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

Sephton CF, Cenik C, Kucukural A, Dammer EB, Cenik B, Han Y, Dewey CM, Roth FP, Herz J, Peng J, Moore MJ, Yu G - J. Biol. Chem. (2010)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Neuroscience, University of Texas Southwestern Medical Center,Dallas, Texas 75390-9111, USA.

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.

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Functional categorization of top TDP-43 RNA targets. A–C, summary of the top 30 most enriched Gene Ontology terms in TDP-43 RNA targets in exonic (A, panel i); intronic (B, panel i); and dual sets (C, panel i). For the complete functional listing, see supplemental Tables S3–S5. A–C, panel ii, snapshots of genes representing each category of binding. A, panel ii, exonic-TDP-43; B, panel ii, intronic-Slit3; and C, panel ii, dual Notch1. The number of uniquely mapped reads to the gene were shown for both the TDP-43 library and the control (CTL) library. The asterisk indicates TG-rich regions. Note the adenine (bolded) in the (TG)n motifs shown for Slit3 and Notch1.
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Figure 4: Functional categorization of top TDP-43 RNA targets. A–C, summary of the top 30 most enriched Gene Ontology terms in TDP-43 RNA targets in exonic (A, panel i); intronic (B, panel i); and dual sets (C, panel i). For the complete functional listing, see supplemental Tables S3–S5. A–C, panel ii, snapshots of genes representing each category of binding. A, panel ii, exonic-TDP-43; B, panel ii, intronic-Slit3; and C, panel ii, dual Notch1. The number of uniquely mapped reads to the gene were shown for both the TDP-43 library and the control (CTL) library. The asterisk indicates TG-rich regions. Note the adenine (bolded) in the (TG)n motifs shown for Slit3 and Notch1.

Mentions: We then asked whether these three categories of TDP-43 RNA targets differed with respect to their functions. We used the Gene Ontology database and searched for statistically significant enrichment of functional categories within these three sets. TDP-43-targeted RNAs were enriched in diverse functional categories (supplemental Tables S3–S6). Remarkably, all three sets revealed distinct functional enrichment profiles (Fig. 4, A–C). In particular, genes with TDP-43 exonic reads were enriched for Gene Ontology terms related to splicing and RNA processing and maturation (Fig. 4A, panel i, and supplemental Table S3), whereas genes with intronic TDP-43 reads were enriched for terms associated with synaptic formation and function and in regulation of neurotransmitter processes (Fig. 4B, panel i, and supplemental Table S4); genes with dual TDP-43 reads were enriched for terms related to various aspects of development (Fig. 4C, panel i, and supplemental Table S5). These results provide an important perspective about how TDP-43 regulates different biological and pathobiological processes.


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

Sephton CF, Cenik C, Kucukural A, Dammer EB, Cenik B, Han Y, Dewey CM, Roth FP, Herz J, Peng J, Moore MJ, Yu G - J. Biol. Chem. (2010)

Functional categorization of top TDP-43 RNA targets. A–C, summary of the top 30 most enriched Gene Ontology terms in TDP-43 RNA targets in exonic (A, panel i); intronic (B, panel i); and dual sets (C, panel i). For the complete functional listing, see supplemental Tables S3–S5. A–C, panel ii, snapshots of genes representing each category of binding. A, panel ii, exonic-TDP-43; B, panel ii, intronic-Slit3; and C, panel ii, dual Notch1. The number of uniquely mapped reads to the gene were shown for both the TDP-43 library and the control (CTL) library. The asterisk indicates TG-rich regions. Note the adenine (bolded) in the (TG)n motifs shown for Slit3 and Notch1.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3020728&req=5

Figure 4: Functional categorization of top TDP-43 RNA targets. A–C, summary of the top 30 most enriched Gene Ontology terms in TDP-43 RNA targets in exonic (A, panel i); intronic (B, panel i); and dual sets (C, panel i). For the complete functional listing, see supplemental Tables S3–S5. A–C, panel ii, snapshots of genes representing each category of binding. A, panel ii, exonic-TDP-43; B, panel ii, intronic-Slit3; and C, panel ii, dual Notch1. The number of uniquely mapped reads to the gene were shown for both the TDP-43 library and the control (CTL) library. The asterisk indicates TG-rich regions. Note the adenine (bolded) in the (TG)n motifs shown for Slit3 and Notch1.
Mentions: We then asked whether these three categories of TDP-43 RNA targets differed with respect to their functions. We used the Gene Ontology database and searched for statistically significant enrichment of functional categories within these three sets. TDP-43-targeted RNAs were enriched in diverse functional categories (supplemental Tables S3–S6). Remarkably, all three sets revealed distinct functional enrichment profiles (Fig. 4, A–C). In particular, genes with TDP-43 exonic reads were enriched for Gene Ontology terms related to splicing and RNA processing and maturation (Fig. 4A, panel i, and supplemental Table S3), whereas genes with intronic TDP-43 reads were enriched for terms associated with synaptic formation and function and in regulation of neurotransmitter processes (Fig. 4B, panel i, and supplemental Table S4); genes with dual TDP-43 reads were enriched for terms related to various aspects of development (Fig. 4C, panel i, and supplemental Table S5). These results provide an important perspective about how TDP-43 regulates different biological and pathobiological processes.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Neuroscience, University of Texas Southwestern Medical Center,Dallas, Texas 75390-9111, USA.

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.

Show MeSH
Related in: MedlinePlus