A conserved abundant cytoplasmic long noncoding RNA modulates repression by Pumilio proteins in human cells

Abstract

Thousands of long noncoding RNA (lncRNA) genes are encoded in the human genome, and hundreds of them are evolutionarily conserved, but their functions and modes of action remain largely obscure. Particularly enigmatic lncRNAs are those that are exported to the cytoplasm, including NORAD—an abundant and highly conserved cytoplasmic lncRNA. Here we show that most of the sequence of NORAD is comprised of repetitive units that together contain at least 17 functional binding sites for the two mammalian Pumilio homologues. Through binding to PUM1 and PUM2, NORAD modulates the mRNA levels of their targets, which are enriched for genes involved in chromosome segregation during cell division. Our results suggest that some cytoplasmic lncRNAs function by modulating the activities of RNA-binding proteins, an activity which positions them at key junctions of cellular signalling pathways.

PUMILIO/FOXP1 signaling drives expansion of hematopoietic stem/progenitor and leukemia cells

“…Their multiple biological activities depend on association with differentially expressed partners, 29 on posttranslational modifications that can be modulated by growth factors, 30 on PUM stability itself, 13 and also on the presence of RNA sponge that binds and sequesters PUM proteins. 27,28 Our data indicate that PUM1 and PUM2 gene expression levels are also regulated along cell differentiation, being maximal in undifferentiated progenitors.…”

“…18 Unexpectedly, overexpression of PUM1/2 was similarly deleterious for HSPC and leukemic cell survival (data not shown), probably reflecting PUM major contribution to chromosome instability, as recently reported. 27,28 These observations indicate that PUM levels are subjected to fine-tuning to control myeloid cell growth.…”

The functions of long noncoding RNAs in development and stem cells

“…The same stoichiometric concerns exist for the cytoplasmic functions of lncRNAs and, in general, the roles of cytoplasmic lncRNAs have been less explored. Some cytoplasmic lncRNAs, including the circular lncRNA CDR1as (Memczak et al, 2013) and NORAD (Lee et al, 2016;Tichon et al, 2016), are abundant enough to bind to and affect the function of RNA-binding proteins (Argonaute and Pumilio, respectively) and thereby modulate their ability to regulate their other targets. Other cytoplasmic lncRNAs have been shown to bind and modulate the stability and translation of other RNAs by base-pairing with them (Carrieri et al, 2012;Gong and Maquat, 2011).…”

Origin and evolution of the metazoan non-coding regulatory genome: Insights from the sponge Amphimedon queenslandica

“…Other lncRNA features that appear to be conserved include syntenic relationships to neighboring genes (Amaral et al, 2016;Hezroni et al, 2015;, secondary structure (Hawkes et al, 2016;Lee et al, 2016;Novikova et al, 2012;Sanbonmatsu, 2016;Tichon et al, 2016), and specific expression patterns (Chodroff et al, 2010;Hezroni et al, 2015;Washietl et al, 2014). The conservation of genomic position of hundreds of deuterostome (i.e., sea urchins and vertebrates) lncRNAs with no detectable sequence similarity (Hezroni et al, 2015) suggests that lncRNA sequences evolve rapidly yet are likely to be functionally conserved.…”

“…The inducible lncRNA DINO binds to and stabilizes the well-known tumor suppressor protein p53 amplifying DNA damage response (Schmitt et al, 2016). The lncRNA NORAD maintains genomic stability by sequestering PUMILIO proteins, which repress the stability and translation of mRNAs to which they bind (Lee et al, 2016;Tichon et al, 2016).…”