Paramutation’s Properties and Puzzles

@article{Chandler2010ParamutationsPA,
  title={Paramutation’s Properties and Puzzles},
  author={Vicki L. Chandler},
  journal={Science},
  year={2010},
  volume={330},
  pages={628 - 629}
}
Paramutation refers to the process by which homologous DNA sequences communicate in trans to establish meiotically heritable expression states. Although mechanisms are unknown, current data are consistent with the hypothesis that the establishment and heritable transmission of specific chromatin states underlies paramutation. Transcribed, noncoding tandem repeats and proteins implicated in RNA-directed transcriptional silencing in plants and yeast are required for paramutation, yet the specific… 
required to maintain repression2 Is a Novel Protein That Facilitates Locus-Specific Paramutation in Maize[W]
TLDR
The RMR2 clade of proteins provides a new entry point for understanding the diversity of epigenomic control operating in higher plants and identifies a novel protein required for paramutation at the maize purple plant1 locus.
Specific Tandem Repeats Are Sufficient for Paramutation-Induced Trans-Generational Silencing
TLDR
Paramutation was achieved using multiple transgenes containing the b1 tandem repeats, including events with tandem repeats of only one half of the repeat unit, demonstrating that these sequences are sufficient for paramutation and an allelic position is not required for the repeats to communicate.
Locus-specific paramutation in Zea mays is maintained by a PICKLE-like chromodomain helicase DNA-binding 3 protein controlling development and male gametophyte function
TLDR
Results show that a CHD3 protein responsible for normal plant ontogeny and sperm transmission also helps maintain meiotically-heritable epigenetic regulatory variation for specific alleles, implicating an intersection of RNA polymerase IV function and nucleosome positioning in the paramutation process.
RNAi and heterochromatin assembly.
TLDR
Heterochromatic small interfering RNAs are produced and how the RNAi machinery participates in the formation and function of heterochromatin is discussed.
Chromatin-associated ncRNA activities
TLDR
Mechanistic insights into chromatin-associated ncRNA activities gained from work with fission yeast are highlighted, and parallels to studies in other eukaryotes that indicate evolutionary conservation are drawn.
Paramutagenicity of a p1 epiallele in maize
TLDR
This work proposes a model in which P1-pr paramutation is triggered by changing epigenetic states of transposons immediately adjacent to a P2-rr enhancer sequence, which could have a significant impact on breeding agronomically important traits.
Mechanism for full-length RNA processing of Arabidopsis genes containing intragenic heterochromatin.
TLDR
It is shown using a flowering plant, Arabidopsis, that full-length transcript formation over intragenic heterochromatin depends on a protein named IBM2 (Increase in Bonsai Methylation 2), which has a Bromo-Adjacent Homology domain and an RNA recognition motif.
Involvement o f M ultiple G ene-Silencing P athways in a P aramutation-lik e P henomenon i n Arabidopsis
TLDR
This study reported a multi-copy pRD29A-LUC transgene in Arabidopsis thaliana that behaves like a paramutation locus and established a model system for the study of paramutation inArabidopsis.
Overlapping RdDM and non-RdDM mechanisms work together to maintain somatic repression of a paramutagenic epiallele of maize pericarp color1
TLDR
It is shown here a direct evidence for small RNAs’ involvement in regulating p1 that has not been demonstrated previously, and that the epigenetic regulation of p1 alleles is controlled both via RdDM as well as non-RdDM mechanisms.
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TLDR
In mice, small RNAs appear sufficient to induce paramutation, whereas in maize, it seems not to be the only player in the process, and potential mechanisms are discussed in relation to the various paramutation phenomena.
RNA-mediated trans-communication can establish paramutation at the b1 locus in maize
TLDR
A role for mop1 is uncovered in the biogenesis of a subset of microRNAs (miRNAs) and it is uncovered that it functions at the level of production of the primary miRNA transcripts.
Transgenic expression of CBBP, a CXC domain protein, establishes paramutation in maize
TLDR
This study reports the identification of a CXC-domain protein CBBP (CXC domain b1-repeat binding protein) that binds to a defined region within the b1 tandem repeat sequence in vivo and in vitro and suggests a model for counting the number of b1 repeats.
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TLDR
Tandem repeats are prone to epigenetic silencing regulated by RNA interference, but siRNAs from single-copy sequences are exhausted by sequential use of downstream primers by RdRP, which could account for the formation of heterochromatin from tandem repeats.
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TLDR
Genomic studies are allowing the mapping of modifications such as DNA methylation on a genome-wide scale, and small RNAs seem to be important in determining the distribution of chromatin modifications, and RNA might also underlie the complex epigenetic interactions that occur between homologous sequences.
The role of DNA methylation, nucleosome occupancy and histone modifications in paramutation.
TLDR
Insight is provided into the mechanisms underlying paramutation and tissue-specific regulation of b1 at the level of chromatin structure and the B' coding region is H3K27 dimethylated in all tissues analyzed, indicating a role in the maintenance of the silenced B' state.
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