression ◽

Early Stage ◽

Nuclear Organization ◽

Nuclear Periphery ◽

Erythroid Differentiation ◽

Elevated Concentration ◽

Erythroid Progenitors ◽

Coiled Bodies ◽

Murine Erythroleukemia ◽

Terminal Erythroid Differentiation

Murine erythroleukemia (MEL) cells are erythroid progenitors that can be induced to undergo terminal erythroid differentiation in culture. We have used MEL cells here as a model system to study the nuclear organization of splicing snRNPs during the physiological changes in gene expression which accompany differentiation. In uninduced MEL cells, snRNPs are widely distributed throughout the nucleoplasm and show an elevated concentration in coiled bodies. Within the first two days after induction of terminal erythroid differentiation, the pattern of gene expression changes, erythroid-specific transcription is activated and transcription of many other genes is repressed. During this early stage splicing snRNPs remain widely distributed through the nucleoplasm and continue to associate with coiled bodies. At later stages of differentiation (four to six days), when total transcription levels have greatly decreased, splicing snRNPs are redistributed. By six days postinduction snRNPs were concentrated in large clusters of interchromatin granules and no longer associated with coiled bodies. At the end-point of erythroid differentiation, just before enucleation, we observe a dramatic segregation of splicing snRNPs from the condensed chromatin. Analysis by EM shows that the snRNPs are packaged into a membrane-associated structure at the nuclear periphery which we term the "SCIM" domain (i.e., SnRNP Clusters Inside a Membrane).

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Viral DNA Sensors IFI16 and Cyclic GMP-AMP Synthase Possess Distinct Functions in Regulating Viral Gene Expression, Immune Defenses, and Apoptotic Responses during Herpesvirus Infection

mBio ◽

10.1128/mbio.01553-16 ◽

2016 ◽

Vol 7 (6) ◽

Cited By ~ 84

Author(s):

Benjamin A. Diner ◽

Krystal K. Lum ◽

Jared E. Toettcher ◽

Ileana M. Cristea

Keyword(s):

Gene Expression ◽

Live Cell Imaging ◽

Nuclear Periphery ◽

Viral Gene Expression ◽

Live Cell ◽

Viral Gene ◽

Viral Dna ◽

Herpes Simplex Virus 1 ◽

Simplex Virus ◽

Hsv 1

ABSTRACTThe human interferon-inducible protein IFI16 is an important antiviral factor that binds nuclear viral DNA and promotes antiviral responses. Here, we define IFI16 dynamics in space and time and its distinct functions from the DNA sensor cyclic dinucleotide GMP-AMP synthase (cGAS). Live-cell imaging reveals a multiphasic IFI16 redistribution, first to viral entry sites at the nuclear periphery and then to nucleoplasmic puncta upon herpes simplex virus 1 (HSV-1) and human cytomegalovirus (HCMV) infections. Optogenetics and live-cell microscopy establish the IFI16 pyrin domain as required for nuclear periphery localization and oligomerization. Furthermore, using proteomics, we define the signature protein interactions of the IFI16 pyrin and HIN200 domains and demonstrate the necessity of pyrin for IFI16 interactions with antiviral proteins PML and cGAS. We probe signaling pathways engaged by IFI16, cGAS, and PML using clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9-mediated knockouts in primary fibroblasts. While IFI16 induces cytokines, only cGAS activates STING/TBK-1/IRF3 and apoptotic responses upon HSV-1 and HCMV infections. cGAS-dependent apoptosis upon DNA stimulation requires both the enzymatic production of cyclic dinucleotides and STING. We show that IFI16, not cGAS or PML, represses HSV-1 gene expression, reducing virus titers. This indicates that regulation of viral gene expression may function as a greater barrier to viral replication than the induction of antiviral cytokines. Altogether, our findings establish coordinated and distinct antiviral functions for IFI16 and cGAS against herpesviruses.IMPORTANCEHow mammalian cells detect and respond to DNA viruses that replicate in the nucleus is poorly understood. Here, we decipher the distinct functions of two viral DNA sensors, IFI16 and cGAS, during active immune signaling upon infection with two herpesviruses, herpes simplex virus 1 (HSV-1) and human cytomegalovirus (HCMV). We show that IFI16 rapidly oligomerizes at incoming herpesvirus genomes at the nuclear periphery to transcriptionally repress viral gene expression and limit viral replicative capacity. We further demonstrate that IFI16 does not initiate upstream activation of the canonical STING/TBK-1/IRF3 signaling pathway but is required for downstream antiviral cytokine expression. In contrast, we find that, upon DNA sensing during herpesvirus infection, cGAS triggers apoptosis in a STING-dependent manner. Our live-cell imaging, mass spectrometry-based proteomics, CRISPR-based cellular assays, and optogenetics underscore the value of integrative approaches to uncover complex cellular responses against pathogens.

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Nup93 and CTCF co-modulate spatiotemporal dynamics and function of the HOXA gene cluster during differentiation

10.1101/646224 ◽

2019 ◽

Author(s):

Ajay S. Labade ◽

Adwait Salvi ◽

Krishanpal Karmodiya ◽

Kundan Sengupta

Keyword(s):

Gene Expression ◽

Gene Locus ◽

Nuclear Periphery ◽

Spatiotemporal Dynamics ◽

Differentiated Cells ◽

Undifferentiated Cells ◽

Dynamics And Function ◽

Hoxa Gene Expression ◽

And Function ◽

Hoxa Gene

ABSTRACTNucleoporins regulate nuclear transport. In addition, nucleoporins also modulate chromatin organization and gene expression. Here we investigated the role of nucleoporin Nup93, in regulating HOXA gene expression during differentiation. ChIP-Seq analysis revealed that Nup93 associates with genes involved in development and differentiation. Furthermore, Nup93 occupancy significantly overlaps with CTCF. Interestingly, Nup93 and CTCF show antagonistic roles in regulating 3’ and 5’ end HOXA genes in undifferentiated cells. The HOXA gene locus untethered from the nuclear periphery upon Nup93 but not CTCF depletion, consistent with its upregulation. Remarkably, occupancy of Nup93 and CTCF on HOXA gene locus progressively declined during differentiation but was restored in differentiated cells, consistent with the rerepression and re-localization of the HOXA gene locus with the nuclear periphery upon differentiation. In summary, Nup93 is a key modulator of the spatiotemporal dynamics and function of the HOXA gene locus during differentiation.

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Clock proteins regulate spatiotemporal organization of clock genes to control circadian rhythms

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2019756118 ◽

2021 ◽

Vol 118 (28) ◽

pp. e2019756118

Author(s):

Yangbo Xiao ◽

Ye Yuan ◽

Mariana Jimenez ◽

Neeraj Soni ◽

Swathi Yadlapalli

Keyword(s):

Gene Expression ◽

Circadian Rhythms ◽

Nuclear Envelope ◽

Molecular Mechanisms ◽

Clock Genes ◽

Nuclear Periphery ◽

Spatiotemporal Organization ◽

Subnuclear Localization ◽

Clock Proteins ◽

Spatial Reorganization

Circadian clocks regulate ∼24-h oscillations in gene expression, behavior, and physiology. While the genetic and molecular mechanisms of circadian rhythms are well characterized, what remains poorly understood are the intracellular dynamics of circadian clock components and how they affect circadian rhythms. Here, we elucidate how spatiotemporal organization and dynamics of core clock proteins and genes affect circadian rhythms in Drosophila clock neurons. Using high-resolution imaging and DNA-fluorescence in situ hybridization techniques, we demonstrate that Drosophila clock proteins (PERIOD and CLOCK) are organized into a few discrete foci at the nuclear envelope during the circadian repression phase and play an important role in the subnuclear localization of core clock genes to control circadian rhythms. Specifically, we show that core clock genes, period and timeless, are positioned close to the nuclear periphery by the PERIOD protein specifically during the repression phase, suggesting that subnuclear localization of core clock genes might play a key role in their rhythmic gene expression. Finally, we show that loss of Lamin B receptor, a nuclear envelope protein, leads to disruption of PER foci and per gene peripheral localization and results in circadian rhythm defects. These results demonstrate that clock proteins play a hitherto unexpected role in the subnuclear reorganization of core clock genes to control circadian rhythms, revealing how clocks function at the subcellular level. Our results further suggest that clock protein foci might regulate dynamic clustering and spatial reorganization of clock-regulated genes over the repression phase to control circadian rhythms in behavior and physiology.

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Deletions of Chromosome 7q Affect Nuclear Organization and HLXB9Gene Expression in Hematological Disorders

Cancers ◽

10.3390/cancers11040585 ◽

2019 ◽

Vol 11 (4) ◽

pp. 585 ◽

Cited By ~ 2

Author(s):

Concetta Federico ◽

Temitayo Owoka ◽

Denise Ragusa ◽

Valentina Sturiale ◽

Domenica Caponnetto ◽

...

Keyword(s):

Gene Expression ◽

Chromosomal Abnormalities ◽

Mechanistic Model ◽

Nuclear Periphery ◽

Single Chromosome ◽

Individual Gene ◽

Hematological Disorders ◽

Nuclear Interior ◽

Spatial Positioning ◽

Chromosome 7Q

The radial spatial positioning of individual gene loci within interphase nuclei has been associated with up- and downregulation of their expression. In cancer, the genome organization may become disturbed due to chromosomal abnormalities, such as translocations or deletions, resulting in the repositioning of genes and alteration of gene expression with oncogenic consequences. In this study, we analyzed the nuclear repositioning of HLXB9 (also called MNX1), mapping at 7q36.3, in patients with hematological disorders carrying interstitial deletions of 7q of various extents, with a distal breakpoint in 7q36. We observed that HLXB9 remains at the nuclear periphery, or is repositioned towards the nuclear interior, depending upon the compositional properties of the chromosomal regions involved in the rearrangement. For instance, a proximal breakpoint leading the guanine-cytosine (GC)-poor band 7q21 near 7q36 would bring HLXB9 to the nuclear periphery, whereas breakpoints that join the GC-rich band 7q22 to 7q36 would bring HLXB9 to the nuclear interior. This nuclear repositioning is associated with transcriptional changes, with HLXB9 in the nuclear interior becoming upregulated. Here we report an in cis rearrangement, involving one single chromosome altering gene behavior. Furthermore, we propose a mechanistic model for chromatin reorganization that affects gene expression via the influences of new chromatin neighborhoods.

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