scholarly journals Tissue-specific DNA methylation loss during ageing and carcinogenesis is linked to chromosome structure, replication timing and cell division rates

2018 ◽  
Vol 46 (14) ◽  
pp. 7022-7039 ◽  
Author(s):  
Marija Dmitrijeva ◽  
Stephan Ossowski ◽  
Luis Serrano ◽  
Martin H Schaefer
Keyword(s):  
Dna Methylation ◽  
Cell Division ◽  
Chromosome Structure ◽  
Replication Timing ◽  
Tissue Specific

Many players, one goal: how chromatin states are inherited during cell division

2005 ◽  
Vol 83 (3) ◽  
pp. 332-343 ◽  
Author(s):  
Raffaella Santoro ◽  
Filomena De Lucia
Keyword(s):  
Dna Methylation ◽  
Cell Division ◽  
Chromatin Remodeling ◽  
Dna Sequences ◽  
Replication Timing ◽  
Histone Variants ◽  
High Fidelity ◽  
Chromatin States ◽  
Initiation Of Replication ◽  
Genomic Material

Replication of genomic material is a process that requires not only high fidelity in the duplication of DNA sequences but also inheritance of the chromatin states. In the last few years enormous effort has been put into elucidating the mechanisms involved in the correct propagation of chromatin states. From all these studies it emerges that an epigenetic network is at the base of this process. A coordinated interplay between histone modifications and histone variants, DNA methylation, RNA components, ATP-dependent chromatin remodeling, and histone-specific assembly factors regulates establishment of the replication timing program, initiation of replication, and propagation of chromatin domains. The aim of this review is to examine, in light of recent findings, how so many players can be coordinated with each other to achieve the same goal, a correct inheritance of the chromatin state.Key words: replication, histone variants, histone modification, DNA methylation, chromatin remodeling factors.

scholarly journals Atlas of Age- and Tissue-specific DNA Methylation during Early Development of Barley (Hordeum vulgare)

2018 ◽  
Author(s):  
Moumouni Konate ◽  
Michael J. Wilkinson ◽  
Banjamin Mayne ◽  
Eileen Scott ◽  
Bettina Berger ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Hordeum Vulgare ◽  
Organ Function ◽  
Tissue Specific ◽  
Organ Differentiation ◽  
Differentiated Cells ◽  
Differentially Methylated Genes ◽  
Organ Specific ◽  
Development And Differentiation ◽  
Methylation Patterns

The barley (Hordeum vulgare) genome comprises over 32,000 genes, with differentiated cells expressing only a subset of genes; the remainder being silent. Mechanisms by which tissue-specific genes are regulated are not entirely understood, although DNA methylation is likely to be involved. DNA methylation patterns are not static during plant development, but it is still unclear whether different organs possess distinct methylation profiles. Methylation-sensitive GBS was used to generate DNA methylation profiles for roots, leaf-blades and leaf-sheaths from five barley varieties, using seedlings at the three-leaf stage. Differentially Methylated Markers (DMMs) were characterised by pairwise comparisons of roots, leaf-blades and leaf-sheaths of three different ages. While very many DMMs were found between roots and leaf parts, only a few existed between leaf-blades and leaf-sheaths, with differences decreasing with leaf rank. Organ-specific DMMs appeared to target mainly repeat regions, implying that organ differentiation partially relies on the spreading of DNA methylation from repeats to promoters of adjacent genes. Furthermore, the biological functions of differentially methylated genes in the different organs correlated with functional specialisation. Our results indicate that different organs do possess diagnostic methylation profiles and suggest that DNA methylation is important for both tissue development and differentiation and organ function.

scholarly journals Non-canonical RNA-directed DNA methylation participates in maternal and environmental control of seed dormancy

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Mayumi Iwasaki ◽  
Lena Hyvärinen ◽  
Urszula Piskurewicz ◽  
Luis Lopez-Molina
Keyword(s):  
Dna Methylation ◽  
Seed Dormancy ◽  
Environmental Control ◽  
Negative Regulator ◽  
Paternal Allele ◽  
Seed Progeny ◽  
Tissue Specific ◽  
Parental Allele ◽  
Allele Expression ◽  
Premature Germination

Seed dormancy is an adaptive trait preventing premature germination out of season. In a previous report (Piskurewicz et al., 2016) we showed that dormancy levels are maternally inherited through the preferential maternal allele expression in the seed endosperm of ALLANTOINASE (ALN), a negative regulator of dormancy. Here we show that suppression of ALN paternal allele expression is imposed by non-canonical RNA-directed DNA methylation (RdDM) of the paternal ALN allele promoter. Dormancy levels are further enhanced by cold during seed development. We show that DNA methylation of the ALN promoter is stimulated by cold in a tissue-specific manner through non-canonical RdDM, involving RDR6 and AGO6. This leads to suppression of ALN expression and further promotion of seed dormancy. Our results suggest that tissue-specific and cold-induced RdDM is superimposed to parental allele imprints to deposit in the seed progeny a transient memory of environmental conditions experienced by the mother plant.

DNA methylation versus gene expression

Development ◽  
1984 ◽  
Vol 83 (Supplement) ◽  
pp. 31-40
Author(s):  
Adrian P. Bird
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Cell Division ◽  
Methylation Pattern ◽  
Current Evidence ◽  
Evolutionary Perspective ◽  
Cell Type ◽  
Versus Gene ◽  
Daughter Cells ◽  
The Relationship

Vertebrate DNA is methylated at a high proportion of cytosine residues in the sequence CpG, and it has been suggested that the distribution of methylated and non-methylated CpGs in a given cell type influences the pattern of gene expression in those cells. Since a DNA methylation pattern is normally transmitted faithfully to daughter cells via cell division, this idea suggests an origin for stable, clonally inherited patterns of gene expression. This article discusses some of the current evidence for a relationship between DNA methylation and gene expression. Although the evidence is incomplete, it appears already that the relationship is variable: transcription of some genes is repressed by the presence of 5-methylcytosine at certain CpGs, and may be controlled by methylation, while transcription of other genes is indifferent to methylation. In attempting to explain this variability it is helpful to adopt an evolutionary perspective.

scholarly journals DNA methylation and histone acetylation of rat methionine adenosyltransferase 1A and 2A genes is tissue-specific

2000 ◽  
Vol 32 (4) ◽  
pp. 397-404 ◽  
Author(s):  
Luis Torres ◽  
Gerardo López-Rodas ◽  
M.Ujue Latasa ◽  
M.Victoria Carretero ◽  
Abdelhalim Boukaba ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Histone Acetylation ◽  
Methionine Adenosyltransferase ◽  
Tissue Specific

scholarly journals Age-related DNA methylation changes are tissue-specific with ELOVL2 promoter methylation as exception

2018 ◽  
Vol 11 (1) ◽  
Author(s):  
Roderick C. Slieker ◽  
Caroline L. Relton ◽  
Tom R. Gaunt ◽  
P. Eline Slagboom ◽  
Bastiaan T. Heijmans
Keyword(s):  
Dna Methylation ◽  
Promoter Methylation ◽  
Tissue Specific ◽  
Age Related

scholarly journals Analysis of the structural variability of topologically associated domains as revealed by Hi-C

2019 ◽  
Vol 2 (1) ◽  
Author(s):  
Natalie Sauerwald ◽  
Akshat Singhal ◽  
Carl Kingsford
Keyword(s):  
Structural Changes ◽  
Chromosome Structure ◽  
Three Dimensional ◽  
Replication Timing ◽  
Building Blocks ◽  
Structural Features ◽  
Genetic Sequence ◽  
Experimental Variation ◽  
Topologically Associated Domains ◽  
Integral Role

Abstract Three-dimensional chromosome structure plays an integral role in gene expression and regulation, replication timing, and other cellular processes. Topologically associated domains (TADs), building blocks of chromosome structure, are genomic regions with higher contact frequencies within the region than outside the region. A central question is the degree to which TADs are conserved or vary between conditions. We analyze 137 Hi-C samples from 9 studies under 3 measures to quantify the effects of various sources of biological and experimental variation. We observe significant variation in TAD sets between both non-replicate and replicate samples, and provide initial evidence that this variability does not come from genetic sequence differences. The effects of experimental protocol differences are also measured, demonstrating that samples can have protocol-specific structural changes, but that TADs are generally robust to lab-specific differences. This study represents a systematic quantification of key factors influencing comparisons of chromosome structure, suggesting significant variability and the potential for cell-type-specific structural features, which has previously not been systematically explored. The lack of observed influence of heredity and genetic differences on chromosome structure suggests that factors other than the genetic sequence are driving this structure, which plays an important role in human disease and cellular functioning.

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