The subfamily of C. elegans Argonaute proteins localized to the nucleus is known to participate in transcription regulation. Thus, WAGO Argonautes bind endogenous siRNAs (endo-siRNAs) corresponding to transposable and repetitive elements and maintain the heterochromatic status of these regions [Gu W. et al., 2009]. In contrast to WAGO, nuclear Argonaute CSR-1 [Claycomb J. et al., 2009] was shown to promote sense-oriented RNA polymerase II transcription in active chromatin regions [Cecere G. et al., 2014]. In the previous study, Global Run-On sequencing (GRO-seq) analysis demonstrated both a decrease in active genes transcription and an increase in antisense transcription and expression of silent genes genome-wide. This effect was similar in both
csr-1 hypomorphic strain that has reduced expression of CSR-1 and in a loss-of-function mutant of Dicer-related helicase,
drh-3 [Cecere G. et al., 2014]. Dicer-related helicase (DRH-3) represents an essential component of all C. elegans RNA-dependent RNA polymerase (RdRP) complexes involved in the production of secondary siRNAs, that also exist endogenously. The loss of DRH-3 affects both CSR-1 bound endo-siRNAs and WAGO interacting ones [Gu W. et al., 2009]. Keeping in mind the transcription alterations demonstrated by GRO-Seq, we are focusing on CSR-1 target genes characteristics, their positioning in the nucleus and chromatin organization changes that accompany the transcription alterations. Silent, heterochromatic regions of the genome are localized close to the nuclear periphery [Akhtar A. et al., 2007, Sexton T. et al., 2007] and are anchored there via nuclear membrane proteins [Ikegami K. et al., 2010]. Here, we show that the global changes in transcriptome profile in
drh-3 and
csr-1 loss-of-function mutants occur together with global alterations in chromatin organization. Repeat-rich autosome arms lose their contact with the nuclear envelope. On the contrary, the central gene-rich parts of the chromosomes are coming closer to LEM-2 transmembrane protein as transcription of active genes is decreasing. This effect is more pronounced in
drh-3 mutant, which is depleted of endo-siRNAs belonging to both "silencing" and "activating" pathways. Interestingly,
drh-3 mutant also demonstrates a dramatic decrease in LEM-2 proximity of the chromosome regions associated with the WAGO pathway activity. Therefore, in the absence of WAGO siRNAs, these regions become less heterochromatic and tend to detach from the nuclear membrane. We are further investigating the connection between transcription changes, chromatin organization and histone modifications in
csr-1 and
drh-3 mutants.