scholarly journals Local chromatin context dictates the genetic determinants of the heterochromatin spreading reaction

2020 ◽  
Author(s):  
R.A. Greenstein ◽  
Henry Ng ◽  
Ramon R. Barrales ◽  
Catherine Tan ◽  
Sigurd Braun ◽  
...  
Keyword(s):  
Gene Silencing ◽  
Gene Deletion ◽  
Constitutive Heterochromatin ◽  
De Novo ◽  
Directed Assembly ◽  
Nucleation Site ◽  
Genetic Determinants ◽  
Chromatin Remodelers ◽  
Nucleation Sites ◽  
Deletion Library

AbstractHeterochromatin spreading, the expansion of gene-silencing structures from DNA-encoded nucleation sites, occurs in distinct chromatin contexts. Spreading re-establishes gene-poor constitutive heterochromatin every cell cycle, but also invades gene-rich euchromatin de novo to steer fate decisions. Unlike heterochromatin nucleation and assembly, the determinants of the spreading process remain poorly understood. Our heterochromatin spreading sensor separately records nucleation site-proximal, and distal, heterochromatin gene silencing. By screening a nuclear function gene deletion library in fission yeast, we identified regulators that alter the propensity, both positively and negatively, of a nucleation site to spread heterochromatin. Critically, the involvement of many regulators is conditioned by the chromatin context within which spreading occurs. We find spreading, but not nucleation, within constitutive heterochromatin, requires distinct Clr6 histone deacetylase complexes. However, spreading is universally antagonized by a suite of chromatin remodelers. Our results disentangle the machineries that control lateral heterochromatin spreading from those that instruct DNA-directed assembly.

scholarly journals Capturing the onset of PRC2-mediated repressive domain formation

2018 ◽  
Author(s):  
Ozgur Oksuz ◽  
Varun Narendra ◽  
Chul-Hwan Lee ◽  
Nicolas Descostes ◽  
Gary LeRoy ◽  
...  
Keyword(s):  
Gene Silencing ◽  
Long Range ◽  
De Novo ◽  
Histone H3 ◽  
Domain Formation ◽  
Polycomb Repressive Complex 2 ◽  
Nucleation Sites ◽  
In Cis ◽  
Step Mechanism

SummaryPolycomb repressive complex 2 (PRC2) maintains gene silencing by catalyzing methylation of histone H3 at lysine 27 (H3K27me2/3) within chromatin. By designing a system whereby PRC2-mediated repressive domains were collapsed and then reconstructed in an inducible fashion in vivo, a two-step mechanism of H3K27me2/3 domain formation became evident. First, PRC2 is stably recruited by the actions of JARID2 and MTF2 to a limited number of spatially interacting “nucleation sites”, creating H3K27me3-forming polycomb foci within the nucleus. Second, PRC2 is allosterically activated via its binding to H3K27me3 and rapidly spreads H3K27me2/3 both in cis and in far-cis via long-range contacts. As PRC2 proceeds further from the nucleation sites, its stability on chromatin decreases such that domains of H3K27me3 remain proximal, and those of H3K27me2 distal, to the nucleation sites. This study demonstrates the principles of de novo establishment of PRC2-mediated repressive domains across the genome.

scholarly journals Epigenetic Changes in Host Ribosomal DNA Promoter Induced by an Asymptomatic Plant Virus Infection

Biology ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 91 ◽  
Author(s):  
Miryam Pérez-Cañamás ◽  
Elizabeth Hevia ◽  
Carmen Hernández
Keyword(s):  
Gene Silencing ◽  
Ribosomal Dna ◽  
Plant Virus ◽  
Dna Methyltransferase ◽  
Cytosine Methylation ◽  
De Novo ◽  
Methylation Pattern ◽  
Transcriptional Gene Silencing ◽  
Post Transcriptional Gene Silencing ◽  
The Impact

DNA cytosine methylation is one of the main epigenetic mechanisms in higher eukaryotes and is considered to play a key role in transcriptional gene silencing. In plants, cytosine methylation can occur in all sequence contexts (CG, CHG, and CHH), and its levels are controlled by multiple pathways, including de novo methylation, maintenance methylation, and demethylation. Modulation of DNA methylation represents a potentially robust mechanism to adjust gene expression following exposure to different stresses. However, the potential involvement of epigenetics in plant-virus interactions has been scarcely explored, especially with regard to RNA viruses. Here, we studied the impact of a symptomless viral infection on the epigenetic status of the host genome. We focused our attention on the interaction between Nicotiana benthamiana and Pelargonium line pattern virus (PLPV, family Tombusviridae), and analyzed cytosine methylation in the repetitive genomic element corresponding to ribosomal DNA (rDNA). Through a combination of bisulfite sequencing and RT-qPCR, we obtained data showing that PLPV infection gives rise to a reduction in methylation at CG sites of the rDNA promoter. Such a reduction correlated with an increase and decrease, respectively, in the expression levels of some key demethylases and of MET1, the DNA methyltransferase responsible for the maintenance of CG methylation. Hypomethylation of rDNA promoter was associated with a five-fold augmentation of rRNA precursor levels. The PLPV protein p37, reported as a suppressor of post-transcriptional gene silencing, did not lead to the same effects when expressed alone and, thus, it is unlikely to act as suppressor of transcriptional gene silencing. Collectively, the results suggest that PLPV infection as a whole is able to modulate host transcriptional activity through changes in the cytosine methylation pattern arising from misregulation of methyltransferases/demethylases balance.

Proton Induced Structuring of a Photostructurable Glass

2002 ◽  
Vol 739 ◽  
Author(s):  
Meg Abraham ◽  
Inmaculada Gomez-Morilla ◽  
Mike Marsh ◽  
Geoff Grime
Keyword(s):  
Three Dimensional ◽  
Particle Beam ◽  
Nucleation Site ◽  
Buried Structures ◽  
Corning Glass ◽  
Nucleation Sites ◽  
Initial Nucleation ◽  
Similar Product ◽  
Photon Process ◽  
Meta Silicate

ABSTRACTThe use of photons to create intricate three-dimensional and buried structures [1] in photo-structurable glass has been well demonstrated at several institutions [2]. In these instances the glass used whether it be Foturan™, made by the Schott Group or a similar product made by Corning Glass, forms a silver nucleation sites on exposure to intense UV laser light via a two-photon process. Subsequent annealing causes a localized crystal growth to form a meta-silicate phase which can be etched in dilute hydrofluoric acid at rates of 20 to 50 times that of the unprocessed glass. The same formulation of glass can be “exposed” using a particle beam to create the nucleation site. In the case of particle beam exposure, experiments have shown that the mechanisms that cause this initial nucleation and eventual stochiometric transformation, after annealing, depend largely on the beam energy.

scholarly journals A de novo and heterozygous gene deletion causing a variant of von Willebrand disease

Blood ◽  
1990 ◽  
Vol 75 (3) ◽  
pp. 677-683
Author(s):  
F Bernardi ◽  
G Marchetti ◽  
S Guerra ◽  
A Casonato ◽  
D Gemmati ◽  
...  
Keyword(s):  
Gene Deletion ◽  
De Novo ◽  
Genomic Region ◽  
Restriction Pattern ◽  
Von Willebrand Disease ◽  
De Novo Mutation ◽  
Homologous Protein ◽  
Copy Dna ◽  
Von Willebrand ◽  
Reduced Intensity

An abnormal von Willebrand factor (vWF) gene restriction pattern has been found in a patient with von Willebrand disease. Because this gene alteration is not present in his parents or in 50 normal and 25 affected subjects, and the restriction fragment length polymorphism haplotypes are inherited normally in the patient's family, we suggest that a de novo mutation is present. Bands with reduced intensity and additional fragments, observed in several restriction digests, hybridize with noncontiguous copy DNA (cDNA) portions, thus indicating the presence of a heterozygous gene deletion. The deletion removes a genomic region containing at least codons 1147 through 1854 and corresponding to the D3-A3 homologous protein domains. The extent of the vWF pseudogene on chromosome 22 is roughly similar to that of the deleted area. However, the pseudogenic nature of the deletion is excluded by the mapping of bands with reduced intensity in the patient to the true vWF gene. The vWF antigen levels are one fourth of normal and ristocetin cofactor activity is severely impaired. The reduction of high molecular weight multimers in plasma and platelets and the altered triplet morphology are compatible with the presence of a dominant variant of type II von Willebrand disease.

scholarly journals EGF stimulates an increase in actin nucleation and filament number at the leading edge of the lamellipod in mammary adenocarcinoma cells

1998 ◽  
Vol 111 (2) ◽  
pp. 199-211 ◽  
Author(s):  
A.Y. Chan ◽  
S. Raft ◽  
M. Bailly ◽  
J.B. Wyckoff ◽  
J.E. Segall ◽  
...  
Keyword(s):  
Actin Polymerization ◽  
De Novo ◽  
Leading Edge ◽  
Mammary Adenocarcinoma ◽  
Actin Dynamics ◽  
Actin Nucleation ◽  
Nucleation Sites ◽  
Nucleation Activity ◽  
Pointed End ◽  
Stimulation Of

Stimulation of metastatic MTLn3 cells with EGF causes the rapid extension of lamellipods, which contain a zone of F-actin at the leading edge. In order to establish the mechanism for accumulation of F-actin at the leading edge and its relationship to lamellipod extension in response to EGF, we have studied the kinetics and location of EGF-induced actin nucleation activity in MTLn3 cells and characterized the actin dynamics at the leading edge by measuring the changes at the pointed and barbed ends of actin filaments upon EGF stimulation of MTLn3 cells. The major result of this study is that stimulation of MTLn3 cells with EGF causes a transient increase in actin nucleation activity resulting from the appearance of free barbed ends very close to the leading edge of extending lamellipods. In addition, cytochalasin D causes a significant decrease in the total F-actin content in EGF-stimulated cells, indicating that both actin polymerization and depolymerization are stimulated by EGF. Pointed end incorporation of rhodamine-labeled actin by the EGF stimulated cells is 2.12+/−0.47 times higher than that of control cells. Since EGF stimulation causes an increase in both barbed and pointed end incorporation of rhodamine-labeled actin in the same location, the EGF-stimulated nucleation sites are more likely due either to severing of pre-existing filaments or de novo nucleation of filaments at the leading edge thereby creating new barbed and pointed ends. The timing and location of EGF-induced actin nucleation activity in MTLn3 cells can account for the observed accumulation of F-actin at the leading edge and demonstrate that this F-actin rich zone is the primary actin polymerization zone after stimulation.

scholarly journals Epimutations are associated with CHROMOMETHYLASE 3-induced de novo DNA methylation

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Jered M Wendte ◽  
Yinwen Zhang ◽  
Lexiang Ji ◽  
Xiuling Shi ◽  
Rashmi R Hazarika ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Plant Species ◽  
Dna Methyltransferase ◽  
Constitutive Heterochromatin ◽  
De Novo ◽  
Flowering Plant ◽  
Gene Body ◽  
Gene Body Methylation ◽  
Mechanistic Basis ◽  
Flowering Plant Species

In many plant species, a subset of transcribed genes are characterized by strictly CG-context DNA methylation, referred to as gene body methylation (gbM). The mechanisms that establish gbM are unclear, yet flowering plant species naturally without gbM lack the DNA methyltransferase, CMT3, which maintains CHG (H = A, C, or T) and not CG methylation at constitutive heterochromatin. Here, we identify the mechanistic basis for gbM establishment by expressing CMT3 in a species naturally lacking CMT3. CMT3 expression reconstituted gbM through a progression of de novo CHG methylation on expressed genes, followed by the accumulation of CG methylation that could be inherited even following loss of the CMT3 transgene. Thus, gbM likely originates from the simultaneous targeting of loci by pathways that promote euchromatin and heterochromatin, which primes genes for the formation of stably inherited epimutations in the form of CG DNA methylation.

scholarly journals Post-transcriptional gene silencing triggers dispensable DNA methylation in gene body in Arabidopsis

2019 ◽  
Vol 47 (17) ◽  
pp. 9104-9114 ◽  
Author(s):  
Christelle Taochy ◽  
Agnès Yu ◽  
Nicolas Bouché ◽  
Nathalie Bouteiller ◽  
Taline Elmayan ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Gene Silencing ◽  
De Novo ◽  
Transcriptional Silencing ◽  
Transcriptional Gene Silencing ◽  
Gene Body ◽  
Coding Sequence ◽  
Post Transcriptional Gene Silencing ◽  
Methylation Signal ◽  
Rule Out

Abstract Spontaneous post-transcriptional silencing of sense transgenes (S-PTGS) is established in each generation and is accompanied by DNA methylation, but the pathway of PTGS-dependent DNA methylation is unknown and so is its role. Here we show that CHH and CHG methylation coincides spatially and temporally with RDR6-dependent products derived from the central and 3′ regions of the coding sequence, and requires the components of the RNA-directed DNA methylation (RdDM) pathway NRPE1, DRD1 and DRM2, but not CLSY1, NRPD1, RDR2 or DCL3, suggesting that RDR6-dependent products, namely long dsRNAs and/or siRNAs, trigger PTGS-dependent DNA methylation. Nevertheless, none of these RdDM components are required to establish S-PTGS or produce a systemic silencing signal. Moreover, preventing de novo DNA methylation in non-silenced transgenic tissues grafted onto homologous silenced tissues does not inhibit the triggering of PTGS. Overall, these data indicate that gene body DNA methylation is a consequence, not a cause, of PTGS, and rule out the hypothesis that a PTGS-associated DNA methylation signal is transmitted independent of a PTGS signal.

scholarly journals A de novo and heterozygous gene deletion causing a variant of von Willebrand disease

Blood ◽  
1990 ◽  
Vol 75 (3) ◽  
pp. 677-683 ◽  
Author(s):  
F Bernardi ◽  
G Marchetti ◽  
S Guerra ◽  
A Casonato ◽  
D Gemmati ◽  
...  
Keyword(s):  
Gene Deletion ◽  
De Novo ◽  
Genomic Region ◽  
Restriction Pattern ◽  
Von Willebrand Disease ◽  
De Novo Mutation ◽  
Homologous Protein ◽  
Copy Dna ◽  
Von Willebrand ◽  
Reduced Intensity

Abstract An abnormal von Willebrand factor (vWF) gene restriction pattern has been found in a patient with von Willebrand disease. Because this gene alteration is not present in his parents or in 50 normal and 25 affected subjects, and the restriction fragment length polymorphism haplotypes are inherited normally in the patient's family, we suggest that a de novo mutation is present. Bands with reduced intensity and additional fragments, observed in several restriction digests, hybridize with noncontiguous copy DNA (cDNA) portions, thus indicating the presence of a heterozygous gene deletion. The deletion removes a genomic region containing at least codons 1147 through 1854 and corresponding to the D3-A3 homologous protein domains. The extent of the vWF pseudogene on chromosome 22 is roughly similar to that of the deleted area. However, the pseudogenic nature of the deletion is excluded by the mapping of bands with reduced intensity in the patient to the true vWF gene. The vWF antigen levels are one fourth of normal and ristocetin cofactor activity is severely impaired. The reduction of high molecular weight multimers in plasma and platelets and the altered triplet morphology are compatible with the presence of a dominant variant of type II von Willebrand disease.

Carbon Black and Fullerenes: New Discoveries in Early Formation Mechanisms and Nucleation

2000 ◽  
Vol 73 (5) ◽  
pp. 875-888 ◽  
Author(s):  
M. Pontier Johnson ◽  
R. W. Locke ◽  
J. B. Donnet ◽  
T. K. Wang ◽  
C. C. Wang ◽  
...  
Keyword(s):  
Carbon Black ◽  
Mass Spectroscopy ◽  
Photoelectron Spectroscopy ◽  
Nucleation Site ◽  
Formation Mechanisms ◽  
Clear Understanding ◽  
Transmission Electron ◽  
Nucleation Sites ◽  
Buckminster Fullerene ◽  
Secondary Ion

Abstract Recent studies on the formation of carbon black have resulted in the previously unreported finding of buckminster-fullerene, C60, in trace quantities in the toluene extractable materials. High-resolution transmission electron microscopy (HRTEM) experiments indicate the molecule may be functioning as a nucleation site in the formation of primary particles of carbon black. Time-of-flight secondary ion mass spectroscopy (ToF-SIMS) and X-ray photoelectron spectroscopy (XPS) provided the surface chemical analysis of conventional and experimental carbon blacks. The toluene extracts represented the precursor compounds present in the gaseous phase at the time of quench. The extracts were analyzed by Fourier transform infrared (FTIR) spectroscopy, liquid chromatography (LC)/mass spectroscopy (MS) and elemental composition. The data, taken as a whole, have led to a more clear understanding of the competitive chemical pathways occurring during the inception and nucleation of a primary particle of carbon black. Direct observation of nucleation sites and types are possible with HRTEM analysis.

scholarly journals Ice nucleation efficiency of clay minerals in the immersion mode

2012 ◽  
Vol 12 (13) ◽  
pp. 5859-5878 ◽  
Author(s):  
V. Pinti ◽  
C. Marcolli ◽  
B. Zobrist ◽  
C. R. Hoyle ◽  
T. Peter
Keyword(s):  
Clay Minerals ◽  
Clay Mineral ◽  
Differential Scanning Calorimeter ◽  
Pure Water ◽  
Nucleation Site ◽  
Ice Nucleation ◽  
Nucleation Sites ◽  
The One ◽  
Site Classes

Abstract. Emulsion and bulk freezing experiments were performed to investigate immersion ice nucleation on clay minerals in pure water, using various kaolinites, montmorillonites, illites as well as natural dust from the Hoggar Mountains in the Saharan region. Differential scanning calorimeter measurements were performed on three different kaolinites (KGa-1b, KGa-2 and K-SA), two illites (Illite NX and Illite SE) and four natural and acid-treated montmorillonites (SWy-2, STx-1b, KSF and K-10). The emulsion experiments provide information on the average freezing behaviour characterized by the average nucleation sites. These experiments revealed one to sometimes two distinct heterogeneous freezing peaks, which suggest the presence of a low number of qualitatively distinct average nucleation site classes. We refer to the peak at the lowest temperature as "standard peak" and to the one occurring in only some clay mineral types at higher temperatures as "special peak". Conversely, freezing in bulk samples is not initiated by the average nucleation sites, but by a very low number of "best sites". The kaolinites and montmorillonites showed quite narrow standard peaks with onset temperatures 238 K

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