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Complex coding of endogenous siRNA, transcriptional silencing and H3K9 methylation on native targets of germline nuclear RNAi in C. elegans
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Complex coding of endogenous siRNA, transcriptional silencing and H3K9 methylation on native targets of germline nuclear RNAi in C. elegans
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Complex coding of endogenous siRNA, transcriptional silencing and H3K9 methylation on native targets of germline nuclear RNAi in C. elegans
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Journal Article
Complex coding of endogenous siRNA, transcriptional silencing and H3K9 methylation on native targets of germline nuclear RNAi in C. elegans
2014
Overview
Background
Small RNA-guided transcriptional silencing (nuclear RNAi) is fundamental to genome integrity and epigenetic inheritance. Despite recent progress in identifying the capability and genetic requirements for nuclear RNAi in
Caenorhabditis elegans
, the natural targets and cellular functions of nuclear RNAi remain elusive
.
Methods
To resolve this gap, we coordinately examined the genome-wide profiles of transcription, histone H3 lysine 9 methylation (H3K9me) and endogenous siRNAs of a germline nuclear Argonaute (
hrde-1
/
wago-9
) mutant and identified regions on which transcription activity is markedly increased and/or H3K9me level is markedly decreased relative to wild type animals.
Results
Our data revealed a distinct set of native targets of germline nuclear RNAi, with the H3K9me response exhibiting both overlapping and non-overlapping distribution with the transcriptional silencing response. Interestingly LTR retrotransposons, but not DNA transposons, are highly enriched in the targets of germline nuclear RNAi. The genomic distribution of the native targets is highly constrained, with >99% of the identified targets present in five autosomes but not in the sex chromosome. By contrast, HRDE-1
-
associated small RNAs correspond to all chromosomes. In addition, we found that the piRNA pathway is not required for germline nuclear RNAi activity on native targets.
Conclusion
Germline nuclear RNAi in
C. elegans
is required to silence retrotransposons but not DNA transposon. Transcriptional silencing and H3K9me can occur independently of each other on the native targets of nuclear RNAi in
C. elegans
. Our results rule out a simple model in which nuclear Argonaute protein-associated-small RNAs are sufficient to trigger germline nuclear RNAi responses. In addition, the piRNA pathway and germline nuclear RNAi are specialized to target different types of foreign genetic elements for genome surveillance in
C. elegans.
Publisher
BioMed Central,BioMed Central Ltd,Springer Nature B.V
Subject
/ Animal Genetics and Genomics
/ Animals
/ Argonaute Proteins - deficiency
/ Argonaute Proteins - genetics
/ Biomedical and Life Sciences
/ Caenorhabditis elegans - cytology
/ Caenorhabditis elegans - genetics
/ DNA
/ Genomics
/ Lysine
/ Methods
/ Microbial Genetics and Genomics
/ Multicellular invertebrate genomics
/ RNA Polymerase II - metabolism
/ RNA, Small Interfering - genetics
