The mRNA-like noncoding RNA Gomafu constitutes a novel nuclear domain in a subset of neurons

Abstract

Recent transcriptome analyses have revealed that a large body of noncoding regions of mammalian genomes are actually transcribed into RNAs. Our understanding of the molecular features of these noncoding RNAs is far from complete. We have identified a novel mRNA-like noncoding gene, named Gomafu, which is expressed in a distinct set of neurons in the mouse nervous system. Interestingly, spliced mature Gomafu RNA is localized to the nucleus despite its mRNA-like characteristics, which usually act as potent export signals to the cytoplasm. Within the nucleus, Gomafu RNA is detected as numerous spots that do not colocalize with known nuclear domain markers. Gomafu RNA is extremely insoluble and remains intact after nuclear matrix preparation. Furthermore, heterokaryon assays revealed that Gomafu RNA does not shuttle between the nucleus and cytoplasm, but is retained in the nucleus after its transcription. We propose that Gomafu RNA represents a novel family of mRNA-like noncoding RNA that constitutes a cell-type-specific component of the nuclear matrix.

Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals

“…The transcribed DIG-labeled RNA probes were partially digested in alkaline buffer (60 mM Na 2 CO 3 , 40 mM NaHCO 3 at pH 10.2) (Cox et al 1984). FISH was performed to visualize endogenous RNAs according to a previously described protocol (Sone et al 2007). The hybridized probes were detected with standard immunocytochemical procedures, using the following antibodies: anti-DIG sheep monoclonal antibody (Roche) and Alexa Fluor 488-conjugated anti-sheep IgG polyclonal goat antibody (Invitrogen).…”

New meaning in the message: Noncoding RNAs and their role in retinal development

“…Variously termed RNCR2 (Blackshaw et al, 2004), MIAT (Ishii et al, 2006), and Gomafu (Sone et al, 2007), this RNA that is evolutionarily conserved from amphibians to mammals (Rapicavoli and Blackshaw, unpublished data) is 9 kb long, spliced, and like Xist is a nuclear-retained transcript. It is not, however, associated with chromatin but instead binds to specific, though uncharacterized, subdomains of the nuclear matrix (Sone et al, 2007). It is expressed selectively in the developing central and peripheral nervous system (Ishii et al, 2006;Sone et al, 2007), and is also expressed in focal regions of the adult brain .…”

“…It is not, however, associated with chromatin but instead binds to specific, though uncharacterized, subdomains of the nuclear matrix (Sone et al, 2007). It is expressed selectively in the developing central and peripheral nervous system (Ishii et al, 2006;Sone et al, 2007), and is also expressed in focal regions of the adult brain . The transcript is highly abundant in the developing retina, comprising a maximum of 0.2% of polyadenylated RNA at embryonic day 18 in mouse (Blackshaw et al, 2004).…”

Non-Coding RNAs: A Dynamic and Complex Network of Gene Regulation

“…Long ncRNAs are involved in cellular signaling networks associated with human stem cell differentiation [112] Long ncRNAs exihibit cell-type specific repression localized to specific subcellular compartments [113]. Genes once silenced by inclusion into the silent domains of the long ncRNAs are capable of reactivation in a tissue or developmental stage-specific manner by enhancers which are also tissue and development stage-specific [114].…”

“…One polyadenylated long ncRNA occurs exclusively in these speckles [113]. A number of RNA-binding proteins, including paraspeckle-protien-complex-1, together with the RNA-NEAT-1, form parapeckles [143].…”