Identification of neuronal RNA targets of TDP-43-containing ribonucleoprotein complexes.
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.
Department of Neuroscience, University of Texas Southwestern Medical Center,Dallas, Texas 75390-9111, USA.
Chantelle F
CF
Sephton
Can
C
Cenik
Alper
A
Kucukural
Eric B
EB
Dammer
Basar
B
Cenik
Yuhong
Y
Han
Colleen M
CM
Dewey
Frederick P
FP
Roth
Joachim
J
Herz
Junmin
J
Peng
Melissa J
MJ
Moore
Gang
G
Yu
D000818:Animals; D002540:Cerebral Cortex / Q000166:cytology; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism*; D015723:Gene Library; D023281:Genomics; D006367:HeLa Cells; D006801:Humans; D051379:Mice; D008970:Molecular Weight; D009474:Neurons / Q000166:cytology / Q000502:physiology*; D040901:Proteomics; D020871:RNA Stability / Q000502:physiology*; D012333:RNA, Messenger / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism; D051381:Rats; D057177:TDP-43 Proteinopathies / Q000378:metabolism*
D004268:DNA-Binding Proteins; D012333:RNA, Messenger; D016601:RNA-Binding Proteins