RNA regulation of epigenetic processes

@article{Mattick2009RNARO,
  title={RNA regulation of epigenetic processes},
  author={John S. A. Mattick and Paulo P. Amaral and M. Dinger and Tim R. Mercer and Mark F. Mehler},
  journal={BioEssays},
  year={2009},
  volume={31}
}
There is increasing evidence that dynamic changes to chromatin, chromosomes and nuclear architecture are regulated by RNA signalling. Although the precise molecular mechanisms are not well understood, they appear to involve the differential recruitment of a hierarchy of generic chromatin modifying complexes and DNA methyltransferases to specific loci by RNAs during differentiation and development. A significant fraction of the genome‐wide transcription of non‐protein coding RNAs may be involved… 
Impact of nuclear organization and dynamics on epigenetic regulation in the central nervous system: implications for neurological disease states
TLDR
An update of the emerging understanding of genomic architecture, RNA biology, and nuclear organization is provided and the interconnected roles that deregulation of these factors may play in diverse CNS disorders are highlighted.
The impact of histone post-translational modifications on developmental gene regulation
TLDR
This review examines the molecular processes regulating site-specific histone acetylation, methylation and phosphorylation with an emphasis on how these processes underpin differentiation-regulated transcription.
Long non-coding RNAs in nervous system function and disease
The emerging role of epigenetics in stroke: II. RNA regulatory circuitry.
TLDR
The role of these novel ncRNAs in the nervous system is examined and emerging evidence that implicates RNA-based networks in the molecular pathogenesis of stroke is highlighted, as well as the development of future therapeutic strategies for locus-specific and genome-wide regulation of genes and functional gene networks.
Epigenetic modifications and noncoding RNAs in cardiac hypertrophy and failure
TLDR
New insights are summarized into how these two layers of gene-expression regulation might be involved in the pathogenesis of cardiac hypertrophy and failure, and how the authors are only beginning to appreciate the complexity of the interactive network of which they are part.
Epigenetics and gene expression
TLDR
The role epigenetics is believed to have in influencing gene expression is outlined and various RNA-mediated processes thought to influence gene expression chiefly at the level of transcription are outlined.
The Genetic Signatures of Noncoding RNAs
TLDR
It is shown that an historic emphasis, both phenotypically and technically, on mutations in protein-coding sequences, and by presumptions about the nature of regulatory mutations, show that most variations in regulatory sequences produce relatively subtle phenotypic changes, in contrast to mutations in proteins that frequently cause catastrophic component failure.
Non-coding RNAs in homeostasis, disease and stress responses: an evolutionary perspective.
TLDR
The growing evidence that ncRNAs are intrinsically involved in cellular and organismal adaptation processes, in both robustness and protection to stresses, as well as in mechanisms generating evolutionary change is presented.
...
...

References

SHOWING 1-10 OF 120 REFERENCES
Non-coding RNAs, epigenetics and complexity.
Non‐coding RNAs: the architects of eukaryotic complexity
TLDR
It is suggested that the central dogma is incomplete, and that intronic and other non‐coding RNAs have evolved to comprise a second tier of gene expression in eukaryotes, which enables the integration and networking of complex suites of gene activity.
Mechanisms of epigenetic inheritance.
Small RNA-Directed Epigenetic Natural Variation in Arabidopsis thaliana
TLDR
It is reported that, in the model plant Arabidopsis thaliana, a cluster of ∼24 nt siRNAs found at high levels in the ecotype Landsberg erecta (Ler) could direct DNA methylation and heterochromatinization at a hAT element adjacent to the promoter of FLOWERING LOCUS C (FLC).
RNA-directed DNA methylation
TLDR
Double-stranded RNAs and their `diced' small RNA products can guide key developmental and defense mechanisms in eukaryotes and can feed backwards to modulate the accessibility of information stored in the DNA of cognate genes.
Components of the DNA Methylation System of Chromatin Control Are RNA-binding Proteins*
TLDR
A novel set of RNA-binding proteins that are well known for their function in chromatin regulation are identified and it is speculated that DNMTs and MBD proteins allow RNA molecules to participate in DNA methylation-mediated chromatin control.
Noncoding RNA in development
Non-protein-coding sequences increasingly dominate the genomes of multicellular organisms as their complexity increases, in contrast to protein-coding genes, which remain relatively static. Most of
RNA Is an Integral Component of Chromatin that Contributes to Its Structural Organization
TLDR
Results that indicate a general structural role for RNA in eukaryotic chromatin are reported, which is observed both at euchromatic and heterochromatic regions, and proceeds without loss of histone H1 or any significant change in core-histone composition and integrity.
RNA silencing systems and their relevance to plant development.
TLDR
Plant RNA silencing systems are organized into a network with shared components and overlapping functions, and microRNAs, and probably trans-acting small RNAs, help regulate development at the posttranscriptional level.
...
...