Region-specific H3K9me3 gain in aged somatic tissues in Caenorhabditis elegans

Epigenetic alterations occur as organisms age, and lead to chromatin deterioration, loss of transcriptional silencing and genomic instability. Dysregulation of the epigenome has been associated with increased susceptibility to age-related disorders. In this study, we aimed to characterize the age-dependent changes of the epigenome and, in turn, to understand epigenetic processes that drive aging phenotypes. We focused on the aging-associated changes in the repressive histone marks H3K9me3 and H3K27me3 in C. elegans. We observed region-specific gain and loss of both histone marks, but the changes are more evident for H3K9me3. We further found alteration of heterochromatic boundaries in aged somatic tissues. Interestingly, we discovered that the most statistically significant changes reflected H3K9me3-marked regions that are formed during aging, and are absent in developing worms, which we termed “aging-specific repressive regions” (ASRRs). These ASRRs preferentially occur in genic regions that are marked by high levels of H3K9me2 and H3K36me2 in larval stages. Maintenance of high H3K9me2 levels in these regions have been shown to correlate with a longer lifespan. Next, we examined whether the changes in repressive histone marks lead to de-silencing of repetitive DNA elements, as reported for several other organisms. We observed increased expression of active repetitive DNA elements but not global re-activation of silent repeats in old worms, likely due to the distributed nature of repetitive elements in the C. elegans genome. Intriguingly, CELE45, a putative short interspersed nuclear element (SINE), was greatly overexpressed at old age and upon heat stress. SINEs have been suggested to regulate transcription in response to various cellular stresses in mammals. It is likely that CELE45 RNAs also play roles in stress response and aging in C. elegans. Taken together, our study revealed significant and specific age-dependent changes in repressive histone modifications and repetitive elements, providing important insights into aging biology.

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Locus-specific H3K9me3 gain in aged somatic tissues in Caenorhabditis elegans

10.1101/2021.02.22.432236 ◽

2021 ◽

Author(s):

Cheng-Lin Li ◽

Mintie Pu ◽

Wenke Wang ◽

Siu Sylvia Lee

Keyword(s):

Histone Modifications ◽

Repetitive Dna ◽

Repetitive Elements ◽

Histone Marks ◽

C Elegans ◽

Genome Wide ◽

Somatic Tissues ◽

Age Dependent ◽

Dna Elements ◽

Repetitive Dna Elements

AbstractEpigenetic alterations occur as organisms age, and lead to chromatin deterioration, loss of transcriptional silencing and genomic instability. Dysregulated epigenome has been linked to increased susceptibility to age-related disorders. We aim to characterize the age-dependent changes of the epigenome and, in turn, to understand epigenetic processes that drive aging phenotypes. In this study, we focused on the aging-associated changes in the repressive histone marks H3K9me3 and H3K27me3 in C. elegans. We observed redistribution of of both histone marks, but the changes are more significant for H3K9me3. We further found alteration of heterochromatic boundaries in aged somatic tissues. Interestingly, we discovered that the most significant changes reflected H3K9me3-marked regions that are formed during aging, and are absent in developing worms, which we termed “aging-associated repressive domains” (AARDs). These AARDs preferentially occur in genic regions that are marked by high levels of H3K9me2 and H3K36me2 in larval stages. Interestingly, maintenance of high H3K9me2 levels in these regions have been shown to correlate with longer lifespan. Next, we examined whether the changes in repressive histone marks lead to de-silencing of repetitive DNA elements, as reported for several other organisms. We observed increased expression of active repetitive DNA elements but not global re-activation of silent repeats in old worms, likely due to the distributed nature of repetitive elements in the C. elegans genome. Intriguingly, CELE45, a putative short interspersed nuclear elements (SINE), was greatly overexpressed at old age and upon heat stress. SINEs have been suggested to regulate transcription in response to various cellular stresses in mammals, it is likely that CELE45 RNAs also play roles in stress response and aging in C. elegans. Taken together, our study revealed significant and specific age-dependent changes in repressive histone modifications and repetitive elements, providing important insights into aging biology.Author summaryHeterochromatin refers to the portion of the genome that is tightly packed where genes stay silent. Heterochromatin is typically decorated by particular chemical groups called histone modifications, such as trimethylation of lysine 9 or lysine 27 on histone 3 (H3K9me3 or H3K27me3). To understand how the heterochromatin landscape may change from a “youthful” to an “aged” state, we monitored the genome-wide patterns of H3K9me3 and H3K27me3 during aging using the genetic model soil worm C. elegans. We found that while H3K27me3 remained relatively stable with age, H3K9me3 showed profound genome-wide redistribution in aged worms. We observed that new H3K9me3-marked heterochromatin preferentially formed in specific gene-rich regions in aged worms. Interestingly, these particular regions were marked by high levels of three other histone modifications when worms were young. This result suggested that H3K9me3 gain during aging is influenced by the gene-specific landscape of histone modifications established at young age rather than occurs in a stochastic manner. In summary, our study discovered reproducible and gene-specific changes in histone modifications that likely contribute to the aging phenotypes.

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Impact of Repetitive DNA Elements on Snake Genome Biology and Evolution

Cells ◽

10.3390/cells10071707 ◽

2021 ◽

Vol 10 (7) ◽

pp. 1707

Author(s):

Syed Farhan Ahmad ◽

Worapong Singchat ◽

Thitipong Panthum ◽

Kornsorn Srikulnath

Keyword(s):

Repetitive Dna ◽

Repetitive Elements ◽

Model Systems ◽

Satellite Repeats ◽

Evolutionary Features ◽

Dna Elements ◽

Genomic Repeats ◽

The Impact ◽

Repetitive Dna Elements

The distinctive biology and unique evolutionary features of snakes make them fascinating model systems to elucidate how genomes evolve and how variation at the genomic level is interlinked with phenotypic-level evolution. Similar to other eukaryotic genomes, large proportions of snake genomes contain repetitive DNA, including transposable elements (TEs) and satellite repeats. The importance of repetitive DNA and its structural and functional role in the snake genome, remain unclear. This review highlights the major types of repeats and their proportions in snake genomes, reflecting the high diversity and composition of snake repeats. We present snakes as an emerging and important model system for the study of repetitive DNA under the impact of sex and microchromosome evolution. We assemble evidence to show that certain repetitive elements in snakes are transcriptionally active and demonstrate highly dynamic lineage-specific patterns as repeat sequences. We hypothesize that particular TEs can trigger different genomic mechanisms that might contribute to driving adaptive evolution in snakes. Finally, we review emerging approaches that may be used to study the expression of repetitive elements in complex genomes, such as snakes. The specific aspects presented here will stimulate further discussion on the role of genomic repeats in shaping snake evolution.

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Invasion of the human albumin-alpha-fetoprotein gene family by Alu, Kpn, and two novel repetitive DNA elements.

Molecular Biology and Evolution ◽

10.1093/oxfordjournals.molbev.a040420 ◽

1987 ◽

Keyword(s):

Gene Family ◽

Repetitive Dna ◽

Human Albumin ◽

Alpha Fetoprotein ◽

Dna Elements ◽

Repetitive Dna Elements

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A simple method for estimating global DNA methylation using bisulfite PCR of repetitive DNA elements

Nucleic Acids Research ◽

10.1093/nar/gnh032 ◽

2004 ◽

Vol 32 (3) ◽

pp. 38e-38 ◽

Cited By ~ 704

Author(s):

A. S. Yang

Keyword(s):

Dna Methylation ◽

Repetitive Dna ◽

Global Dna Methylation ◽

Simple Method ◽

Dna Elements ◽

Repetitive Dna Elements

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Sequence Organization of Simple, Highly Repetitive DNA Elements inBrassicaspecies

Journal of Experimental Botany ◽

10.1093/jxb/42.2.243 ◽

1991 ◽

Vol 42 (2) ◽

pp. 243-249 ◽

Cited By ~ 7

Author(s):

D. R SIBSON ◽

S. G. HUGHES ◽

J. A. BRYANT ◽

P. N. FITCHETT

Keyword(s):

Repetitive Dna ◽

Sequence Organization ◽

Dna Elements ◽

Highly Repetitive Dna ◽

Repetitive Dna Elements

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A rapid procedure for the isolation of C0t-1 DNA from plants

Genome ◽

10.1139/g97-020 ◽

1997 ◽

Vol 40 (1) ◽

pp. 138-142 ◽

Cited By ~ 137

Author(s):

Michael S. Zwick ◽

Robert E. Hanson ◽

M. Nurul Islam-Faridi ◽

David M. Stelly ◽

Rod A. Wing ◽

...

Keyword(s):

In Situ Hybridization ◽

Repetitive Dna ◽

Copy Number ◽

Genomic Dna ◽

Mammalian Species ◽

Repetitive Dnas ◽

Rapid Procedure ◽

Dna Elements ◽

Repetitive Dna Elements

In situ hybridization (ISH) for the detection of single- or low-copy sequences, particularly large DNA fragments cloned into YAC or BAC vectors, generally requires the suppression or "blocking" of highly-repetitive DNAs. C0t-1 DNA is enriched for repetitive DNA elements, high or moderate in copy number, and can therefore be used more effectively than total genomic DNA to prehybridize and competitively hybridize repetitive elements that would otherwise cause nonspecific hybridization. C0t-1 DNAs from several mammalian species are commercially available, however, none is currently available for plants to the best of our knowledge. We have developed a simple 1-day procedure to generate C0t-1 DNA without the use of specialized equipment.Key words: C0t-1 DNA, in situ hybridization, BACs, plants.

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