scholarly journals Restricted nucleation and piRNA-mediated establishment of heterochromatin during embryogenesis in Drosophila miranda

2021 ◽  
Author(s):  
Kevin H.-C. Wei ◽  
Carolus Chan ◽  
Doris Bachtrog
Keyword(s):  
Genome Stability ◽  
Repetitive Sequences ◽  
Developmental Time ◽  
Wide Distribution ◽  
Promoter Regions ◽  
Architectural Feature ◽  
Genome Wide ◽  
Nucleation Sites ◽  
Zygotic Transcription ◽  
Initial Nucleation

Heterochromatin is a key architectural feature of eukaryotic genomes, crucial for silencing of repetitive elements and maintaining genome stability. Heterochromatin shows stereotypical enrichment patterns around centromeres and repetitive sequences, but the molecular details of how heterochromatin is established during embryogenesis are poorly understood. Here, we map the genome-wide distribution of H3K9me3-dependent heterochromatin in individual embryos of D. miranda at precisely staged developmental time points. We find that canonical H3K9me3 enrichment patterns are established early on before cellularization, and mature into stable and broad heterochromatin domains through development. Intriguingly, initial nucleation sites of H3K9me3 enrichment appear as early as embryonic stage3 (nuclear cycle 9) over transposable elements (TE) and progressively broaden, consistent with spreading to neighboring nucleosomes. The earliest nucleation sites are limited to specific regions of a small number of TE families and often appear over promoter regions, while late nucleation develops broadly across most TEs. Early nucleating TEs are highly targeted by maternal piRNAs and show early zygotic transcription, consistent with a model of co-transcriptional silencing of TEs by small RNAs. Interestingly, truncated TE insertions lacking nucleation sites show significantly reduced enrichment across development, suggesting that the underlying sequences play an important role in recruiting histone methyltransferases for heterochromatin establishment.

scholarly journals Establishment of H3K9me3-dependent heterochromatin during embryogenesis in Drosophila miranda

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Kevin H-C Wei ◽  
Carolus Chan ◽  
Doris Bachtrog
Keyword(s):  
Repetitive Sequences ◽  
Developmental Time ◽  
Wide Distribution ◽  
Ltr Retrotransposons ◽  
Architectural Feature ◽  
Genome Wide ◽  
Nucleation Sites ◽  
Zygotic Transcription ◽  
Initial Nucleation ◽  
Eukaryotic Genomes

Heterochromatin is a key architectural feature of eukaryotic genomes crucial for silencing of repetitive elements. During Drosophila embryonic cellularization, heterochromatin rapidly appears over repetitive sequences but the molecular details of how heterochromatin is established are poorly understood. Here, we map the genome-wide distribution of H3K9me3-dependent heterochromatin in individual embryos of Drosophila miranda at precisely-staged developmental time points. We find that canonical H3K9me3 enrichment is established prior to cellularization, and matures into stable and broad heterochromatin domains through development. Intriguingly, initial nucleation sites of H3K9me3 enrichment appear as early as embryonic stage3 over transposable elements (TE) and progressively broaden, consistent with spreading to neighboring nucleosomes. The earliest nucleation sites are limited to specific regions of a small number of recently active retrotransposon families and often appear over promoter and 5' regions of LTR retrotransposons, while late nucleation develops broadly across the entirety of most TEs. Interestingly, early nucleating TEs are strongly associated with abundant maternal piRNAs and show early zygotic transcription. These results support a model of piRNA-associated co-transcriptional silencing while also suggesting additional mechanisms for site-restricted H3K9me3 nucleation at TEs in pre-cellular Drosophila embryos.

scholarly journals Holocentromeres in Rhynchospora are associated with genome-wide centromere-specific repeat arrays interspersed among euchromatin

2015 ◽  
Vol 112 (44) ◽  
pp. 13633-13638 ◽  
Author(s):  
André Marques ◽  
Tiago Ribeiro ◽  
Pavel Neumann ◽  
Jiří Macas ◽  
Petr Novák ◽  
...  
Keyword(s):  
Repetitive Sequences ◽  
Wide Distribution ◽  
Holocentric Chromosomes ◽  
Metaphase Chromosomes ◽  
Centromeric Repeat ◽  
Gene Coding ◽  
Genome Wide ◽  
Histone H3 Variant ◽  
A Cell ◽  
Cycle Dependent

Holocentric chromosomes lack a primary constriction, in contrast to monocentrics. They form kinetochores distributed along almost the entire poleward surface of the chromatids, to which spindle fibers attach. No centromere-specific DNA sequence has been found for any holocentric organism studied so far. It was proposed that centromeric repeats, typical for many monocentric species, could not occur in holocentrics, most likely because of differences in the centromere organization. Here we show that the holokinetic centromeres of the Cyperaceae Rhynchospora pubera are highly enriched by a centromeric histone H3 variant-interacting centromere-specific satellite family designated “Tyba” and by centromeric retrotransposons (i.e., CRRh) occurring as genome-wide interspersed arrays. Centromeric arrays vary in length from 3 to 16 kb and are intermingled with gene-coding sequences and transposable elements. We show that holocentromeres of metaphase chromosomes are composed of multiple centromeric units rather than possessing a diffuse organization, thus favoring the polycentric model. A cell-cycle–dependent shuffling of multiple centromeric units results in the formation of functional (poly)centromeres during mitosis. The genome-wide distribution of centromeric repeat arrays interspersing the euchromatin provides a previously unidentified type of centromeric chromatin organization among eukaryotes. Thus, different types of holocentromeres exist in different species, namely with and without centromeric repetitive sequences.

scholarly journals Role of the male specific lethal (msl) Genes in Modifying the Effects of Sex Chromosomal Dosage in Drosophila

Genetics ◽  
1999 ◽  
Vol 152 (1) ◽  
pp. 249-268 ◽  
Author(s):  
Utpal Bhadra ◽  
Manika Pal-Bhadra ◽  
James A Birchler
Keyword(s):  
X Chromosome ◽  
Wide Distribution ◽  
Individual Gene ◽  
Genome Wide ◽  
Nucleation Sites ◽  
Inverse Effect ◽  
Male Specific Lethal ◽  
Msl Complex ◽  
Normal Males ◽  
Male Specific

Abstract Immunostaining of chromosomes shows that the male-specific lethal (MSL) proteins are associated with all female chromosomes at a low level but are sequestered to the X chromosome in males. Histone-4 Lys-16 acetylation follows a similar pattern in normal males and females, being higher on the X and lower on the autosomes in males than in females. However, the staining pattern of acetylation and the mof gene product, a putative histone acetylase, in msl mutant males returns to a uniform genome-wide distribution as found in females. Gene expression on the autosomes correlates with the level of histone-4 acetylation. With minor exceptions, the expression levels of X-linked genes are maintained with either an increase or decrease of acetylation, suggesting that the MSL complex renders gene activity unresponsive to H4Lys16 acetylation. Evidence was also found for the presence of nucleation sites for association of the MSL proteins with the X chromosome rather than individual gene binding sequences. We suggest that sequestration of the MSL proteins occurs in males to nullify on the autosomes and maintain on the X, an inverse effect produced by negatively acting dosage-dependent regulatory genes as a consequence of the evolution of the X/Y sex chromosomal system.

scholarly journals Author Correction: Determinants of genome-wide distribution and evolution of uORFs in eukaryotes

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Hong Zhang ◽  
Yirong Wang ◽  
Xinkai Wu ◽  
Xiaolu Tang ◽  
Changcheng Wu ◽  
...  
Keyword(s):  
Wide Distribution ◽  
Genome Wide

A Correction to this paper has been published: https://doi.org/10.1038/s41467-021-22435-2

scholarly journals Genome-Wide Identification and Expression Analyses of CONSTANS-Like Family Genes in Cucumber (Cucumis sativus L.)

2021 ◽  
Author(s):  
Zhen Tian ◽  
Xiaodong Qin ◽  
Hui Wang ◽  
Ji Li ◽  
Jinfeng Chen
Keyword(s):  
Floral Induction ◽  
Structural Characteristics ◽  
Expression Patterns ◽  
Evolutionary Relationship ◽  
Biological Functions ◽  
Promoter Regions ◽  
Cucumis Sativus L ◽  
Cis Acting ◽  
Genome Wide ◽  
Induction Process

AbstractThe CONSTANS-like (COL) gene family is one of the plant-specific transcription factor families that play important roles in plant growth and development. However, the knowledge of COLs related in cucumber is limited, and their biological functions, especially in the photoperiod-dependent flowering process, are still unclear. In this study, twelve CsaCOL genes were identified in the cucumber genome. Phylogenetic and conserved motif analyses provided insights into the evolutionary relationship between the CsaCOLs. Further, the comparative genome analysis revealed that COL genes are conserved in different plant species, especially collinearity gene pairs related to CsaCOL5. Ten kinds of cis-acting elements were vividly detected in CsaCOLs promoter regions, including five light-responsive elements, which echo the diurnal rhythm expression patterns of seven CsaCOL genes under SD and LD photoperiod regimes. Combined with the expression data of developmental stage, three CsaCOL genes are involved in the flowering network and play pivotal roles for the floral induction process. Our results provide useful information for further elucidating the structural characteristics, expression patterns, and biological functions of COL family genes in many plants

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.

Distinctive patterns of age-dependent hypomethylation in interspersed repetitive sequences

2010 ◽  
Vol 41 (2) ◽  
pp. 194-200 ◽  
Author(s):  
Pornrutsami Jintaridth ◽  
Apiwat Mutirangura
Keyword(s):  
Mononuclear Cells ◽  
Repetitive Sequences ◽  
Endogenous Retrovirus ◽  
Human Endogenous Retrovirus ◽  
Cellular Functions ◽  
Peripheral Blood Mononuclear ◽  
Global Methylation ◽  
Short Interspersed Elements ◽  
Genome Wide ◽  
Age Dependent

Interspersed repetitive sequences (IRSs) are a major contributor to genome size and may contribute to cellular functions. IRSs are subdivided according to size and functionally related structures into short interspersed elements, long interspersed elements (LINEs), DNA transposons, and LTR-retrotransposons. Many IRSs may produce RNA and regulate genes by a variety of mechanisms. The majority of DNA methylation occurs in IRSs and is believed to suppress IRS activities. Global hypomethylation, or the loss of genome-wide methylation, is a common epigenetic event not only in senescent cells but also in cancer cells. Loss of LINE-1 methylation has been characterized in many cancers. Here, we evaluated the methylation levels of peripheral blood mononuclear cells of LINE-1, Alu, and human endogenous retrovirus K (HERV-K) in 177 samples obtained from volunteers between 20 and 88 yr of age. Age was negatively associated with methylation levels of Alu (r = −0.452, P < 10−3) and HERV-K (r = −0.326, P < 10−3) but not LINE-1 (r = 0.145, P = 0.055). Loss of methylation of Alu occurred during ages 34–68 yr, and loss of methylation of HERV-K occurred during ages 40–63 yr and again during ages 64–83 yr. Interestingly, methylation of Alu and LINE-1 are directly associated, particularly at ages 49 yr and older (r = 0.49, P < 10−3). Therefore, only some types of IRSs lose methylation at certain ages. Moreover, Alu and HERV-K become hypomethylated differently. Finally, there may be several mechanisms of global methylation. However, not all of these mechanisms are age-dependent. This finding may lead to a better understanding of not only the biological causes and consequences of genome-wide hypomethylation but also the role of IRSs in the aging process.

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