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RNAi-mediated pathways in the nucleus

Key Points

  • There is increasing evidence that RNA interference (RNAi)-mediated pathways have important roles in gene regulation at the nuclear-genome level. Key proteins of the RNAi machinery (Dicer, Argonaute, RNA-dependent RNA polymerase) function together with small RNAs to target epigenetic modifications and silencing of homologous regions of the genome.

  • RNA-directed DNA methylation has been well documented in plants and recent reports indicate that it might occur in mammalian cells. RNA-directed DNA methylation can target DNA sequences that are as short as 30 bp for dense cytosine methylation, in contrast to histone modifications, which take place in the context of nucleosomes and comprise 147 bp of DNA.

  • RNAi-mediated heterochromatin formation is important for centromere stucture and function in fission yeast, Drosophila melanogaster, mammals and perhaps other organisms. RNAi-mediated heterochromatin can also be induced at non-centromeric, interstitial regions to silence retrotransposons and regulate endogenous genes.

  • In Neurospora crassa, unpaired DNA can be silenced during meiosis by an RNAi-related pathway. This process might silence new transposon inserts. A similar pathway operates during meiosis in Caenorhabditis elegans.

  • Pairing-sensitive silencing in D. melanogaster, which involves greater silencing of somatically paired transgenes than unpaired copies, is intensified by mutations in the RNAi pathway.

  • RNAi-mediated heterochromatin marks internal eliminated sequences for deletion in developing macronuclei of Tetrahymena thermophila, perhaps to remove transposons that have invaded the germline genome of micronuclei.

  • Transposable elements and related repeats are primary targets for RNAi-mediated pathways in the nucleus, consistent with a role for RNAi in host defence against invasive sequences.

  • Despite the importance of RNAi-mediated pathways in establishing epigenetic modifications, not all DNA methylation and heterochromatin formation is induced by RNA. For example, N. crassa, which has the machinery for RNAi, does not seem to use the RNAi pathway for heterochromatin formation or DNA methylation.

  • Important questions for future research concern the universality of various RNAi-mediated nuclear pathways and the molecular composition of nuclear silencing-effector complexes.

Abstract

RNA interference (RNAi) is an evolutionarily conserved mechanism that uses short antisense RNAs that are generated by 'dicing' dsRNA precursors to target corresponding mRNAs for cleavage. However, recent developments have revealed that there is also extensive involvement of RNAi-related processes in regulation at the genome level. dsRNA and proteins of the RNAi machinery can direct epigenetic alterations to homologous DNA sequences to induce transcriptional gene silencing or, in extreme cases, DNA elimination. Furthermore, in some organisms RNAi silences unpaired DNA regions during meiosis. These mechanisms facilitate the directed silencing of specific genomic regions.

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Figure 1: RNA-directed DNA methylation.
Figure 2: RNA interference-mediated heterochromatin assembly.
Figure 3: RNA interference (RNAi) and DNA elimination in Tetrahymena thermophila.
Figure 4: Silencing of unpaired DNA during meiosis.

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Acknowledgements

We thank Kathy Barton, Rodolfo Aramayo, Tim Bestor and Mary Groll for preprints and Rodolfo Aramayo, Maarten Koornneef, Tim Bestor, Chris Schaefer, Thomas Tuschl and Antonius Matzke for helpful comments. We are grateful to Eric Meyer for valuable discussions and advice on DNA elimination in ciliates. We acknowledge the financial support of the Austrian Fonds zur Förderung der wissenschaftlichen Forschung and the European Union (M.A.M.) and the US National Science Foundation (J.A.B.).

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Correspondence to Marjori A. Matzke or James A. Birchler.

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DATABASES

Entrez Gene

FWA

piwi

aubergine

homeless

white

NCBI Taxonomy

Neurospora crassa

Arabidopsis thaliana

Drosophila melanogaster

Tetrahymena thermophila

Paramecium tetraurelia

Ascobolus immersus

Caenorhabditis elegans

FURTHER INFORMATION

Arabidopsis small RNA Project

ChromDB: The Plant Chromatin Database

The miRNA registry

Glossary

EPIGENETIC

Refers to mitotically and/or meiotically heritable changes in gene expression that do not involve a change in DNA sequence.

VIROIDS

These are tiny plant pathogens consisting solely of a non-protein-coding, circular rod-shaped RNA that is several hundred base pairs in length.

NUCLEOSOME

The basic unit of chromatin. The nucleosome core consists of an octamer made up of two copies of each of the histones H2A, H2B, H3 and H4, around which 147 bp of DNA is wrapped approximately twice. The histone N-terminal tails protrude from the core and are targets of various post-translational covalent modifications, such as methylation and acetylation.

ENDOSPERM

The seeds of flowering plants contain two fertilization products: the diploid embryo and the triploid endosperm, a terminally differentiated tissue that serves as a nutrient source for the developing embryo.

BASE-EXCISION REPAIR

(BER). The replacement of DNA bases that are altered by small chemical modifications through the excision of only the damaged nucleotide (short-patch BER) or through the removal of 2–13 nucleotides containing the damaged nucleotide (long-patch BER).

SNF2-CHROMATIN-LIKE REMODELLING PROTEINS

First identified in budding yeast as sucrose non-fermenter, or mating type switching defective (Swi) mutants, these proteins use energy from ATP breakdown to enhance the accessibility of nucleosomal DNA to regulatory factors.

CHROMODOMAIN

(Chromatin organization modifier domain). Initially identified in the Drosophila melanogaster HP1 and polycomb proteins, this is an 50-amino-acid domain that binds to histone tails that are methylated at certain lysine residues.

KINETOCHORE

A large protein complex that mediates the attachment of chromosomes to the meiotic and mitotic spindles.

SILENT MATING TYPE

The unexpressed copy of the mating-type locus.

POLYCOMB COMPLEX

A group of repressive chromatin proteins that maintain states of gene expression throughout development.

GENE CONVERSION

The non-reciprocal transfer of DNA-sequence information during meiotic recombination owing to heteroduplex formation.

HERMAPHRODITE

Individuals with both male and female sexual organs.

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Matzke, M., Birchler, J. RNAi-mediated pathways in the nucleus. Nat Rev Genet 6, 24–35 (2005). https://doi.org/10.1038/nrg1500

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