The Paf1 complex represses small-RNA-mediated epigenetic gene silencing

Small non-protein coding RNAs are involved in pathways that control the genome at the level of chromatin. In Schizosaccharomyces pombe, small interfering RNAs (siRNAs) are required for the faithful propagation of heterochromatin that is found at peri-centromeric repeats. In contrast to repetitive DNA, protein-coding genes are refractory to siRNA-mediated heterochromatin formation, unless siRNAs are expressed in mutant cells. Here we report the identification of 20 novel mutant alleles that enable de novo formation of heterochromatin at a euchromatic protein-coding gene by using trans-acting siRNAs as triggers. For example, a single amino acid substitution in the pre-mRNA cleavage factor Yth1 enables siRNAs to trigger silent chromatin formation with unparalleled efficiency. Our results are consistent with a kinetic nascent transcript processing model for the inhibition of small-RNA-directed de novo formation of heterochromatin and lay a foundation for further mechanistic dissection of cellular activities that counteract epigenetic gene silencing.

Download Full-text

Faculty Opinions recommendation of ROR1/RPA2A, a putative replication protein A2, functions in epigenetic gene silencing and in regulation of meristem development in Arabidopsis.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1029787.347561 ◽

2005 ◽

Author(s):

Shigeru Iida

Keyword(s):

Gene Silencing ◽

Replication Protein ◽

Epigenetic Gene Silencing ◽

Meristem Development

Download Full-text

Faculty Opinions recommendation of E-cadherin is transcriptionally activated via suppression of ZEB1 transcriptional repressor by small RNA-mediated gene silencing.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.13436964.14811067 ◽

2012 ◽

Author(s):

Marjori Matzke

Keyword(s):

Gene Silencing ◽

Small Rna ◽

Transcriptional Repressor ◽

E Cadherin

Download Full-text

Faculty Opinions recommendation of Epigenetic gene silencing underlies C-fiber dysfunctions in neuropathic pain.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.2953960.2624060 ◽

2010 ◽

Author(s):

Michael Andresen

Keyword(s):

Neuropathic Pain ◽

Gene Silencing ◽

Epigenetic Gene Silencing ◽

C Fiber

Download Full-text

Nickel and Epigenetic Gene Silencing

Genes ◽

10.3390/genes4040583 ◽

2013 ◽

Vol 4 (4) ◽

pp. 583-595 ◽

Cited By ~ 27

Author(s):

Hong Sun ◽

Magdy Shamy ◽

Max Costa

Keyword(s):

Gene Silencing ◽

Epigenetic Gene Silencing

Download Full-text

FOXO regulates RNA interference in Drosophila and protects from RNA virus infection

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1517124112 ◽

2015 ◽

Vol 112 (47) ◽

pp. 14587-14592 ◽

Cited By ~ 33

Author(s):

Michael J. Spellberg ◽

Michael T. Marr

Keyword(s):

Rna Interference ◽

Virus Infection ◽

Gene Silencing ◽

Small Rna ◽

Stress Responses ◽

Posttranscriptional Regulation ◽

Rna Virus ◽

Regulation Of Gene Expression ◽

Cellular Physiology ◽

Metabolic Conditions

Small RNA pathways are important players in posttranscriptional regulation of gene expression. These pathways play important roles in all aspects of cellular physiology from development to fertility to innate immunity. However, almost nothing is known about the regulation of the central genes in these pathways. The forkhead box O (FOXO) family of transcription factors is a conserved family of DNA-binding proteins that responds to a diverse set of cellular signals. FOXOs are crucial regulators of cellular homeostasis that have a conserved role in modulating organismal aging and fitness. Here, we show that Drosophila FOXO (dFOXO) regulates the expression of core small RNA pathway genes. In addition, we find increased dFOXO activity results in an increase in RNA interference (RNAi) efficacy, establishing a direct link between cellular physiology and RNAi. Consistent with these findings, dFOXO activity is stimulated by viral infection and is required for effective innate immune response to RNA virus infection. Our study reveals an unanticipated connection among dFOXO, stress responses, and the efficacy of small RNA-mediated gene silencing and suggests that organisms can tune their gene silencing in response to environmental and metabolic conditions.

Download Full-text

Potato Virus X Amplicons in Arabidopsis Mediate Genetic and Epigenetic Gene Silencing

The Plant Cell ◽

10.2307/3870942 ◽

2000 ◽

Vol 12 (3) ◽

pp. 369 ◽

Cited By ~ 6

Author(s):

Tamas Dalmay ◽

Andrew Hamilton ◽

Elisabeth Mueller ◽

David C. Baulcombe

Keyword(s):

Gene Silencing ◽

Potato Virus ◽

Potato Virus X ◽

Epigenetic Gene Silencing

Download Full-text

Modulations of SIR-nucleosome interactions of reconstructed yeast silent pre-heterochromatin by O-acetyl-ADP-ribose and magnesium

Molecular Biology of the Cell ◽

10.1091/mbc.e16-06-0359 ◽

2017 ◽

Vol 28 (3) ◽

pp. 381-386 ◽

Cited By ~ 7

Author(s):

Shu-Yun Tung ◽

Sue-Hong Wang ◽

Sue-Ping Lee ◽

Shu-Ping Tsai ◽

Hsiao-Hsuian Shen ◽

...

Keyword(s):

Gene Silencing ◽

Chromatin Condensation ◽

Epigenetic Inheritance ◽

Assembly System ◽

Sir Proteins ◽

Epigenetic Gene Silencing ◽

In Vitro Assembly ◽

The Individual

Yeast silent heterochromatin provides an excellent model with which to study epigenetic inheritance. Previously we developed an in vitro assembly system to demonstrate the formation of filament structures with requirements that mirror yeast epigenetic gene silencing in vivo. However, the properties of these filaments were not investigated in detail. Here we show that the assembly system requires Sir2, Sir3, Sir4, nucleosomes, and O-acetyl-ADP-ribose. We also demonstrate that all Sir proteins and nucleosomes are components of these filaments to prove that they are SIR-nucleosome filaments. Furthermore, we show that the individual localization patterns of Sir proteins on the SIR-nucleosome filament reflect those patterns on telomeres in vivo. In addition, we reveal that magnesium exists in the SIR-nucleosome filament, with a role similar to that for chromatin condensation. These results suggest that a small number of proteins and molecules are sufficient to mediate the formation of a minimal yeast silent pre-heterochromatin in vitro.

Download Full-text

Small RNAs in Plant Immunity and Virulence of Filamentous Pathogens

Annual Review of Phytopathology ◽

10.1146/annurev-phyto-121520-023514 ◽

2021 ◽

Vol 59 (1) ◽

Author(s):

Yongli Qiao ◽

Rui Xia ◽

Jixian Zhai ◽

Yingnan Hou ◽

Li Feng ◽

...

Keyword(s):

Gene Silencing ◽

Small Rna ◽

Small Rnas ◽

Plant Immunity ◽

Receptor Gene ◽

Current Status ◽

Annual Review ◽

Publication Date ◽

Small Interfering Rnas ◽

Host Pathogen

Gene silencing guided by small RNAs governs a broad range of cellular processes in eukaryotes. Small RNAs are important components of plant immunity because they contribute to pathogen-triggered transcription reprogramming and directly target pathogen RNAs. Recent research suggests that silencing of pathogen genes by plant small RNAs occurs not only during viral infection but also in nonviral pathogens through a process termed host-induced gene silencing, which involves trans-species small RNA trafficking. Similarly, small RNAs are also produced by eukaryotic pathogens and regulate virulence. This review summarizes the small RNA pathways in both plants and filamentous pathogens, including fungi and oomycetes, and discusses their role in host–pathogen interactions. We highlight secondary small interfering RNAs of plants as regulators of immune receptor gene expression and executors of host-induced gene silencing in invading pathogens. The current status and prospects of small RNAs trafficking at the host–pathogen interface are discussed. Expected final online publication date for the Annual Review of Phytopathology, Volume 59 is August 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Download Full-text