FUS-dependent loading of SUV39H1 to OCT4 pseudogene-lncRNA programs a silencing complex with OCT4 promoter specificity

Michele Scarola,Massimo Rosso,Elisa Comisso,Giannino Del Sal,Claudio Schneider,Stefan Schoeftner,Roberta Benetti

doi:10.1038/s42003-020-01355-9

Michele Scarola, Massimo Rosso + Show 5 more

Open Access

https://doi.org/10.1038/s42003-020-01355-9

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Abstract

The resurrection of pseudogenes during evolution produced lncRNAs with new biological function. Here we show that pseudogene-evolution created an Oct4 pseudogene lncRNA that is able to direct epigenetic silencing of the parental Oct4 gene via a 2-step, lncRNA dependent mechanism. The murine Oct4 pseudogene 4 (mOct4P4) lncRNA recruits the RNA binding protein FUS to allow the binding of the SUV39H1 HMTase to a defined mOct4P4 lncRNA sequence element. The mOct4P4-FUS-SUV39H1 silencing complex holds target site specificity for the parental Oct4 promoter and interference with individual components results in loss of Oct4 silencing. SUV39H1 and FUS do not bind parental Oct4 mRNA, confirming the acquisition of a new biological function by the mOct4P4 lncRNA. Importantly, all features of mOct4P4 function are recapitulated by the human hOCT4P3 pseudogene lncRNA, indicating evolutionary conservation. Our data highlight the biological relevance of rapidly evolving lncRNAs that infiltrate into central epigenetic regulatory circuits in vertebrate cells.

Highlights

The resurrection of pseudogenes during evolution produced long noncoding RNAs (lncRNAs) with new biological function
We recently reported on a new mechanism of ancestral gene regulation that depends on pseudogene lncRNA dependent recruitment of an epigenetic silencing complex to the Oct[4] promoter in trans[17]
Performing murine Oct4 pseudogene 4 (mOct4P4) lncRNA pulldown experiments and a mOct4P4 lncRNA deletion analysis we demonstrate that the RNA binding protein FUS and a 200 nucleotide mOct4P4/hOCT4P3 region are essential for Oct4/ OCT4 silencing in mouse and human cells

Summary

Introduction

The resurrection of pseudogenes during evolution produced lncRNAs with new biological function. The resulting nuclear restricted mOct4P4 lncRNA forms a complex with the HMTase SUV39h1 and targets H3K9me[3] and HP1 to the promoter of the parental Oct[4] gene on chromosome 17, leading to gene silencing in trans. This mechanism does not involve pairing of Oct[4] sense and pseudogene antisense RNAs. Importantly, this mechanism does not involve pairing of Oct[4] sense and pseudogene antisense RNAs To this end, lncRNA sequence determinants and evolutional importance for mOct4P4 pseudogene lncRNA dependent silencing of Oct[4] are not known. The 200nt mOct4P4/hOCT4P3 lncRNA sequence element is sufficient to guide SUV39H1 dependent Oct4/OCT4 silencing, even in the absence of FUS

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