A conserved RNA degradation complex required for spreading and epigenetic inheritance of heterochromatin.

Gergana Shipkovenska,Danesh Moazed,Steven P Gygi,Alexander Durango,Marian Kalocsay

doi:10.7554/elife.54341

Gergana Shipkovenska, Danesh Moazed + Show 3 more

Open Access

https://doi.org/10.7554/elife.54341

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Journal: eLife	Publication Date: Jun 3, 2020
Citations: 33	License type: CC BY 4.0

Affiliation: Howard Hughes Medical Institute, Harvard University

Abstract

Heterochromatic domains containing histone H3 lysine 9 methylation (H3K9me) can be epigenetically inherited independently of underlying DNA sequence. To gain insight into the mechanisms that mediate epigenetic inheritance, we used a Schizosaccharomyces pombe inducible heterochromatin formation system to perform a genetic screen for mutations that abolish heterochromatin inheritance without affecting its establishment. We identified mutations in several pathways, including the conserved and essential Rix1-associated complex (henceforth the rixosome), which contains RNA endonuclease and polynucleotide kinase activities with known roles in ribosomal RNA processing. We show that the rixosome is required for spreading and epigenetic inheritance of heterochromatin in fission yeast. Viable rixosome mutations that disrupt its association with Swi6/HP1 fail to localize to heterochromatin, lead to accumulation of heterochromatic RNAs, and block spreading of H3K9me and silencing into actively transcribed regions. These findings reveal a new pathway for degradation of heterochromatic RNAs with essential roles in heterochromatin spreading and inheritance.

Highlights

Heterochromatic domains of DNA are a conserved feature of eukaryotic chromosomes and play central roles in regulation of transcription, inactivation of transposons, and maintenance of genome integrity (Allshire and Madhani, 2018; Saksouk et al, 2015)
Since the requirements for establishment and maintenance of heterochromatin cannot be readily separated at endogenous sites, the identification of pathways required for epigenetic inheritance of heterochromatin has not been possible
The rixosome is recruited to heterochromatin by the HP1 protein, Swi6, to promote the degradation of RNAs transcribed by RNA pol II within heterochromatic domains

Summary

Introduction

Heterochromatic domains of DNA are a conserved feature of eukaryotic chromosomes and play central roles in regulation of transcription, inactivation of transposons, and maintenance of genome integrity (Allshire and Madhani, 2018; Saksouk et al, 2015). Cell Biology Chromosomes and Gene Expression independently of any input from underlying DNA sequence (Ragunathan et al, 2015; Audergon et al, 2015) In these studies, H3K9 methylation is induced by fusion of a Clr fragment, containing the methyltransferase domain but lacking the chromodomain (CD) required for recognition of H3K9me, to the bacterial Tetracycline Repressor (TetR-Clr4DCD), which binds to tetO arrays inserted at a euchromatic locus. We show that the rixosome targets heterochromatic RNAs for degradation through the conserved 5’À3’ exoribonuclease pathway to clear a path for Clr4-mediated read-write

Results

10 Silver stain

D RNA Pol II ChIP E RNA Pol II ChIP

Discussion

Materials and methods

Funding Funder National Institutes of Health