RN7SK small nuclear RNA controls bidirectional transcription of highly expressed gene pairs in skin

Roberto Bandiera,Michaela Frye,Thiago Britto-Borges,Susanne Bornelöv,Rebecca E Wagner,Christoph Dieterich,Sabine Dietmann

doi:10.1038/s41467-021-26083-4

Abstract

Pausing of RNA polymerase II (Pol II) close to promoters is a common regulatory step in RNA synthesis, and is coordinated by a ribonucleoprotein complex scaffolded by the noncoding RNA RN7SK. The function of RN7SK-regulated gene transcription in adult tissue homoeostasis is currently unknown. Here, we deplete RN7SK during mouse and human epidermal stem cell differentiation. Unexpectedly, loss of this small nuclear RNA specifically reduces transcription of numerous cell cycle regulators leading to cell cycle exit and differentiation. Mechanistically, we show that RN7SK is required for efficient transcription of highly expressed gene pairs with bidirectional promoters, which in the epidermis co-regulated cell cycle and chromosome organization. The reduction in transcription involves impaired splicing and RNA decay, but occurs in the absence of chromatin remodelling at promoters and putative enhancers. Thus, RN7SK is directly required for efficient Pol II transcription of highly transcribed bidirectional gene pairs, and thereby exerts tissue-specific functions, such as maintaining a cycling cell population in the epidermis.

Highlights

Pausing of RNA polymerase II (Pol II) close to promoters is a common regulatory step in RNA synthesis, and is coordinated by a ribonucleoprotein complex scaffolded by the noncoding RNA RN7SK
To remove Rn7sk in the interfollicular epidermis (IFE) (Rn7sk conditional knockout mice (cKO)), the mice were crossed to a transgenic line carrying an inducible oestrogen receptor domain under the control of the keratin 14 promoter (Krt14:Cre-ERT2), targeting all undifferentiated basal cells in the IFE
We observed the same phenotype when we deleted Rn7sk during skin morphogenesis starting from postnatal day 4 (P4) (Fig. 1g−i)

Summary

Introduction

Pausing of RNA polymerase II (Pol II) close to promoters is a common regulatory step in RNA synthesis, and is coordinated by a ribonucleoprotein complex scaffolded by the noncoding RNA RN7SK. We show that RN7SK is required for efficient transcription of highly expressed gene pairs with bidirectional promoters, which in the epidermis co-regulated cell cycle and chromosome organization. RN7SK is directly required for efficient Pol II transcription of highly transcribed bidirectional gene pairs, and thereby exerts tissue-specific functions, such as maintaining a cycling cell population in the epidermis. Pol II pausing is a common feature of gene regulation during development and embryonic stem cell differentiation[21,22,23,24], and orchestrates rapid and dynamic changes in transcription, in particular of regulators involved in signal transduction[24,25,26,27]. Depletion experiments in mouse embryonic stem cells revealed impaired neuronal differentiation[29], and identified RN7SK as regulator of bidirectionally transcribed enhancers and transcription termination[30,31]. Our work identifies a functional role of the 7SK snRNP complex in regulating RNA synthesis during cellular differentiation in adult skin

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Results

Conclusion