Identification of neuronal RNA targets of TDP-43-containing ribonucleoprotein complexes.

Abstract

TAR DNA-binding protein 43 (TDP-43) is associated with a spectrum of neurodegenerative diseases. Although TDP-43 resembles heterogeneous nuclear ribonucleoproteins, its RNA targets and physiological protein partners remain unknown. Here we identify RNA targets of TDP-43 from cortical neurons by RNA immunoprecipitation followed by deep sequencing (RIP-seq). The canonical TDP-43 binding site (TG)(n) is 55.1-fold enriched, and moreover, a variant with adenine in the middle, (TG)(n)TA(TG)(m), is highly abundant among reads in our TDP-43 RIP-seq library. TDP-43 RNA targets can be divided into three different groups: those primarily binding in introns, in exons, and across both introns and exons. TDP-43 RNA targets are particularly enriched for Gene Ontology terms related to synaptic function, RNA metabolism, and neuronal development. Furthermore, TDP-43 binds to a number of RNAs encoding for proteins implicated in neurodegeneration, including TDP-43 itself, FUS/TLS, progranulin, Tau, and ataxin 1 and -2. We also identify 25 proteins that co-purify with TDP-43 from rodent brain nuclear extracts. Prominent among them are nuclear proteins involved in pre-mRNA splicing and RNA stability and transport. Also notable are two neuron-enriched proteins, methyl CpG-binding protein 2 and polypyrimidine tract-binding protein 2 (PTBP2). A PTBP2 consensus RNA binding motif is enriched in the TDP-43 RIP-seq library, suggesting that PTBP2 may co-regulate TDP-43 RNA targets. This work thus reveals the protein and RNA components of the TDP-43-containing ribonucleoprotein complexes and provides a framework for understanding how dysregulation of TDP-43 in RNA metabolism contributes to neurodegeneration.

• Authors: Chantelle F Sephton, Can Cenik, Alper Kucukural, Eric B Dammer, Basar Cenik, Yuhong Han, Colleen M Dewey, Frederick P Roth, Joachim Herz, Junmin Peng, Melissa J Moore, Gang Yu
• Journal: The Journal of biological chemistry (J Biol Chem) Vol. 286 Issue 2 Pg. 1204-15 (Jan 14 2011) ISSN: 1083-351X [Electronic] United States
• PMID: 21051541 (Publication Type: Journal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't)

Chemical References

• DNA-Binding Proteins
• RNA, Messenger
• RNA-Binding Proteins

Topics

• Animals
• Cerebral Cortex (cytology)
• DNA-Binding Proteins (chemistry, metabolism)
• Gene Library
• Genomics
• HeLa Cells
• Humans
• Mice
• Molecular Weight
• Neurons (cytology, physiology)
• Proteomics
• RNA Stability (physiology)
• RNA, Messenger (metabolism)
• RNA-Binding Proteins (chemistry, metabolism)
• Rats
• TDP-43 Proteinopathies (metabolism)