Allele-specific repression of Sox2 through the long non-coding RNA Sox2ot

Tobias C Messemaker,Harald M M Mikkers,Anke E J ‘T Jong,Patrick R Van Den Berg,Robert-Jan Palstra,Selina M Van Leeuwen,Stefan Semrau,Rob C Hoeben

doi:10.1038/s41598-017-18649-4

Tobias C Messemaker, Harald M M Mikkers + Show 6 more

Open Access

https://doi.org/10.1038/s41598-017-18649-4

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Abstract

The transcription factor Sox2 controls the fate of pluripotent stem cells and neural stem cells. This gatekeeper function requires well-regulated Sox2 levels. We postulated that Sox2 regulation is partially controlled by the Sox2 overlapping long non-coding RNA (lncRNA) gene Sox2ot. Here we show that the RNA levels of Sox2ot and Sox2 are inversely correlated during neural differentiation of mouse embryonic stem cells (ESCs). Through allele-specific enhanced transcription of Sox2ot in mouse Sox2eGFP knockin ESCs we demonstrate that increased Sox2ot transcriptional activity reduces Sox2 RNA levels in an allele-specific manner. Enhanced Sox2ot transcription, yielding lower Sox2 RNA levels, correlates with a decreased chromatin interaction of the upstream regulatory sequence of Sox2 and the ESC-specific Sox2 super enhancer. Our study indicates that, in addition to previously reported in trans mechanisms, Sox2ot can regulate Sox2 by an allele-specific mechanism, in particular during development.

Highlights

Correct gene regulation, which relies on the temporally and spatially controlled expression of lineage specific transcription factors, determines the success of development
Primers recognizing an exon of Sox2otb that is the first exon of Sox2otc could amplify Sox2ot transcripts in early passage neurospheres, which is in agreement with two recent studies[31,35]
We identified one previously undescribed exon located between Sox2otb exon 2 and Sox2otc exon 1 (Fig. 1a)

Summary

Introduction

Correct gene regulation, which relies on the temporally and spatially controlled expression of lineage specific transcription factors, determines the success of development. Sox[2] activity is controlled by post-translational modifications, such as serine- and threonine phosphorylation, sumoylation, ubiquitination, and acytelation[16] These modifications affect localization, DNA binding and stability. To date several studies investigating the function of Sox2ot have been reported[32,33,34] These studies utilized knockdown or overexpression of Sox2ot in cancer cell lines and the results have indicated a role of Sox2ot in regulating proliferation as well as regulating Sox[2]. On basis of our data we propose that during development Sox2ot expression is mainly restricted to neural cell types and that, in contrast to previous reports, enhanced Sox2ot transcriptional activity negatively affects Sox[2] RNA levels in an allele-specific manner

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