Paupar RNA Regulates Olfactory Bulb Neurogenesis

A non-coding RNA, called Paupar (PAX6 Upstream Antisense RNA), which influences how healthy brains develop during early life, has been identified by scientists from the Universities of Edinburgh, Bath, and Oxford. They have shown that Paupar orchestrates proteins that control neurodevelopment.

Since the human genome was first sequenced in 2001, scientists have puzzled over swathes of our DNA that despite apparently lacking function are made into ribonucleic acid (RNA) by the cell.

Why make RNA at all when it is not then used to make proteins, which perform fundamental biological tasks? Perhaps these so-called non-coding RNAs perform critical, but as yet unknown, tasks?

Binding To KAP1

The researchers investigated KAP1, a gene that codes for an essential protein associated with several fundamental processes in neurodevelopment. The KAP1 protein acts as a regulator for several other genes which allow the brain to grow healthily and develop several types of brain cell.

RNP complex with long non‐coding RNA

The formation of an RNP complex containing a long non‐coding RNA (lncRNA), a chromatin regulator and transcription factor illustrates how a single nuclear lncRNA can regulate transcription of multiple target genes in trans.
Credit: Ioanna Pavlaki, et al. CC-BY

Using molecular biology techniques they discovered that Paupar can act as a switch, modulating how KAP1 acts by binding to it – thus influencing the development of healthy brains in mice. It is the first time that a non-coding RNA has been shown to bind to KAP1.

Dr Keith Vance, from the University of Bath Department of Biology & Biochemistry led the research.

“It is now clear that the genome expresses many non-coding RNAs that are not made into protein. Despite this, there is a lot of controversy regarding their function. Some groups argue that these non-coding RNAs are a result of transcriptional noise with no apparent use whilst others think that the vast majority of them must be doing something important. We have shown here good evidence that one of these genes, called Paupar, is important for development of the brain,”

said Vance.

Long Non-coding RNA

Long non-coding RNAs (long ncRNAs, lncRNA) are defined as transcripts longer than 200 nucleotides that are not translated into protein. This somewhat arbitrary limit distinguishes long ncRNAs from small non-coding RNAs such as microRNAs (miRNAs), short interfering RNAs (siRNAs), Piwi-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), and other short RNAs.

LncRNAs are sometimes referred to as long intergenic noncoding RNAs (lincRNAs), which specifies that they are found in between coding genes rather than antisense to them or within introns.

KAP1 chromatin regulatory protein

Overview of the pulldown assay.
In vitro‐transcribed biotinylated Paupar RNA was immobilised on streptavidin beads and incubated with N2A cell nuclear extract.
Bound RNA protein complexes were extensively washed and specific Paupar‐associated proteins, which do not interact with a control mRNA of a similar size, identified by mass spectrometry.
Credit: Ioanna Pavlaki, et al. CC-BY

It is known that Paupar, an lncRNA expressed during central nervous system (CNS) development, controls neuroblastoma cell growth by binding and modulating the activity of transcriptional regulatory elements in a genome‐wide manner. It’s mechanisms of action, however, remain poorly understood.

“It’s a young field, but I think it’s clear we have to reassess the central dogma of molecular biology that DNA is transcribed to RNA that codes for a protein. We’re now seeing that some RNAs can go off and do something themselves. Our findings also help us understand the essential role of KAP1, which is something we’re really interested in as we look at the development of the central nervous system,”

Vance said.

The findings in this study provide insights into the trans‐acting modes of lncRNA‐mediated epigenetic regulation and the mechanisms of KAP1 genomic recruitment, and identify Paupar and Kap1 as regulators of neurogenesis in vivo.

Funding for the work came from the Biotechnology and Biological Sciences Research Council, Medical Research Council, European Research Council and Wellcome Trust.

Ioanna Pavlaki, Farah Alammari, Bin Sun, Neil Clark, Tamara Sirey, Sheena Lee, Dan J Woodcock, Chris P Ponting, Francis G Szele, Keith W Vance
The long non‐coding RNA Paupar promotes KAP1‐dependent chromatin changes and regulates olfactory bulb neurogenesis
The EMBO Journal (2018) e98219 DOI 10.15252/embj.201798219

Top Image: cross section of the mouse olfactory bulb. Green is electroporated neuroblasts born in the sub ventricular zone that migrated into the olfactory bulb. Blue is a DAPI nuclear counterstain. Credit: Francis Szele