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分子遗传学阅读文献:基因表达调控之四

已有 6117 次阅读 2008-9-3 17:13 |个人分类:科学感想|系统分类:科研笔记| 基因, 分子遗传学阅读文献, 表达调控

the expanding world of small RNAs

 

Grosshans H, Filipowicz W. Molecular biology: the expanding world of small RNAs. Nature. 2008 Jan 24; 451 (7177): 414-6.

 

the expanding world of small RNAs

Impact of small RNAs

 

Obernosterer G, Meister G, Poy MN, Kuras A. The impact of small RNAs. Microsymposium on small RNAs. EMBO Rep. 2007 Jan; 8 (1): 23-7. Epub 2006 Dec 15.

 Impact of small RNAs

 

Small RNAs as big players in plant abiotic stress response and nutrient deprivation

 

Sunkar R, Chinnusamy V, Zhu J, Zhu JK. Small RNAs as big players in plant abiotic stress responses and nutrient deprivation. Trends Plant Sci. 2007 Jul; 12 (7): 301-9. Epub 2007 Jun 18.

 

Abiotic stress is one of the primary causes of crop losses worldwide. Much progress has been made in unraveling the complex stress response mechanisms, particularly in the identification of stress responsive protein-coding genes. In addition to protein coding genes, recently discovered microRNAs (miRNAs) and endogenous small interfering RNAs (siRNAs) have emerged as important players in plant stress responses. Initial clues suggesting that small RNAs are involved in plant stress responses stem from studies showing stress regulation of miRNAs and endogenous siRNAs, as well as from target predictions for some miRNAs. Subsequent studies have demonstrated an important functional role for these small RNAs in abiotic stress responses. This review focuses on recent advances, with emphasis on integration of small RNAs in stress regulatory networks.

 Small RNAs as big players in plant abiotic stress response and nutrient deprivation

 

RNA silencing: small RNAs as ubiquitous regulators of gene expression

 

Voinnet O. RNA silencing: small RNAs as ubiquitous regulators of gene expression. Curr Opin Plant Biol. 2002 Oct; 5 (5): 444-51.

 

'RNA silencing' is the suppression of gene expression through nucleotide sequence-specific interactions that are mediated by RNA. Initially identified as an immune system that is targeted against transposons and viruses, RNA silencing is emerging as a fundamental regulatory process that is likely to affect many layers of endogenous gene expression in most, if not all, eukaryotes.

 RNA silencing-small RNAs as ubiquitous regulators of gene expression

 

Specialization and evolution of endogenous small RNA pathways

 

Chapman EJ, Carrington JC. Specialization and evolution of endogenous small RNA pathways. Nat Rev Genet. 2007 Nov; 8 (11): 884-96.

 

The specificity of RNA silencing is conferred by small RNA guides that are processed from structured RNA or dsRNA. The core components for small RNA biogenesis and effector functions have proliferated and specialized in eukaryotic lineages, resulting in diversified pathways that control expression of endogenous and exogenous genes, invasive elements and viruses, and repeated sequences. Deployment of small RNA pathways for spatiotemporal regulation of the transcriptome has shaped the evolution of eukaryotic genomes and contributed to the complexity of multicellular organisms.

 Specialization and evolution of endogenous small RNA pathways

 

Targets of RNA-directed DNA methylation

 

Matzke M, Kanno T, Huettel B, Daxinger L, Matzke AJ. Targets of RNA-directed DNA methylation. Curr Opin Plant Biol. 2007 Oct; 10 (5): 512-9. Epub 2007 Aug 16.

 

RNA-directed DNA methylation contributes substantially to epigenetic regulation of the plant genome. Methylation is guided to homologous DNA target sequences by 24 nt 'heterochromatic' small RNAs produced by nucleolar-localized components of the RNAi machinery and a plant-specific RNA polymerase, Pol IV. Plants contain unusually large and diverse populations of small RNAs, many of which originate from transposons and repeats. These sequences are frequent targets of methylation, and they are able to bring plant genes in their vicinity under small RNA-mediated control. RNA-directed DNA methylation can be removed by enzymatic demethylation, providing plants with a versatile system that facilitates epigenetic plasticity. In addition to subduing transposons, RNA-directed DNA methylation has roles in plant development and, perhaps, stress responses.

 Targets of RNA-directed DNA methylation

 

Signaling in gene silencing

Signaling in gene silencing

Nucleolar dominance and silencing of transcription

 

Pikaard CS. Nucleolar dominance and silencing of transcription. Trends Plant Sci. 1999 Dec; 4 (12): 478-483.

 

Nucleolar dominance is a phenomenon in plant and animal hybrids whereby one parental set of ribosomal RNA (rRNA) genes is transcribed, but the hundreds of rRNA genes inherited from the other parent are silent. The phenomenon gets it name because only transcriptionally active rRNA genes give rise to a nucleolus, the site of ribosome assembly. Nucleolar dominance provided the first clear example of DNA methylation and histone deacetylation acting in partnership in a gene-silencing pathway. However, the sites of chromatin modification and the ways in which one set of rRNA genes are targeted for repression remain unclear. Another unresolved question is whether the units of regulation are the individual rRNA genes or the multi-megabase chromosomal domains that encompass the rRNA gene clusters.

 Nucleolar dominance and silencing of transcription

 

Small RNAs and transposon silencing in plants

 

Hidetaka Ito. Small RNAs and transposon silencing in plants. Develop. Growth Differ., 2011. doi: 10.1111/j.1440-169X.2011.01309.x

 

Transposons are highly conserved in plants and have created a symbiotic relationship with the host genome. An important factor of the successful communication between transposons and host plants is epigenetic modifications including DNA methylation and the modifications of the histone tail. In plants, small interfering RNAs (siRNAs) are responsible for RNA-directed DNA methylation (RdDM) that suppresses transposon activities. Although most transposons are silent in their host plants, certain genomic shocks, such as an environmental stress or a hybridization event, might trigger transposon activation. Further, since transposons can affect the regulation mechanisms of host genes, it is possible that transposons have co-evolved as an important mechanism for plant development and adaptation. Recent new findings reveal that siRNAs control not only transcriptional activation, but also suppress transgenerational transposition of mobile elements making siRNAs critically important towards maintaining genome stability. Together these data suggest host-mediated siRNA regulation of transposons appears to have been adapted for controlling essential systems of plant development, morphogenesis, and reproduction.

Small RNAs and transposon silencing in plants.pdf

 

 



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