Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43.

Nature neuroscience 2011

We used cross-linking and immunoprecipitation coupled with high-throughput sequencing to identify binding sites in 6,304 genes as the brain RNA targets for TDP-43, an RNA binding protein that, when mutated, causes amyotrophic lateral sclerosis. Massively parallel sequencing and splicing-sensitive junction arrays revealed that levels of 601 mRNAs were changed (including Fus (Tls), progranulin and other transcripts encoding neurodegenerative disease-associated proteins) and 965 altered splicing events were detected (including in sortilin, the receptor for progranulin) following depletion of TDP-43 from mouse adult brain with antisense oligonucleotides. RNAs whose levels were most depleted by reduction in TDP-43 were derived from genes with very long introns and that encode proteins involved in synaptic activity. Lastly, we found that TDP-43 autoregulates its synthesis, in part by directly binding and enhancing splicing of an intron in the 3' untranslated region of its own transcript, thereby triggering nonsense-mediated RNA degradation.

12 Figures Extracted

TDP-43 binds distal introns of pre-mRNA transcripts through UG-rich sites in vivo

(a) Autoradiograph of TDP-43-RNA complexes trimmed by different concentrations of micrococcal nuclease (MNase) (left panel). Complexes within red box ...

(a) Strategy for depletion of TDP-43 in mouse striatum. TDP-43-specific or control ASOs were injected into the striatum of adult mice. TDP-43 mRNA was...

In vivo depletion of TDP-43 in mouse brain with antisense oligonucleotides (ASOs)

(a) Correlation between RNA-seq and CLIP-seq data. Genes were ranked upon their degree of regulation after TDP-43 depletion (x-axis) and the mean numb...

Binding of TDP-43 on long transcripts enriched in brain sustains their normal mRNA levels

(a) Schematic representation of different exon classes defined by EST and mRNA libraries, RNA-seq or splicing-sensitive microarray data as indicated (...

TDP-43-mediates alternative splicing regulation of its RNA targets

Autoregulation of TDP-43 through binding on the 3′UTR of its own transcript

(a) CLIP-seq reads and clusters on TDP-43 transcript showing binding mainly within an alternatively spliced part of the 3′ untranslated region (3′UTR)...

TDP-43 regulates expression of FUS/TLS and Progranulin

(a) CLIP-seq reads and clusters on Fus/Tls transcript showing TDP-43 binding within introns 6 and 7 (also annotated as an alternative 3′UTR) and the c...