Psip1/p52 regulates posterior Hoxa genes through activation of lncRNA Hottip.

Andrew J Wood,Shipra Bhatia,Madapura M Pradeepa,Hemant Bengani,Wendy A Bickmore,Gillian C A Taylor,Fionnuala Mckenna,Graeme R Grimes

doi:10.1371/journal.pgen.1006677

Abstract

Long noncoding RNAs (lncRNAs) have been implicated in various biological functions including the regulation of gene expression, however, the functionality of lncRNAs is not clearly understood and conflicting conclusions have often been reached when comparing different methods to investigate them. Moreover, little is known about the upstream regulation of lncRNAs. Here we show that the short isoform (p52) of a transcriptional co-activator—PC4 and SF2 interacting protein (Psip1), which is known to be involved in linking transcription to RNA processing, specifically regulates the expression of the lncRNA Hottip–located at the 5’ end of the Hoxa locus. Using both knockdown and knockout approaches we show that Hottip expression is required for activation of the 5’ Hoxa genes (Hoxa13 and Hoxa10/11) and for retaining Mll1 at the 5’ end of Hoxa. Moreover, we demonstrate that artificially inducing Hottip expression is sufficient to activate the 5’ Hoxa genes and that Hottip RNA binds to the 5’ end of Hoxa. By engineering premature transcription termination, we show that it is the Hottip lncRNA molecule itself, not just Hottip transcription that is required to maintains active expression of posterior Hox genes. Our data show a direct role for a lncRNA molecule in regulating the expression of developmentally-regulated mRNA genes in cis.

Highlights

The mammalian genome encodes ~10,000 long noncoding RNAs[1]
We show that a transcriptional co activator—Psip1 regulates the expression of the Long noncoding RNAs (lncRNAs) Hottip
We recently demonstrated that the transcriptional co-activator Psip1/p75 and Mll co-occupy expressed Hox genes, and that loss of Psip1 leads to reduced Mll1 occupancy at active Hox genes[35]

Summary

Introduction

Very few of these molecules have been functionally characterised, a small number have been shown to function by binding to various protein complexes to regulate gene expression[2,3,4,5,6]. Some lncRNAs have been reported to affect gene expression in trans[7,8], whereas others, such as Kcnq1ot, Xact, Xist and Tsix, function in cis (reviewed in[9]). Other lncRNAs likely function in the cytoplasm through binding to other regulatory RNAs, e.g. miRNAs[10]. It has been difficult to distinguish whether lncRNA function is conferred by the process of transcription or by the RNA molecule itself. Concerns have been raised with respect to limitations and discrepancies in various methodologies used to study lncRNA function[11,12,13]. Contrasting conclusions have often been reached when comparing knockdown and knockout studies of lncRNA loci—e.g. HOTAIR, MALAT1 and Halr [14,15,16,17]

Methods

Results

Discussion

Conclusion