Table 1.
LncRNAs in neurodevelopment and neurodevelopmental disorders.
| lncRNA | Classification | Function | References |
|---|---|---|---|
| AK055040 | Promoter-associated | Located upstream of CACN2D1; interacts with SUZ12 and is required for neural induction of ES cells | Ng et al. (2012) |
| AK091713 | Overlapping | Contains miRNAs Mir125B and LET7A and the nuclear encoded mitochondrial protein BLID within its introns; required for neural induction of ES cells by regulated expression of miRNAs that promote neurogenesis | Ng et al. (2012) |
| AK124684 | lincRNA | Interacts with the master negative regulator of neurogenesis, REST; required for neural induction of ES cells | Ng et al. (2012) |
| ANRIL/CDKN2B-AS | Antisense | CDKN2B located on the opposite strand within ANRIL intron1; binds chromatin-modifying complexes to regulate CDKN2A/B expression; mutations in promoter and transcript sequence correlate with multiple genetic disorders | Yap et al. (2010), Aguilo et al. (2011), Kotake et al. (2011), Pasmant et al. (2011a,b), Congrains et al. (2013) |
| BACE1-AS | NAT | Positive regulator of BACE1 expression; increased expression correlates with Alzheimer’s disease pathology | Faghihi et al. (2008), |
| Modarresi et al. (2011) | |||
| BDNF-AS | NAT | Negative regulation of BDNF through recruitment of chromatin-modifying complex to BDNF locus | Modarresi et al. (2012) |
| CDRas1 | circRNA | miR-7 decoy; over-expression results in the reduced size of the zebrafish midbrain, similar to miR-7 loss-of-function | Memczak et al. (2013) |
| Cyrano | lincRNA | Loss of function results in small eyes and brains due to a reduction in neural specification; may function as a miR-7 decoy transcript | Ulitsky et al. (2011) |
| Dlx1AS | Enhancer-associated and NAT | Overlaps conserved enhancer between Dlx1/2; inhibits Dlx1 expression; loss causes increased interneuron number; required for neuronal differentiation of ES cells | Dinger et al. (2008), Mercer et al. (2010), Kraus et al. (2013) |
| Evf2/Dlx6AS | Enhancer-associated | Overlaps conserved enhancer between Dlx5/6; recruits Dlx1/2 and MECP2 to Dlx5/6 enhancer to control GABAergic interneuron specification; loss causes reduced GABAergic neuron number and reduced inhibition of CA1 pyramidal neurons | Feng et al. (2006), Bond et al. (2009), Berghoff et al. (2013) |
| GDNF-OS | Promoter-associated opposite strand | Negative regulation of GDNF | Airavaara et al. (2011), Modarresi et al. (2012) |
| Gomafu/Miat/RNCR2 | lincRNA | Interacts with splicing factors to regulate alternative splicing; inhibits amacrine cell specification; associated in GWAS studies with eye movement disorders in schizophrenia; down-regulated in schizophrenic brains | Takahashi et al. (2003), Rapicavoli et al. (2010), Tsuiji et al. (2011), Barry et al. (2013) |
| Kcna2AS | NAT | Inhibits expression of Kcna2; results in decreased voltage-gated potassium currents and increased resting membrane potential leading to pain hypersensitivity | Zhao et al. (2013) |
| Linc-Brn1b | lincRNA | Loss causes reduced Brn1 expression, reduced proliferation of intermediate progenitors in the SVZ of the dorsal telencephalon and fewer upper layer cortical neurons | Sauvageau et al. (2013) |
| Linc00299 | lincRNA | Deletion/interruption results in cognitive developmental delay in humans caused by improper neural development | Talkowski et al. (2012) |
| Malat1 | lincRNA | Regulation of alternative splicing through recruitment of slicing factors to paraspeckles; regulation of synaptogenesis through gene splicing; cis- regulation of gene expression | Bernard et al. (2010), Tripathi et al. (2010), Zong et al. (2011), Zhang et al. (2012) |
| Megamind | lincRNA | Loss of function results in small eyes and brains due to a reduction in neural specification | Ulitsky et al. (2011) |
| Neat1 | lincRNA | Induction of paraspeckle formation | Clemson et al. (2009) |
| Paupar | lincRNA; Promoter-associated? | Negative regulation of Pax6 expression; regulation of Pax6 target gene (and others) expression through occupancy of promoter sequences | Vance et al. (2014) |
| RMST | lincRNA | Binds to Sox2 and the promoters of Sox2 targets to facilitate Sox2-dependent neural induction | Ng et al. (2012, 2013) |
| Six3OS | Promoter-associated opposite strand | Regulation of Six3 targets through interactions with Eya proteins and the chromatin-modifying protein Ezh2; required for neural specification of ES cells | Alfano et al. (2005), Zhao et al. (2010), Rapicavoli et al. (2011) |
| Sox2dot | Enhancer-associated | Overlaps a distal enhancer of Sox2; expressed in neurogenic regions of the brain | Amaral et al. (2009) |
| Tug1 | lincRNA | Up-regulated in response to taurine; inhibition of cone photoreceptor specification through PRC2 complex-mediated chromatin modifications affecting cell-cycle regulation | Altshuler et al. (1993), Young et al. (2005), Khalil et al. (2009) |
| TUNA | lincRNA | Regulates pluripotency by recruiting RNA biding proteins to Sox2, Nanog, and Fgf4 promoters; required for neural specification of ES cells | Lin et al. (2014) |
| utNgn1 | Enhancer-associated | Located ~6 kb upstream of Neurog1gene; required for proper Neurog1 transcription and mouse cortical progenitor differentiation | Onoguchi et al. (2012) |
| Vax2OS | Promoter-associated opposite strand | Maintenance of proliferation through alterations to cell cycle progression in neural progenitors | Meola et al. (2012) |