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NOVA2-mediated RNA regulation is required for axonal pathfinding during development.

Saito Y, Miranda-Rottmann S, Ruggiu M, Park CY, Fak JJ, Zhong R, Duncan JS, Fabella BA, Junge HJ, Chen Z, Araya R, Fritzsch B, Hudspeth AJ, Darnell RB - Elife (2016)

Bottom Line: The neuron specific RNA-binding proteins NOVA1 and NOVA2 are highly homologous alternative splicing regulators.NOVA proteins regulate at least 700 alternative splicing events in vivo, yet relatively little is known about the biologic consequences of NOVA action and in particular about functional differences between NOVA1 and NOVA2.Thus we have discovered that NOVA2 uniquely regulates alternative splicing of a coordinate set of transcripts encoding key components in cortical, brainstem and spinal axon guidance/outgrowth pathways during neural differentiation, with severe functional consequences in vivo.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Molecular Neuro-Oncology, Howard Hughes Medical Institute, The Rockefeller University, New York, United States.

ABSTRACT
The neuron specific RNA-binding proteins NOVA1 and NOVA2 are highly homologous alternative splicing regulators. NOVA proteins regulate at least 700 alternative splicing events in vivo, yet relatively little is known about the biologic consequences of NOVA action and in particular about functional differences between NOVA1 and NOVA2. Transcriptome-wide searches for isoform-specific functions, using NOVA1 and NOVA2 specific HITS-CLIP and RNA-seq data from mouse cortex lacking either NOVA isoform, reveals that NOVA2 uniquely regulates alternative splicing events of a series of axon guidance related genes during cortical development. Corresponding axonal pathfinding defects were specific to NOVA2 deficiency: Nova2-/- but not Nova1-/- mice had agenesis of the corpus callosum, and axonal outgrowth defects specific to ventral motoneuron axons and efferent innervation of the cochlea. Thus we have discovered that NOVA2 uniquely regulates alternative splicing of a coordinate set of transcripts encoding key components in cortical, brainstem and spinal axon guidance/outgrowth pathways during neural differentiation, with severe functional consequences in vivo.

No MeSH data available.


Related in: MedlinePlus

RNA-seq analysis in the midbrain and hindbrain of Nova1-/- versus littermate wild-type control.(A) Summary of NOVA2-dependent (cortex) and NOVA1-dependent (midbrain and hindbrain) alternative splicing changes that showed /ΔI/>=0.1 (FDR<0.1). (B) Correlation of Nova2-deficient (cortex) and Nova1-deficient (midbrain and hindbrain) impact on alternative splicing events. X-axis and Y-axis indicated ΔI of wild-type vs Nova2-/- (cortex) and vs Nova1-/- (midbrain and hindbrain), respectively. (C) Examples of alternative splicing changes of the NOVA2-regulated axon guidance genes in the cortex of Nova2-/- and Nova1-/- and in the midbrain and hindbrain of Nova1-/- mice. Low expression genes in midbrain and hindbrain samples were filtered out. Y-axis indicated ΔI. Blue; Nova2-/- (cortex), red; Nova1-/- (cortex), orange; Nova1-/- (midbrain and hindbrain). *p<0.05.DOI:http://dx.doi.org/10.7554/eLife.14371.016
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fig3s4: RNA-seq analysis in the midbrain and hindbrain of Nova1-/- versus littermate wild-type control.(A) Summary of NOVA2-dependent (cortex) and NOVA1-dependent (midbrain and hindbrain) alternative splicing changes that showed /ΔI/>=0.1 (FDR<0.1). (B) Correlation of Nova2-deficient (cortex) and Nova1-deficient (midbrain and hindbrain) impact on alternative splicing events. X-axis and Y-axis indicated ΔI of wild-type vs Nova2-/- (cortex) and vs Nova1-/- (midbrain and hindbrain), respectively. (C) Examples of alternative splicing changes of the NOVA2-regulated axon guidance genes in the cortex of Nova2-/- and Nova1-/- and in the midbrain and hindbrain of Nova1-/- mice. Low expression genes in midbrain and hindbrain samples were filtered out. Y-axis indicated ΔI. Blue; Nova2-/- (cortex), red; Nova1-/- (cortex), orange; Nova1-/- (midbrain and hindbrain). *p<0.05.DOI:http://dx.doi.org/10.7554/eLife.14371.016

Mentions: RNA-seq analysis in the E18.5 midbrain and hindbrain of wild-type and Nova1-/- mice, where NOVA1 is more abundantly expressed, identified that 119 of 1991 NOVA2-dependent alternative splicing events were changed in Nova1-/- mice (/ΔI/>=0.1, FDR<0.1) (Figure 3—figure supplement 4A). There was no correlation between ΔI of wild-type versus Nova1-/- (mid- and hindbrain) and wild-type versus Nova2-/- (cortex) (R=0.20) (Figure 3—figure supplement 4B) as well as identified between ΔI of wild-type versus Nova1-/- (cortex) and wild-type versus Nova2-/- (cortex). In the midbrain and hindbrain of Nova1-/- mice, only one alternative splicing event (Robo2 exon 6b) was significantly changed in the NOVA2-regulated genes list of KEGG axon guidance pathway but it was smaller change when compared with ΔI of wild-type versus Nova2-/- (cortex) (Figure 3—figure supplement 4C). Taken together, these data suggest that NOVA2 regulates a distinct set of transcripts related, in particular, to axon guidance, in the E18.5 mouse cortex.


NOVA2-mediated RNA regulation is required for axonal pathfinding during development.

Saito Y, Miranda-Rottmann S, Ruggiu M, Park CY, Fak JJ, Zhong R, Duncan JS, Fabella BA, Junge HJ, Chen Z, Araya R, Fritzsch B, Hudspeth AJ, Darnell RB - Elife (2016)

RNA-seq analysis in the midbrain and hindbrain of Nova1-/- versus littermate wild-type control.(A) Summary of NOVA2-dependent (cortex) and NOVA1-dependent (midbrain and hindbrain) alternative splicing changes that showed /ΔI/>=0.1 (FDR<0.1). (B) Correlation of Nova2-deficient (cortex) and Nova1-deficient (midbrain and hindbrain) impact on alternative splicing events. X-axis and Y-axis indicated ΔI of wild-type vs Nova2-/- (cortex) and vs Nova1-/- (midbrain and hindbrain), respectively. (C) Examples of alternative splicing changes of the NOVA2-regulated axon guidance genes in the cortex of Nova2-/- and Nova1-/- and in the midbrain and hindbrain of Nova1-/- mice. Low expression genes in midbrain and hindbrain samples were filtered out. Y-axis indicated ΔI. Blue; Nova2-/- (cortex), red; Nova1-/- (cortex), orange; Nova1-/- (midbrain and hindbrain). *p<0.05.DOI:http://dx.doi.org/10.7554/eLife.14371.016
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fig3s4: RNA-seq analysis in the midbrain and hindbrain of Nova1-/- versus littermate wild-type control.(A) Summary of NOVA2-dependent (cortex) and NOVA1-dependent (midbrain and hindbrain) alternative splicing changes that showed /ΔI/>=0.1 (FDR<0.1). (B) Correlation of Nova2-deficient (cortex) and Nova1-deficient (midbrain and hindbrain) impact on alternative splicing events. X-axis and Y-axis indicated ΔI of wild-type vs Nova2-/- (cortex) and vs Nova1-/- (midbrain and hindbrain), respectively. (C) Examples of alternative splicing changes of the NOVA2-regulated axon guidance genes in the cortex of Nova2-/- and Nova1-/- and in the midbrain and hindbrain of Nova1-/- mice. Low expression genes in midbrain and hindbrain samples were filtered out. Y-axis indicated ΔI. Blue; Nova2-/- (cortex), red; Nova1-/- (cortex), orange; Nova1-/- (midbrain and hindbrain). *p<0.05.DOI:http://dx.doi.org/10.7554/eLife.14371.016
Mentions: RNA-seq analysis in the E18.5 midbrain and hindbrain of wild-type and Nova1-/- mice, where NOVA1 is more abundantly expressed, identified that 119 of 1991 NOVA2-dependent alternative splicing events were changed in Nova1-/- mice (/ΔI/>=0.1, FDR<0.1) (Figure 3—figure supplement 4A). There was no correlation between ΔI of wild-type versus Nova1-/- (mid- and hindbrain) and wild-type versus Nova2-/- (cortex) (R=0.20) (Figure 3—figure supplement 4B) as well as identified between ΔI of wild-type versus Nova1-/- (cortex) and wild-type versus Nova2-/- (cortex). In the midbrain and hindbrain of Nova1-/- mice, only one alternative splicing event (Robo2 exon 6b) was significantly changed in the NOVA2-regulated genes list of KEGG axon guidance pathway but it was smaller change when compared with ΔI of wild-type versus Nova2-/- (cortex) (Figure 3—figure supplement 4C). Taken together, these data suggest that NOVA2 regulates a distinct set of transcripts related, in particular, to axon guidance, in the E18.5 mouse cortex.

Bottom Line: The neuron specific RNA-binding proteins NOVA1 and NOVA2 are highly homologous alternative splicing regulators.NOVA proteins regulate at least 700 alternative splicing events in vivo, yet relatively little is known about the biologic consequences of NOVA action and in particular about functional differences between NOVA1 and NOVA2.Thus we have discovered that NOVA2 uniquely regulates alternative splicing of a coordinate set of transcripts encoding key components in cortical, brainstem and spinal axon guidance/outgrowth pathways during neural differentiation, with severe functional consequences in vivo.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Molecular Neuro-Oncology, Howard Hughes Medical Institute, The Rockefeller University, New York, United States.

ABSTRACT
The neuron specific RNA-binding proteins NOVA1 and NOVA2 are highly homologous alternative splicing regulators. NOVA proteins regulate at least 700 alternative splicing events in vivo, yet relatively little is known about the biologic consequences of NOVA action and in particular about functional differences between NOVA1 and NOVA2. Transcriptome-wide searches for isoform-specific functions, using NOVA1 and NOVA2 specific HITS-CLIP and RNA-seq data from mouse cortex lacking either NOVA isoform, reveals that NOVA2 uniquely regulates alternative splicing events of a series of axon guidance related genes during cortical development. Corresponding axonal pathfinding defects were specific to NOVA2 deficiency: Nova2-/- but not Nova1-/- mice had agenesis of the corpus callosum, and axonal outgrowth defects specific to ventral motoneuron axons and efferent innervation of the cochlea. Thus we have discovered that NOVA2 uniquely regulates alternative splicing of a coordinate set of transcripts encoding key components in cortical, brainstem and spinal axon guidance/outgrowth pathways during neural differentiation, with severe functional consequences in vivo.

No MeSH data available.


Related in: MedlinePlus