Plant Gene Silencing PDF
Preview Plant Gene Silencing
PLANT GENE SILENCING PLANT GENE SILENCING Edited by M.A. MATZKE and A.J.M. MATZKE Institute of Molecular Biology, Austrian Academy of Sciences, Salzburg, Austria Reprinted from Plant Molecular Biology, Volume 43 (2-3),2000 SPRINGER SCIENCE+BUSINESS MEDIA, B.V. A C.I.P. Catalogue record for this book is available from the Library of Congress ISBN 978-94-010-5821-6 ISBN 978-94-011-4183-3 (eBook) DOI 10.1007/978-94-011-4183-3 Printed on acid-free paper AII Rights Reserved © 2000 Springer Science+Business Media Dordrecht Originally published by Kluwer Academic Publishers in 2000 Softcover reprint ofthe hardcover lst edition 2000 No part of the material protected by this copyright notice may be reproduced or utilized in any form or by any means, electronic or mechanical, including photocopying, recording or by any information storage and retrieval system, without written permis sion from the copyright owner. CONTENTS Preface vii-ix Paramutation in maize v.L. Chandler, WB. Eggleston, J.E. Dorweiler 1-25 Genomic imprinting in plants: observations and evolutionary implications M. Alleman, J. Doctor 27-41 Nucleolar dominance: uniparental gene silencing on a multi-megabase scale in genetic hybrids C.S. Pikaard 43-57 Epigenetic aspects of somaclonal variation in plants S.M. Kaeppler, H.F. Kaeppler, Y. Rhee 59-68 Plant DNA methyltransferases E.J. Finnegan, KA Kovac 69-81 RNA-directed DNA methylation M. VVassenegger 83-100 Transcriptional transgene silencing and chromatin components P. Meyer 101-114 Transcriptional gene silencing mutants O. Mittelsten Scheid, J. Paszkowski 115-121 Role of inverted DNA repeats in transcriptional and post-transcriptional gene Silencing M.WM. Muskens, A.PA Vissers, J.N.M. Mol, J.M. Kooter 123-140 RNA degradation and models for post-transcriptional gene silencing F.MeinsJr. 141-153 Post-transcriptional gene silencing mutants J.-B. Morel, H. Vaucheret 155-164 Systemic silencing signal(s) M. Fagard, H. Vaucheret 165-173 RNA viruses as inducers, suppressors and targets of post-transcriptional gene silen- cing R. Marathe, R. Anandalakshmi, T.H. Smith, G.J. Pruss, V.B. Vance 175-186 Plant DNA viruses and gene silencing S.N. Covey, N.S. AI-Kaff 187-202 Transgene silencing in monocots L.M. Iyer, S.P. Kumpatla, M.B. Chandrasekharan, T.C. Hall 203-226 Plants as bioreactors for protein production: avoiding the problem of transgene silen- cing C. De VVilde, H. Van Houdt, S. De Buck, G. Angenon, G. De Jaeger, A. Depicker 227-239 Use of matrix attachment regions (MARs) to minimize transgene silencing G.C. Allen, S. Spiker, WF. Thompson 241-256 Gene silencing in potato: allelic differences and effect of ploidy A.-MA VVolters, R.G.F. Visser 257-266 Genetic and epigenetic interactions in allopolyploid plants L. Comai 267-279 Transgenic silencing by the host genome defense: implications for the evolution of epigenetic control mechanisms in plants and vertebrates M.A. Matzke, M.F. Mette, A.J.M. Matzke 281-295 Index 297-298 Cover illustration Imprinting of the r1 gene in the maize endosperm is demonstrated visually with reciprocal crosses between a colorless kernel r1 allele (r-g) and colored kernel alleles or epialleles. According to convention, maternal parents are shown on the right side in a cross. Shown are ears from crosses in which a weakly paramutant r1 allele is transmitted maternally with either Mdr1-w22 or mdr1-r, a mutant of the imprinting control gene. The crosses are: (right ear) R-r:std r-g x r-gfr-g (left ear) R-r:stdf rog, Mdr1-w221mdr1-r x r-gfr-g Kernel genotypes (left ear): (colorless kernels) r-g, r-gfr-g (solid kernels) R-r:std, R-r:stdf rog; Mdr1-w22, Mdr1-w22IMdr1-w22 (mottled kernels) R-r:std, R-r:stdf rog; mdr1-r, mdr1-rIMdr1-w22 Plant Molecular Biology 43, pp. 147-161. Plant Molecular Biology 43: vii-ix, 2000. M.A. Matzke and AJ.M. Matzke (Eds.), Plant Gene Silencing. VB " Preface The rapid pace of discovery in plant gene silencing re- trans-silencing phenomenon similar to those observed search and the explosive growth in our understanding more recently with transgenes. As detailed by Chan- of novel epigenetic silencing phenomena over the past dler et at., maize provides a rich source of para- decade have few parallels in modern plant science. mutation systems that can be used to derive general Couple this with the fact that plant scientists have per- principles of epigenetic regulation and to probe the formed groundbreaking work on different aspects of basis of meiotically heritable epigenetic states. Mary epigenetic silencing that are now being 'rediscovered' Alleman and John Doctor discuss parental imprinting, in animals and it is easy to see why this field attracts another epigenetic effect that was discovered first at so much attention and devoted experimental effort. the single-gene level in plants by Jerry Kermicle in We hope that the collection of reviews in this special the 1970s. While maize has traditionally been used issue of Plant Molecular Biology will convey some to study imprinting, considerable progress has been of this excitement and also illustrate the wide range made recently in Arabidopsis, which is challenging of gene silencing phenomena and their considerable some previous assumptions about imprinting in plants. importance for basic and applied plant science. Craig Pikaard reviews nucleolar dominance in genetic Many of the reviews in this issue discuss silencing hybrids, a third natural epigenetic phenomenon dis- effects observed in transgenic plants, which have for- covered first in plants. Nucleolar dominance is a truly tuitously provided excellent tools for discovering and impressive example of silencing on a multi-megabase analyzing different silencing phenomena. Transgenes scale, with the potential to contribute significantly to a can be silenced in plants by classical position effects, wider understanding of gene expression, chromosome in which the genomic environment influences trans- dynamics and allelic discrimination. gene expression, and by homology-dependent gene The fourth review by Shawn Kaeppler, Heidi silencing (HDGS), a type of epigenetic inactivation Kaeppler and Yong Rhee considers epigenetic aspects that is based on interactions between homologous nu- of somaclonal variation in plants. Long considered an cleic acid sequences. HDGS phenomena have been outcome of genetic changes incurred during tissue cul- described in diverse organisms and are probably com- ture, somaclonal variation is increasingly viewed as mon to most eukaroytes. In plants, HDGS can occur having a substantial epigenetic component. Moreover, at the transcriptional or posttranscriptionallevels, and the frequent lethality and developmental abormalities involve DNA-DNA, RNA-DNA or RNA-RNA asso- observed with cloned mammals are reminiscent of ciations, respectively. While the mechanisms of these somaclonal variation and might also have a strong epi- silencing effects are still under investigation, it is clear genetic basis. It is thus possible that many of the older that they are revealing unanticipated ways in which in- as well as more recent observations on somaclonal teractions between nucleic acid sequences can regulate variation in plants will be recognized and scrutinized gene expression in the nucleus and in the cytoplasm. by mammalian cloners. Although transgenic plants have been instrumen- Many epigentic silencing effects are accompanied tal in the identification and characterization of gene by reversible DNA modifications, such as cytosine silencing effects, silencing was not observed first with methylation and alterations in chromatin structure, but transgenes. The first three reviews cover silencing phe- we are still far from understanding how these mod- nomena that have been known for some time to affect ifications are induced or the enzymology involved. endogenous genes. Vicki Chandler, William Eggle- Jean Finnegan and Kathryn Kovac provide an up-to- ston and Jane Dorweiler provide a comprehensive date account of plant DNA methyltransferases. With treatment of paramutation in maize. Paramutation, dis- the imminent completion of the Arabidopsis genome covered in the 1950s in maize by Alexander Brink and sequence, we should soon have in hand the com- in tomato by Rudolf Hagemann, can legitimately be plete repertoire of these enzymes from this species, considered the first example of a homology-dependent allowing their different roles in plant development viii and genome defense to be dissected. DNA methy- cover their work on Arabidopsis PTGS mutants, which lation associated with HDGS is thought to be trig- are also being isolated by others from Neurospora gered by homologous DNA or RNA sequences. RNA- and Caenorhabditis elegan~. Some of these mutants directed DNA methylation, discovered first in plants are validating the original insightful suggestion of by Wassenegger and colleagues, is reviewed in depth William Dougherty and coworkers that PTGS involves in this issue by Michael Wassenegger. RNA-directed an RNA-dependent RNA polymerase, whose activ- DNA methylation is gaining in prominence, as its ity is required for the sequence specificity of RNA potential role in mammalian epigenetic effects that in- degradation that is the hallmark of PTGS. volve noncoding RNAs and DNA methylation, such as The stunning demonstration several years ago parental imprinting and X-inactivation, becomes more by Vaucheret and coworkers that PTGS is graft- widely appreciated. transmissible is discussed and elaborated by Mathilde Transcriptional gene silencing (TGS) can involve Fagard and Herve Vaucheret in their review on sys- DNA methylation in promoter regions but perhaps temic silencing signal(s). The existence of mobile even more relevant is the role played by chromatin silencing signals that travel through the plant vascular conformation, which is universal among eukaryotic system is one of several observations that suggests a organisms, even those that do not methylate their relationship between PTGS and plant viruses. A strong DNA. Peter Meyer offers a systematic account of chro- connection between PTGS and a natural form of resis- matin components from all types of organisms and tance to RNA viruses is detailed by Rajendra Marathe, relates this to TGS of transgenes. Studies of plant Radhamani Anandalakshmi, Trent Smith, Gail Pruss chromatin structure are just beginning and surely we and Vicki Vance. RNA viruses can act as inducers and can expect rapid progress in this area as plant ho- targets of gene silencing, and - as the Vance group mologues to yeast and animal chromatin proteins are was one of the first to show - some of these viruses characterized. Genetic approaches are being used to encode suppressors of gene silencing. The identifica- identify molecular components of TGS in Arabidop- tion of these viral suppressors is a significant advance sis. Ortrun Mittelsten Scheid and Jurek Paszkowski that has opened the door to a fuller understanding of describe their pioneering efforts and other work in this the mechanism of PTGS, and has solidified the link area in their review on TGS mutants. between PTGS and a natural plant defense to viruses. The first discovery of post-transcriptional gene DNA viruses provide more examples of gene si- silencing (PTGS), now considered to be essentially lencing phenomena. As discussed by Simon Covey the same phenomenon as quelling in Neurospora and and Nadia AI-Kaff, the two major groups of plant RNAi in animals, was made in plants by the groups DNA viruses, geminiviruses and pararetroviruses, of Richard Jorgensen, Jos Mol and Don Grierson. induce silencing effects resembling both TGS and PTGS/quelling/RNAi is currently a hot area of inves- PTGS. Given the multiple effects elicited by DNA tigation that is benefiting from multiple approaches viruses, the frequent silencing of transgenes driven by and different experimental systems. Four reviews in the cauliflower mosaic (pararetro)virus 35S promoter this volume cover various aspects of PTGS. Fred is perhaps not surprising. Meins, the originator of the influential 'biochemical In addition to its inherent interest, gene silenc- switch model', discusses models for PTGS in the ing has had a substantial impact on applications in light of the most recent data on RNA degradation. agricultural biotechnology. The potential for unwanted Marielle Muskens, Adrienne Vissers, Jos Mol and Jan silencing of trans genes in genetically engineered lines Kooter consider the roles of inverted DNA repeats is a concern, particularly in major crop plants. Laksmi- (IRs), which have been implicated repeatedly in vari- narayan Iyer, Siva Kumpatla, Mahesh Chandrasekha- ous HDGS effects. IRs might be frequently associated ran and Tim Hall consolidate a considerable amount with gene silencing because they are particularly adept of information on gene silencing in monocot plants. at DNA-DNA interactions or because they can be tran- Silencing effects similar to those seen in dicots have scribed to produce double-stranded RNA, which is also been observed in monocots, where the problem another recurring molecule in various cases of gene might even be exacerbated due to the transformation silencing. techniques used and the complex genomes of many Mutants defective in PTGS are helping to un- plants in this group. Strategies to avoid silencing of derstand the molecular machinery and mechanism of introduced genes are discussed by Chris De Wilde, this process. Jean-Benoit Morel and Herve Vaucheret Helena Van Houdt, Sylvie De Buck, Geert Angenon, ix Geert De Jaeger and Ann Depicker in their review often exhibit genome instability and unusual pheno- on using plants as large-scale bioreactors for protein types. Further insight into these effects could lead production. As these authors point out, plants have a to, among other things, an improved understanding number of advantages for producing heterologous pro- of hybrid vigor. As discussed above, PTGS has clear teins such as antibodies, but stable transgene expres- links to a protective response to RNA viruses that sion must be ensured by taking into account construct replicate in the cytoplasm. The host defense angle design, genomic integration regions, growth condi- can be considered further with respect to a genome tions and other factors. A potential means to minimize defense that targets and transcriptionally inactivates transgene silencing by using matrix-attachment re- natural invasive DNA sequences, such as transposable gions (MARs) in transgene constructs is considered elements, via DNA methylation. Keeping in mind the by George Allen, Steve Spiker and Bill Thompson. overwhelming presence of TEs in most plant genomes Certainly the identification of sequences that would in- and the association of TE remnants with many plant sulate trans genes from silencing effects would benefit genes, Marjori Matzke, Florian Mette and Antonius enormously the agricultural biotechnology industry. Matzke consider whether epigenetic control mecha- Finally, gene silencing can be considered in the nisms in (polyploid) plants and vertebrates, both of context of genome evolution. HOGS, which results which require DNA methylation for proper develop- from recognition of nucleic acid sequence homology, ment, have evolved by recruiting the genome defense would be expected to assume a major role in poly- to regulate host gene expression. ploids, where whole genomes are duplicated, and in The topics in this volume run the gamut from species that contain substantial repetitive DNA, which descriptions of various silencing phenomena, to si- includes many higher plants. Providing a bridge be- lencing models and mechanisms, to practical consid- tween the genome evolution aspect and the applied erations of silencing, and lastly, to the links between chapters is the review by Annemarie Wolters and silencing, host defense and genome evolution. It is Richard Visser, who detail their work on gene si- hoped that this broad perspective will inform and stim- lencing in potato, a vegetatively propagated, highly ulate interested readers, and inspire a new generation heterozygous autopolyploid. As they discuss, special of scientists to pursue research on the beautiful epi- considerations appear to apply when using HOGS to genetic gene silencing systems available in the plant inactivate specific genes to improve tuber characteris- kingdom. tics. Luca Comai provides an account of genetic and M.A. MATZKE AND A.J.M. MATZKE epigenetic interactions in allopolyploid plants, which Plant Molecular Biology 43: 121-145,2000, M,A. Matzke and AJ.M. Matzke (Eds.), Plant Gene Silencing. 121 © 2000 Kluwer Academic Publishers. Printed in the Netherlands. Paramutation in maize Vicki L. Chandler1,*, William B. Eggleston2 and Jane E. Dorweiler1 lDepartment of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA (*author for correspondence; e-mail: 122 This review focuses on paramutation in maize. r1 alleles are genetically complex (reviewed in Dooner Similarities and differences in the phenomenology et al., 1991), containing multiple r1 coding regions between the r1 , b 1 and pll loci will be reviewed. separated by anywhere from a few kilobases to over Recombination experiments to localize sequences re- 100 kb (Robbins et al., 1991; Eggleston et aI., 1995; quired for paramutation, presence or absence of DNA Walker et aI., 1995; Matzke et al., 1996; Panavas methylation or chromatin structure correlations with et ai., 1999; W. Eggleston, unpublished data). For this paramutation, and trans-acting mutants affecting para- reason, rl alleles are referred to as haplotypes, with mutation will be described. Potential relationships be- each haplotype containing zero to several r 1 genes. tween paramutation and trans gene silencing, models Each rl gene is regulated independently, although the for paramutation, and potential roles for paramutation r1 genes within a particular haplotype may have the will be discussed. same or different expression patterns. In some com- plex haplotypes unrelated genes are located between the rl genes (Dooner and Kermicle, 1976; Kermicle Anthocyanin regulatory genes and Axtell, 1981; Robbins et ai., 1991; J. Kermicle and W. Eggleston, unpublished data). The majority The maize loci that undergo paramutation all encode of r1 haplotypes that participate in paramutation are transcription factors that activate structural genes in expressed in the aleurone layer of the seed and it is the anthocyanin biosynthetic pathways. Several fea- this expression that is most susceptible to paramuta- tures of this pathway likely contributed to paramu- tion (reviewed in Brink et aI., 1968; Brink, 1973). In tation being discovered at these loci. The pathways contrast, all known bl alleles are simple, with a single produce pigments that are not essential and easily ob- coding region (Patterson et aI., 1991, 1993; Selinger served. In addition, the amount of pigment observed and Chandler, 1999). The bl alleles that participate in often reflects the levels of the regulatory proteins and paramutation primarily are expressed in the epidermal even subtle changes (2-3-fold) in RNA levels are layer of most vegetative parts of the plant, the tassel, easily visualized as changes in pigment intensity (Pat- the cob and the peri carp of the seed. terson et aI., 1993; Hollick et aI., 2000). In most The pll (purple plantl) locus encodes a myb- tissues, where and when the biosynthetic pathways are related transcription factor (Cone et ai., 1993) that expressed is determined at the level of where and when functions together with the b-HLH protein(s) encoded the regulatory proteins are expressed (Dooner, 1979; by rl or bl to activate the anthocyanin pathway (Goff Ludwig and Wessler, 1990; Radicella et aI., 1992). et al., 1992). All described pll alleles also are simple There are numerous alleles at each locus. Different al- (Cone et al., 1993; Hollick et ai., 2000), and the alleles leles have distinct 5' regulatory sequences and display that participate in paramutation are expressed in the a wide diversity of tissue-specific expression patterns epidermal layer of most vegetative plant parts, anthers, (Styles et aI., 1973; Coe, 1979). Only a subset of pericarp and in young seedlings. For pll , paramutation alleles at each locus participate in paramutation, and is typically monitored in the anthers (Hollick et aI., where it has been tested, there are no paramutation 1995; Hollick and Chandler, 1998), a tissue where bi interactions between loci (Brink et aI., 1960; Hollick and r 1 paramutation does not occur. Paramutation has et aI., 2000). not been described for the pll orthologue expressed in The bl (booster!) and rl (redl) loci encode func- the seed, c1 (colorlessl). tionally duplicate basic helix-loop-helix (b-HLH) pro- teins that activate the genes in the anthocyanin biosyn- thetic pathway, which produce red/purple pigments. Properties of paramutation Sequence similarities, the syntenic map position of these two genes, and the ability of the proteins to All examples of paramutation involve an interaction substitute for each other (Styles et aI., 1973; Goff between alleles that leads to a heritable reduction et al., 1990; Ludwig et aI., 1990; Radicella et al., in the expression of one of the alleles. Alleles sen- 1991) suggest that they are orthologues. The dupli- sitive to altered expression are termed paramutable, cation resulted from an ancient allotetraploidization and alleles inducing the change, paramutagenic. After that occurred in maize evolution (Gaut and Doebley, paramutation, sensitive alleles are termed paramutant 1997). Alleles at the two loci are organized very differ- (or paramutated) and designated with an apostrophe ently and exhibit distinct patterns of expression. Many (i.e., generically, B', PI', R', etc.). Many alleles at rI, [2]
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