Epigenetic Dynamics
(A summary of reviews; courtesy to Nature America,Inc, 2013)
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The epigenetic processes that modulate access to DNA in response to upstream signals include DNA methylation, covalent modification of histones, nucleosome remodeling, nuclear dynamics and chromatin interaction with regulatory noncoding RNAs. Nucleosomes represent the most basic level of chromatin organization. The covalent modification of histones is a vital means by which the cell modulates nucleosome mobility and turnover. As such, histone modifications are linked to essentially every cellular process requiring DNA access, including transcription, replication and repair. Nucleosome positioning is critical for transcription and other DNA related processes, and nucleosomes occupy favored positions in the genome. The erasure and re-establishment of DNA methylation patterns during mammalian development is a classical example of epigenetic dynamics. Bergman and Cedar (p. 274) describe the dynamics of DNA methylation patterns during normal development in vivo, starting from fertilization through embryogenesis and postnatal growth, and the combination of sequence information and trans-acting factors that mediate the methylation and demethylation machinery.
Although genomes and epigenomes have been characterized for many species, cell types and cellular conditions, the genome’s threedimensional organization and the importance of its topology for genomic functions such as transcription, replication and repair remain relatively poorly understood. Last but not least, the discovery of noncoding RNAs has added an entire new level of complexity to our understanding of functional elements involved in gene regulation. Long noncoding RNAs (lncRNAs) have emerged as an abundant and functionally diverse group of regulatory RNAs that have been linked to the regulation of almost every stage of gene expression.
1.Regulation of nucleosome dynamics by histone modifications:
Eukaryotic genomes are tightly wraps around octamers of core histone proteins to form nucleosomes, the basic unit of chromatin. Nucleosomes must be densely packed to achieve the 10,000–20,000-fold compaction necessary to fit a genome into the small volume of the nucleus but must also allow proteins involved in transcription, replication and repair to access DNA. Histone modifications have been of great interest ever since the discovery that histones which are associated with highly transcribed genes are hyperacetylated. Histone modifications range from the well known, such as lysine methylation, lysine acetylation
and serine/threonine phosphorylation, to more exotic modifications such as crotonylation; [See http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3176443/ and http://biobabel.wordpress.com/2012/01/18/lysine-crotonylation-and-the-histone-code/].
*crotonylation means posttranslational modicfication of lysine residues in a histone by the introduction of crotonyl groups; The univalent radical "CH3-CH=CH-CO-" derived from crotonic acid.
With the advent of genome-wide chromatin immunoprecipitation (ChIP)-based techniques such as ChIP with tiled microarray analysis (ChIP-chip) or high-throughput sequencing (ChIP-seq), mapping of global patterns of histone modifications has become commonplace and has been performed in many organisms. One insight that has emerged from such studies is the association of particular modifications with distinct types of cis-regulatory elements. Promoters are generally marked with high levels of H3K4me3 regardless of their transcriptional state. Putative enhancers tend to be marked with H3K4me1 alone or in combination with H3K27ac or H3K27me3, depending on the transcriptional activity of putatively regulated genes. How and why certain histone modifications are established at
specific genomic loci remains unclear.
DNA accessthrough histone acetylation
Histone acetylation, discovered in 1961, was the first described histone modification. Early studies revealed the association of hyperacetylated histones with actively transcribed genes, indicating a role for histone acetylation in facilitating transcription. . Acetylation neutralizes the positive charge of lysine residues, weakening charge-dependent interactions between a histone and nucleosomal DNA, linker DNA or adjacent histones, and thus increasing the accessibility of DNA to the transcription machinery. Histone lysine acetylation also functions in other cellular processes that require DNA access. Before DNA replication, chromatin regulates the accessibility of DNA to replication factors and modulates the firing and efficiency of replication origins, with a nucleosome-depleted, DNase-hypersensitive chromatin configuration conducive to proper origin firing. It has recently been shown that histone acetylation is associated with productive origin activation, suggesting that charge neutralization of lysines is important not only for proper transcription but also for efficient DNA replication by relaxing histone-DNA contacts. Histone acetylation also occurs at DNA double-strand breaks and may therefore be used to increase DNA access for repair factors.
Lysine acylation
In addition to acetylation, a variety of less well understood histone lysine coenzyme A– dependent acylations have recently been described; crotonylation, formylation, succinylation, malonylation, propionylation and butyrylation. Similar to acetylation, these acylations neutralize the positive charge of lysine, outwardly weakening histone-DNA contacts.
Histone methylation
Mono-, di- or trimethylation of a lysine residue does not affect its positive charge, and so the effect of methylation on nucleosome dynamics is thought to be less direct than that of acetylation. Histones can also be mono- or dimethylated on arginines, but much less is known
about the effects of histone arginine methylation on nucleosome dynamics.
6.Structure and function of long noncoding RNAs in
*crotonylation means posttranslational modicfication of lysine residues in a histone by the introduction of crotonyl groups; The univalent radical "CH3-CH=CH-CO-" derived from crotonic acid.
With the advent of genome-wide chromatin immunoprecipitation (ChIP)-based techniques such as ChIP with tiled microarray analysis (ChIP-chip) or high-throughput sequencing (ChIP-seq), mapping of global patterns of histone modifications has become commonplace and has been performed in many organisms. One insight that has emerged from such studies is the association of particular modifications with distinct types of cis-regulatory elements. Promoters are generally marked with high levels of H3K4me3 regardless of their transcriptional state. Putative enhancers tend to be marked with H3K4me1 alone or in combination with H3K27ac or H3K27me3, depending on the transcriptional activity of putatively regulated genes. How and why certain histone modifications are established at
specific genomic loci remains unclear.
DNA accessthrough histone acetylation
Histone acetylation, discovered in 1961, was the first described histone modification. Early studies revealed the association of hyperacetylated histones with actively transcribed genes, indicating a role for histone acetylation in facilitating transcription. . Acetylation neutralizes the positive charge of lysine residues, weakening charge-dependent interactions between a histone and nucleosomal DNA, linker DNA or adjacent histones, and thus increasing the accessibility of DNA to the transcription machinery. Histone lysine acetylation also functions in other cellular processes that require DNA access. Before DNA replication, chromatin regulates the accessibility of DNA to replication factors and modulates the firing and efficiency of replication origins, with a nucleosome-depleted, DNase-hypersensitive chromatin configuration conducive to proper origin firing. It has recently been shown that histone acetylation is associated with productive origin activation, suggesting that charge neutralization of lysines is important not only for proper transcription but also for efficient DNA replication by relaxing histone-DNA contacts. Histone acetylation also occurs at DNA double-strand breaks and may therefore be used to increase DNA access for repair factors.
Lysine acylation
In addition to acetylation, a variety of less well understood histone lysine coenzyme A– dependent acylations have recently been described; crotonylation, formylation, succinylation, malonylation, propionylation and butyrylation. Similar to acetylation, these acylations neutralize the positive charge of lysine, outwardly weakening histone-DNA contacts.
Histone methylation
Mono-, di- or trimethylation of a lysine residue does not affect its positive charge, and so the effect of methylation on nucleosome dynamics is thought to be less direct than that of acetylation. Histones can also be mono- or dimethylated on arginines, but much less is known
about the effects of histone arginine methylation on nucleosome dynamics.
2.Determinants of nucleosome positioning:
We define the term ‘nucleosome positioning’ broadly to indicate where nucleosomes are located with respect to the genomic DNA sequence. Nucleosome positioning is a dynamic process, but sequencing-based mapping approaches identify the positions of individual nucleosomes in a single cell at a specific time. Nucleosome positioning can vary from perfect positioning, in which a nucleosome is located at a given 147-bp stretch in all DNA molecules in a cell population, to no positioning, in which nucleosomes are located at all possible genomic positions with equal frequency across a cell population. Eukaryotic genomes are packaged into chromatin, whose basic repeating unit is a nucleosome that consists of a histone octamer wrapped around 147 base pairs (bp) of DNA. Nucleosomes are arranged into regularly spaced arrays, with the length of the linker region between nucleosomes varying among species and cell types.
3.DNA methylation dynamics in health and disease:
DNA methylation is a unique form of gene regulation because, unlike other gene-control mechanisms based on protein-DNA interactions, it involves covalent changes to the genome that provide long-term stability. DNA methylation is a chemical marking system for annotating genetic information by causing gene repression through its ability to affect factor binding and chromatin structure.
4.Epigenetic programming and reprogramming during development:
In vivo and in vitro studies have demonstrated the intrinsic reversibility and plasticity of the differentiated state. the roles of different epigenetic modifiers that can confer or remove histone and DNA modifications during in vivo and in vitro programming and reprogramming. The emerging data suggest that ‘active’ enzymatic activities can be complemented by the ‘passive’ loss of DNA and chromatin modifications during DNA replication, and that the relative contribution of each is probably context dependent.
5.Functional implications of genome topology:
The fundamental cell biological unit of genomes is the chromosome. Clever fluorescence in situ hybridization (FISH) experiments in the 1980s showed that in mammalian cells the genetic material of an individual chromosome occupies a spatially limited territory, typically roughly spherical in shape and 2–4 µm in diameter. These chromosome territories are tightly packed in the nucleus, and they abut at their borders to create a continuous body of chromatin. Whereas in higher eukaryotes chromosome territories intermingle only at their peripheries, in the yeast Saccharomyces cerevisiae chromosome territories are spatially less well defined and intermix to a much greater extent, most probably reflecting the globally more decondensed nature of yeast chromatin, its lack of large heterochromatin domains, and possibly the smaller size of the genome, which might require less spatial organization to ensure functionality.
6.Structure and function of long noncoding RNAs in
epigenetic regulation:
Global transcriptional analyses have revealed that the vast majority of the human genome is dynamically and differentially transcribed to produce a range and complexity of lncRNAs. The abundance of lncRNAs, in conjunction with these emerging functional insights, has fuelled considerable excitement and enthusiasm for research into lncRNA biology.
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