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Distinct mechanisms determine transposon inheritance and methylation via small interfering RNA and histone modification.

Lippman Z, May B, Yordan C, Singer T, Martienssen R - PLoS Biol. (2003)

Bottom Line: More recently, transposon silencing has been associated with DNA methylation, histone H3 lysine-9 methylation (H3mK9), and RNA interference (RNAi).According to their pattern of transposon regulation, the mutants can be divided into two groups, which suggests that there are distinct, but interacting, complexes or pathways involved in transposon silencing.Furthermore, different transposons tend to be susceptible to different forms of epigenetic regulation.

View Article: PubMed Central - PubMed

Affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.

ABSTRACT
Heritable, but reversible, changes in transposable element activity were first observed in maize by Barbara McClintock in the 1950s. More recently, transposon silencing has been associated with DNA methylation, histone H3 lysine-9 methylation (H3mK9), and RNA interference (RNAi). Using a genetic approach, we have investigated the role of these modifications in the epigenetic regulation and inheritance of six Arabidopsis transposons. Silencing of most of the transposons is relieved in DNA methyltransferase (met1), chromatin remodeling ATPase (ddm1), and histone modification (sil1) mutants. In contrast, only a small subset of the transposons require the H3mK9 methyltransferase KRYPTONITE, the RNAi gene ARGONAUTE1, and the CXG methyltransferase CHROMOMETHYLASE3. In crosses to wild-type plants, epigenetic inheritance of active transposons varied from mutant to mutant, indicating these genes differ in their ability to silence transposons. According to their pattern of transposon regulation, the mutants can be divided into two groups, which suggests that there are distinct, but interacting, complexes or pathways involved in transposon silencing. Furthermore, different transposons tend to be susceptible to different forms of epigenetic regulation.

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siRNA Differentially Accumulates in Chromatin MutantssiRNA Northern blots were hybridized with sense RNA probes for each of the transposons indicated in (A) and (B) in order to detect 25 nt antisense siRNA from each of the sequences tested. AtMu1 is single copy so that autoradiographic exposure was increased substantially. A 22 oligonucleotide size marker is indicated, and the 21 nt miRNA miR-171 was used as a loading control. It is unaffected in the mutants tested.
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pbio.0000067-g004: siRNA Differentially Accumulates in Chromatin MutantssiRNA Northern blots were hybridized with sense RNA probes for each of the transposons indicated in (A) and (B) in order to detect 25 nt antisense siRNA from each of the sequences tested. AtMu1 is single copy so that autoradiographic exposure was increased substantially. A 22 oligonucleotide size marker is indicated, and the 21 nt miRNA miR-171 was used as a loading control. It is unaffected in the mutants tested.

Mentions: We looked for siRNA in each of the mutants (Figure 4). Long siRNA (25 nt) is a hallmark of transposons targeted by RNAi (Llave et al. 2002) and is presumably the product of a DICER-like (DCL) enzyme specialized for this purpose (Hamilton et al. 2002). As a control, a 21 nt microRNA (miRNA) derived from hairpin precursors (Rhoades et al. 2002) accumulated to normal levels in all genotypes examined. miRNA is the product of DICER-LIKE1 (DCL1) (At1g01040), and dcl1-9 mutants (Jacobsen et al. 1999) had no effect on any of the transposons tested (data not shown). While we could not detect siRNA corresponding to ATCOPIA4, ATLINE1-4, or ATLANTYS2, 25 nt siRNAs corresponding to AtMu1 and ATGP1, as well as the short interspersed nuclear retroelement AtSN1 (Hamilton et al. 2002), accumulated in WT plants. These siRNAs accumulated to normal levels in sil1, kyp, and cmt3, but AtMu1 and AtSN1 were absent or nearly so in met1 and ddm1 (Figure 4; data not shown). In contrast, siRNA from the LTR and coding sequence of ATGP1 was normal in met1 and ddm1 (Figure 4; data not shown). siRNA in ago1 had the opposite pattern: transposon siRNA accumulated to normal levels except for ATGP1, which had reduced levels (Figure 4). This indicates a role for MET1 and DDM1 in siRNA accumulation and a role for siRNA in epigenetic inheritance.


Distinct mechanisms determine transposon inheritance and methylation via small interfering RNA and histone modification.

Lippman Z, May B, Yordan C, Singer T, Martienssen R - PLoS Biol. (2003)

siRNA Differentially Accumulates in Chromatin MutantssiRNA Northern blots were hybridized with sense RNA probes for each of the transposons indicated in (A) and (B) in order to detect 25 nt antisense siRNA from each of the sequences tested. AtMu1 is single copy so that autoradiographic exposure was increased substantially. A 22 oligonucleotide size marker is indicated, and the 21 nt miRNA miR-171 was used as a loading control. It is unaffected in the mutants tested.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC300680&req=5

pbio.0000067-g004: siRNA Differentially Accumulates in Chromatin MutantssiRNA Northern blots were hybridized with sense RNA probes for each of the transposons indicated in (A) and (B) in order to detect 25 nt antisense siRNA from each of the sequences tested. AtMu1 is single copy so that autoradiographic exposure was increased substantially. A 22 oligonucleotide size marker is indicated, and the 21 nt miRNA miR-171 was used as a loading control. It is unaffected in the mutants tested.
Mentions: We looked for siRNA in each of the mutants (Figure 4). Long siRNA (25 nt) is a hallmark of transposons targeted by RNAi (Llave et al. 2002) and is presumably the product of a DICER-like (DCL) enzyme specialized for this purpose (Hamilton et al. 2002). As a control, a 21 nt microRNA (miRNA) derived from hairpin precursors (Rhoades et al. 2002) accumulated to normal levels in all genotypes examined. miRNA is the product of DICER-LIKE1 (DCL1) (At1g01040), and dcl1-9 mutants (Jacobsen et al. 1999) had no effect on any of the transposons tested (data not shown). While we could not detect siRNA corresponding to ATCOPIA4, ATLINE1-4, or ATLANTYS2, 25 nt siRNAs corresponding to AtMu1 and ATGP1, as well as the short interspersed nuclear retroelement AtSN1 (Hamilton et al. 2002), accumulated in WT plants. These siRNAs accumulated to normal levels in sil1, kyp, and cmt3, but AtMu1 and AtSN1 were absent or nearly so in met1 and ddm1 (Figure 4; data not shown). In contrast, siRNA from the LTR and coding sequence of ATGP1 was normal in met1 and ddm1 (Figure 4; data not shown). siRNA in ago1 had the opposite pattern: transposon siRNA accumulated to normal levels except for ATGP1, which had reduced levels (Figure 4). This indicates a role for MET1 and DDM1 in siRNA accumulation and a role for siRNA in epigenetic inheritance.

Bottom Line: More recently, transposon silencing has been associated with DNA methylation, histone H3 lysine-9 methylation (H3mK9), and RNA interference (RNAi).According to their pattern of transposon regulation, the mutants can be divided into two groups, which suggests that there are distinct, but interacting, complexes or pathways involved in transposon silencing.Furthermore, different transposons tend to be susceptible to different forms of epigenetic regulation.

View Article: PubMed Central - PubMed

Affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.

ABSTRACT
Heritable, but reversible, changes in transposable element activity were first observed in maize by Barbara McClintock in the 1950s. More recently, transposon silencing has been associated with DNA methylation, histone H3 lysine-9 methylation (H3mK9), and RNA interference (RNAi). Using a genetic approach, we have investigated the role of these modifications in the epigenetic regulation and inheritance of six Arabidopsis transposons. Silencing of most of the transposons is relieved in DNA methyltransferase (met1), chromatin remodeling ATPase (ddm1), and histone modification (sil1) mutants. In contrast, only a small subset of the transposons require the H3mK9 methyltransferase KRYPTONITE, the RNAi gene ARGONAUTE1, and the CXG methyltransferase CHROMOMETHYLASE3. In crosses to wild-type plants, epigenetic inheritance of active transposons varied from mutant to mutant, indicating these genes differ in their ability to silence transposons. According to their pattern of transposon regulation, the mutants can be divided into two groups, which suggests that there are distinct, but interacting, complexes or pathways involved in transposon silencing. Furthermore, different transposons tend to be susceptible to different forms of epigenetic regulation.

Show MeSH
Related in: MedlinePlus