Gene Silencing in Plants


The term gene silencing refers to an epigenetic phenomenon, the heritable inactivation of gene expression that does not involve any changes to the deoxyribonucleic acid (DNA) sequence. While this phenomenon has initially been studied in transgenic plants, its relevance in the regulation of endogenous plant genes has become increasingly apparent.

Keywords: DNA methylation; post‐transcriptional gene silencing; heterochromatin; RNA; interference; transgene silencing

Figure 1.

Paramutation of the maize r1 gene. The series of crosses shown involves three alleles of r1, the R‐r complex (paramutable allele) the R‐mb complex (paramutagenic allele) and a recessive tester allele, r. R‐r confers solid purple pigmentation to the aleurone layer of the seeds; R‐mb confers a marbled pattern of pigmentation to the aleurone; the r tester allele confers no colour to aleurone. Paramutation is observed following test crossing of the R‐r/R‐mb heterozygote. Half of the kernels on the test cross ear carry the R‐mb allele, which, when transmitted through the female, confers a marbled pattern of pigmentation in aleurone, but when transmitted through the male confers extremely infrequent sectors rendering the aleurones mostly colourless. The R‐r allele transmitted from the R‐r/R‐mb heterozygote is referred to as being ‘paramutant’ and is designated as R‐r′ to indicate this new epigenetic state. Male transmission of R‐r′ results in a pale mottled pattern of pigmentation in the aleurone, while female transmission of R‐r′ results in a normal solid colour pattern of aleurone pigmentation. From Walker .

Figure 2.

Cosuppression of the petunia. Chalcone synthase (CHS) gene. CHS regulates floral pigmentation. Overexpression of a chimaeric petunia CHS gene in a wild‐type plant (back) induces coexpression effects in some sectors. The white cells in these sectors have lost the blue pigment due to the mutual inactivation of the transferred and the endogenous CHS copy. From Napoli et al. .

Figure 3.

Environmental effects can induce epigenetic changes. The left picture shows isogenic petunia transformants that have been transformed with a recombinant maize A1 construct. A1 activity leads to the accumulation of a red pigment in the flowers. The right picture shows the same field at a later stage after a period of intense heat and sunlight. Many new flowers that have emerged from the plants display a white floral phenotype indicative for the inactivation of the A1 transgene, which is accompanied by DNA methylation and a condensed chromatin structure of the A1 transgene. From Meyer et al. .

Figure 4.

An illustration of some key enzymes and their involvement in gene silencing pathways in Arabidopsis thaliana. See Note for details.



Brink RA (1956) A genetic change associated with the R locus in maize. Genetics 41: 872–889.

Fire A, Xu SQ and Montgomery MK et al. (1998) Potent and specific genetic interference by double‐stranded RNA in Caenorhabditis elegans. Nature 391: 806–811.

Hamilton AJ and Baulcombe DC (1999) A species of small antisense RNA in post‐transcriptional gene silencing in plants. Science 286: 950–952.

Hollick JB and Chandler VL (2001) Genetic factors required to maintain repression of a paramutagenic maize pl1 allele. Genetics 157: 369–378.

Matzke MA, Primig M, Trnovsky J and Matzke AJM (1989) Reversible methylation and inactivation of marker genes in sequentially transformed tobacco plants. EMBO Journal 8: 643–649.

Mette M F, Aufsatz W, van der Winden J, Matzke MA and Matzke AJM (2000) Transcriptional silencing and promoter methylation triggered by double stranded RNA. EMBO Journal 19: 5194–5201.

Meyer P, Linn F and Heidmann I et al. (1992) Endogenous and environmental factors influence 35S promoter methylation of a maize A1 gene construct in transgenic petunia and its colour phenotype. Molecular & General Genetics 231(3): 345–352.

Napoli C, Lemieux C and Jorgensen R (1990) Introduction of a chimeric chalcone synthase gene into petunia results in reversible co‐suppression of homologous genes in trans. Plant Cell 2: 279–289.

Vanderkrol AR, Mur LA, Beld M, Mol JNM and Stuitje AR (1990) Flavonoid genes in petunia – addition of a limited number of gene copies may lead to a suppression of gene‐expression. Plant Cell 2: 291–299.

Walker EL (1998) Paramutation of the r1 locus of maize is associated with increased cytosine methylation. Genetics 148: 1973–1981.

Wassenegger M, Heimes S, Riedel L and Sänger HL (1994) RNA‐directed de novo methylation of genomic sequences in plants. Cell 76: 567–576.

Further Reading

Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281–297.

Baulcombe DC (2004) RNA silencing in plants. Nature 431: 356–363.

Bender J (2004) DNA methylation and epigenetics. Annual Review of Plant Biology 55: 41–68.

Floyd SK and Bowman JL (2004) Ancient microRNA regulation of gene expression in land plants. Nature 428: 485–548.

Matzke MA and Birchler AJ (2005) RNAi‐mediated pathways in the nucleus. Nature Reviews 6: 24–35.

Meins F Jr, Si‐Ammour A and Blevins T (2005) RNA silencing systems and their relevance to plant development. Annual Review of Cell and Developmental Biology 21: 297–318.

Meyer P (ed.) (2005) Annual Plant Reviews: Plant Epigenetics. Oxford: Blackwell Publishing.

Schubert D, Clarenz O and Goodrich J (2005) Epigenetic control of plant development by Polycomb‐group proteins. Current Opinion in Plant Biology 5: 553–561.

Turner BM (1993) Decoding the nucleosome. Cell 75: 5–8.

Waterhouse PM and Helliwell CA (2003) Exploring plant genomes by RNA‐induced gene silencing. Nature Reviews Genetics 4: 29–38.

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How to Cite close
Meyer, Peter(Sep 2006) Gene Silencing in Plants. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0002022.pub2]