A Multidisciplinary Approach to RNA Localisation - Biophysical Approaches to Translational Control of Gene Expression - page 215

and pseudoknots to be formed. As RNA structure is important to protein-RNA
recognition, bases important for maintaining RNA secondary structure are under
evolutionary pressure and are usually well conserved between homologous
sequences. Compensatory mutations in the RNA sequence allow the maintenance of
specific base pairings and of the secondary structure of the RNA. The RNA tertiary
structures are organised from the secondary structure elements, with inter-helical
contacts, contact between loops, docking of adenine-platforms and other interac-
tions (Lunde et al. 2007 ; Hamilton and Davis 2007, 2011 ) . RNA binding proteins
recognise tertiary and secondary structural elements, but the most common recogni-
tion site for RNA binding proteins is in the single stranded RNA regions joining
structured areas.
A well-characterised cis -acting spatial code, defined by non-canonical base pair-
ings that forms a kink-turn (KT) motif, has been identified in several mRNAs local-
ising in the nervous system (Tiedge 2006 ) (Fig. 11.3d ). The kink-turn motif is
characterised by a pair of non-canonical G:A base pairings adjacent to an internal
loop of 3 nt and flanked by canonical, often G:C rich helical stems. In low Ca 2+ or
Mg 2+ concentrations the kink-turn motif is in an extended conformation with a mini-
mal kink. The kink is induced by high concentrations of Ca 2+ , found during innerva-
tions decreasing in concentration away from the synapse towards the soma, and
Mg 2+ found during depolymerisation events. The KT motif, known as a dendritic
targeting element (DTE), specifically binds to heteronuclear ribonucleoprotein A2
(hnRNP A2), also required for correct localisation (Tiedge 2006 ) . Myelin basic
protein (MBP) mRNA contains a KT motif in the 3¢ UTR in a 21 nt region previ-
ously identified as an hnRNP A2 response element (A2RE). BC1, a member of the
non-coding small brain-specific cytoplasmic class of RNAs, contains a KT motif in
its 5¢ UTR and its transport has been shown to be microtubule dependent (Cristofanilli
et al. 2006 ). Activity-regulated cytoskeleton-associated (Arc) mRNA contains two
KT motifs in its 3¢ UTR responsible for targeting (Kobayashi et al. 2005 ) . Protein
kinase M d (PKM d) mRNA contains a KT motif in a 44 nt stem-loop in the 3¢ UTR.
CamKII also has a predicted KT motif in a region of the 3¢ UTR previously shown
to be responsible for targeting (Blichenberg et al. 2001 ). A reverse KT motif has
recently been described where the kink opens up the major groove rather than the
minor groove found and differs by just one nucleotide from the classical KT motif
(Antonioli et al. 2010 ). There is also a database of sequences containing KT motifs
from experimental and theoretical structures (Schroeder et al. 2010 ) .
There are several neurodegenerative diseases linked to defective RNA localisa-
tion including Fragile X-associated tremor/ataxia syndrome (FXTAS), character-
ised by the expansion of CGG repeats in the fragile X mental retardation 1 (FMR1)
mRNA (Jacquemont et al. 2007 ). The CGG repeats form stable stem-loop structures
containing non-canonical G:G base pairings and have been shown to interact with
hnRNP A2 (Muslimov et al. 2011 ). The CGG repeats were shown to compete with
hnRNP A2 binding to the KT motifs of BC1 and PKMd, and in the case of the
expanded CGG repeats (>55) this leads to reduced targeting of mRNAs containing
kink-turn motifs.