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

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

Research output: Contribution to journalArticle

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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) nTA(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.

Original languageEnglish (US)
Pages (from-to)1204-1215
Number of pages12
JournalJournal of Biological Chemistry
Volume286
Issue number2
DOIs
StatePublished - Jan 14 2011

Fingerprint

Ribonucleoproteins
DNA-Binding Proteins
RNA
Polypyrimidine Tract-Binding Protein
RNA Stability
Proteins
Metabolism
Introns
Libraries
Neurons
Exons
Methyl-CpG-Binding Protein 2
RNA Transport
Heterogeneous-Nuclear Ribonucleoproteins
Neurodegenerative diseases
High-Throughput Nucleotide Sequencing
Gene Ontology
RNA Precursors
Adenine
Nuclear Proteins

ASJC Scopus subject areas

  • Biochemistry
  • Cell Biology
  • Molecular Biology

Cite this

Identification of neuronal RNA targets of TDP-43-containing ribonucleoprotein complexes. / Sephton, Chantelle F.; Cenik, Can; Kucukural, Alper; Dammer, Eric B.; Cenik, Basar; Han, YuHong; Dewey, Colleen M.; Roth, Frederick P.; Herz, Joachim; Peng, Junmin; Moore, Melissa J.; Yu, Gang.

In: Journal of Biological Chemistry, Vol. 286, No. 2, 14.01.2011, p. 1204-1215.

Research output: Contribution to journalArticle

Sephton, CF, Cenik, C, Kucukural, A, Dammer, EB, Cenik, B, Han, Y, Dewey, CM, Roth, FP, Herz, J, Peng, J, Moore, MJ & Yu, G 2011, 'Identification of neuronal RNA targets of TDP-43-containing ribonucleoprotein complexes', Journal of Biological Chemistry, vol. 286, no. 2, pp. 1204-1215. https://doi.org/10.1074/jbc.M110.190884
Sephton, Chantelle F. ; Cenik, Can ; Kucukural, Alper ; Dammer, Eric B. ; Cenik, Basar ; Han, YuHong ; Dewey, Colleen M. ; Roth, Frederick P. ; Herz, Joachim ; Peng, Junmin ; Moore, Melissa J. ; Yu, Gang. / Identification of neuronal RNA targets of TDP-43-containing ribonucleoprotein complexes. In: Journal of Biological Chemistry. 2011 ; Vol. 286, No. 2. pp. 1204-1215.
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AU - Cenik, Basar

AU - Han, YuHong

AU - Dewey, Colleen M.

AU - Roth, Frederick P.

AU - Herz, Joachim

AU - Peng, Junmin

AU - Moore, Melissa J.

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AB - 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) nTA(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.

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