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. 2017 Feb 16;65(4):659-670.e5.
doi: 10.1016/j.molcel.2017.01.034.

Stable Heritable Germline Silencing Directs Somatic Silencing at an Endogenous Locus

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Free PMC article

Stable Heritable Germline Silencing Directs Somatic Silencing at an Endogenous Locus

Olga Minkina et al. Mol Cell. .
Free PMC article

Abstract

The importance of transgenerationally inherited epigenetic states to organismal fitness remains unknown as well-documented examples are often not amenable to mechanistic analysis or rely on artificial reporter loci. Here we describe an induced silenced state at an endogenous locus that persists, at 100% transmission without selection, for up to 13 generations. This unusually persistent silencing enables a detailed molecular genetic analysis of an inherited epigenetic state. We find that silencing is dependent on germline nuclear RNAi factors and post-transcriptional mechanisms. Consistent with these later observations, inheritance does not require the silenced locus, and we provide genetic evidence that small RNAs embody the inherited silencing signal. Notably, heritable germline silencing directs somatic epigenetic silencing. Somatic silencing does not require somatic nuclear RNAi but instead requires both maternal germline nuclear RNAi and chromatin-modifying activity. Coupling inherited germline silencing to somatic silencing may enable selection for physiologically important traits.

Keywords: C. elegans; epigenetics; nuclear RNAi; piRNAs; sid-1; transgenerational inheritance.

Figures

Figure 1
Figure 1. Transgenerational epigenetic sid-1 silencing
(A) RNAi sensitivity of >100 progeny of L4 worms. mRNA expression in (B) mixed stage worms (biological replicate average in red), (C) single young adults (25°C, each bar represents a single worm and two technical replicates), and (D) synchronized young adults. (E) Silenced region. (F) Fraction of dpy-11 RNAi resistant F2 Psid-1 array lines (n). (G) Inherited RNAi resistance of average 103 (a, b) or 870 (c, d) progeny from 3 (a, b) or 20 (c, d) L4 larvae fed dpy-11 RNAi. (H) sid-1 expression in mixed stage line b. Expression is relative to gpd-2/3, wild-type is set to 1.0. Average ± SD of two technical replicates, unless otherwise noted. See also Figure S1.
Figure 2
Figure 2. Maternally transmitted epigenetic silencing
(A) Normalized sid-1 mRNA levels (relative to cpf-1) in single silenced and non-silenced parents and progeny (see Figure S2B for non-normalized data). Average ± SD of at least two technical replicates. (B) RNAi sensitivity of progeny (average of 62 per worm) from (n) F2 cross progeny described in (A) and their subsequent self-progeny fed dpy-11 RNAi. (C) RNAi sensitivity of progeny (average 68 per worm) from (n) F2 sid-1+/nDf32 hemizygous or sid-1+/sid-1+ cross progeny fed dpy-11 RNAi. (D) qRT-PCR measurement of sid-1 intron 4 and intron 6 expression in single worm adults relative to cpf-1 intron 5 expression. cDNA used for qRT-PCR was generated using a gene specific primer amplifying sid-1 and cpf-1. Average ± SD of at least two technical replicates is shown. See also Figure S2.
Figure 3
Figure 3. Transgenerational sid-1 silencing is associated with an increase in HRDE-1-dependent small RNAs
(A–B). Frequency and distribution of sense (red) and antisense (blue) 21–26 nucleotide small RNAs over the (A) sid-1 promoter and (B) the sid-1 gene (start codon to 3′ UTR). Total read counts (upper corner) are normalized to all 21–26nt reads that map to genes. (C–D) Reads (both strands) are highly enriched for (C) 22 nucleotide RNAs with (D) a 5′ guanine in all libraries. Four Psid-1::gfp libraries and two libraries for all other genotypes were combined as replicates. See also Figure S3.
Figure 4
Figure 4. Genetic requirements for sid-1 silencing
(A) sid-1 mRNA expression in mixed stage worms. Average (red bar) of biological replicates relative to gpd-2/3. (B) Maintenance and initiation crosses (silencing competent hermaphrodite germline is highlighted). (C) RNAi sensitivity of progeny of (n) F2 L4 larvae produced by crosses in (B). (D) Putative piRNA 14927-1 binding site and mutant Psid-1(piRNA-4A) sequence. (E) RNAi sensitivity of progeny of (n) F2 lines produced by injected wild-type or piRNA-4A Psid-1 DNA. N.S. = Not significant, * = p < 0.05, ** = p < 0.002 (Mann-Whitney test). Resistant and slightly Dpy values were combined for statistics. In A–C, the Psid-1::gfp array is integrated on the X chromosome. See also Figure S4.
Figure 5
Figure 5. HRDE-1 is required to execute transgenerational silencing
Crosses to test hrde-1 necessity and sufficiency for transgenerational silencing. Pie charts show RNAi sensitivity of progeny of singled L4 larvae on dpy-11 RNAi food. Below each pie chart is the number of L4 parents and the number of progeny scored (in parentheses). Early progeny are the first progeny laid, late progeny are progeny laid subsequently by F3 parent. See also Figure S5.
Figure 6
Figure 6. Transgenerational somatic silencing
(A) Progeny of wild-type or Psid-1::gfp larvae (two generations) or embryos (one generation) placed on dpy-11 RNAi food. (B–D) RNAi sensitivity of (n) worms hatched on dpy-11 RNAi food, scored as adults. To determine sid-1 genotype in (B), adults were fed act-5 RNAi (L1 arrest). (E) qRT-PCR analysis of sid-1 mRNA levels (normalized, relative to gpd-2/3) in young adults. Average ± SD of at least two technical replicates. (F) RNAi sensitivity of methyltransferase mutants after dpy-11 dsRNA exposure for one (n worms scored) or two generations (average of 116 progeny from (n) L4 larvae scored). See also Figure S6.

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