Nuclear factor TDP‐43 can affect selected microRNA levels

Buratti, Emanuele; Conti, Laura De; Stuani, Cristiana; Romano, Maurizio; Baralle, Marco; Baralle, Francisco E.

doi:10.1111/j.1742-4658.2010.07643.x

Cited by 208 publications

(185 citation statements)

References 64 publications

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“…Unfortunately, we could not detect the reduced expression of let7b, which has recently been reported as the only microRNA that was down-regulated after TDP-43 knockdown in human Hep-3B cells (23). Although this can be attributed to the difference in the expression levels of each miRNA among the cell lines examined, it also remains to be elucidated how TDP-43 affects the biogenesis of let-7b.…”

Section: Discussioncontrasting

confidence: 47%

“…In contrast, EMSA demonstrated that recTDP-43 bound to pre-miR-574 (Fig. 2D), which is in contrast to a previous report, which demonstrated that premiR-574 did not bind to GST-TDP-43 in vitro (23). To investigate the site within pre-miR-574 that is recognized by TDP-43, first we mutated two nucleotides within the terminal loop to extend the dsRNA region (Fig.…”

Section: Identification Of Mirnas Whose Expression Is Altered By Tdp-43contrasting

confidence: 51%

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TDP-43 promotes microRNA biogenesis as a component of the Drosha and Dicer complexes

Kawahara

Mieda-Sato

2012

Proc. Natl. Acad. Sci. U.S.A.

373

376

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Although aberrant microRNA (miRNA) expression is linked to human diseases including cancer, the mechanisms that regulate the expression of each individual miRNA remain largely unknown. TAR DNA-binding protein-43 (TDP-43) is homologous to the heterogeneous nuclear ribonucleoproteins (hnRNPs), which are involved in RNA processing, and its abnormal cellular distribution is a key feature of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD), two neurodegenerative diseases. Here, we show that TDP-43 facilitates the production of a subset of precursor miRNAs (pre-miRNAs) by both interacting with the nuclear Drosha complex and binding directly to the relevant primary miRNAs (primiRNAs). Furthermore, cytoplasmic TDP-43, which interacts with the Dicer complex, promotes the processing of some of these premiRNAs via binding to their terminal loops. Finally, we show that involvement of TDP-43 in miRNA biogenesis is indispensable for neuronal outgrowth. These results support a previously uncharacterized role for TDP-43 in posttranscriptional regulation of miRNA expression in both the nucleus and the cytoplasm.M icroRNAs (miRNAs), small noncoding RNAs of ∼20-22 nt, have emerged as novel regulatory factors of gene expression (1). The expression of each individual miRNA is tightly regulated in a development-and cell-specific manner through transcriptional or posttranscriptional control. As a result, miRNAs can act as regulatory switches for development, organogenesis, and cellular differentiation and control distinct functions that are required for the maintenance of different cell subtypes. Moreover, the altered expression of certain miRNAs is involved in the pathogenesis of developmental abnormalities and human diseases such as cancer and Parkinson's disease (2, 3). As a consequence, understanding the mechanisms that regulate the expression of each individual miRNA is essential to elucidate the molecular pathogenesis of human diseases.MiRNAs are generated from long primary transcripts, termed pri-miRNAs, which consist of a short dsRNA region and a loop. The nuclear Drosha complex cleaves pri-miRNAs to release intermediate precursors that are termed pre-miRNAs. Pre-miRNAs are then transported by Exportin-5 into the cytoplasm where they are cleaved further by the Dicer complex to generate mature miRNAs. Finally, mature miRNAs are incorporated into the RNA-induced silencing complex (RISC), after which they can hybridize to the 3′-untranslated region (UTR) of their target mRNAs to repress translation or degrade these mRNAs (4). DGCR8 is a partner protein that is indispensable for the processing of pri-miRNAs by Drosha (5). In addition, recent work has identified multiple proteins that modulate the processing of specific miRNAs by interacting with the Drosha complex or by binding directly to pri-miRNAs or both (6, 7). Compared with the number of regulatory proteins that are involved in Drosha cleavage, only a few proteins have been identified that regulate the processing of pre-miRNAs by Dicer (6, 7)....

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Section: Discussioncontrasting

confidence: 47%

Section: Identification Of Mirnas Whose Expression Is Altered By Tdp-43contrasting

confidence: 51%

TDP-43 promotes microRNA biogenesis as a component of the Drosha and Dicer complexes

Kawahara

Mieda-Sato

2012

Proc. Natl. Acad. Sci. U.S.A.

373

376

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“…Alternatively, binding to RNA via RRM1 may induce allosteric changes to TDP-43, which in turn regulates interactions with transcriptional complexes. Previous reports suggested that TDP-43 may bind to messenger RNA as well as small microRNAs (25,26,32). Our future work will focus on identification of the RNA molecules that bind to TDP-43 to regulate its transcriptional function.…”

Section: Discussionmentioning

confidence: 99%

TDP-43 Is a Transcriptional Repressor

Lalmansingh¹,

Urekar

Reddi

2011

Journal of Biological Chemistry

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Here we address TDP-43 function using spermatogenesis as a model system. We previously showed that TDP-43 binds to the testis-specific mouse acrv1 gene promoter in vitro via two GTGTGT-motifs and that mutation of these motifs led to premature transcription in spermatocytes of an otherwise round spermatid-specific promoter. The present study tested the hypothesis that TDP-43 represses acrv1 gene transcription in spermatocytes. Plasmid chromatin immunoprecipitation demonstrated that TDP-43 binds to the acrv1 promoter through GTGTGT motifs in vivo. Reporter gene assays showed that TDP-43 represses acrv1 core promoter-driven transcription via the N-terminal RRM1 domain in a histone deacetylase-independent manner. Consistent with repressor role, ChIP on physiologically isolated germ cells confirmed that TDP-43 occupies the endogenous acrv1 promoter in spermatocytes. Surprisingly, however, TDP-43 remains at the promoter in round spermatids, which express acrv1 mRNA. We show that RNA binding-defective TDP-43, but not splice variant isoforms, relieve repressor function. Transitioning from repressive to active histone marks has little effect on TDP-43 occupancy. Finally, we found that RNA polymerase II is recruited but paused at the acrv1 promoter in spermatocytes. Because mutation of TDP-43 sites caused premature transcription in spermatocytes in vivo, TDP-43 may be involved in pausing RNAPII at the acrv1 promoter in spermatocytes. Overall, our study shows that TDP-43 is a transcriptional repressor and that it regulates spatiotemporal expression of the acrv1 gene during spermatogenesis.TAR DNA-binding protein of 43 kDa 3 is an evolutionarily conserved, ubiquitously expressed DNA/RNA binding nuclear protein. It was originally identified from a HeLa cell cDNA library as a transcription factor binding to the HIV transactivation response region (1). In vitro transcription as well as transient transfection assays showed that TDP-43 repressed HIV transactivation response mediated transcription (1). Since that initial report, the role of TDP-43 in transcription has not been studied. Subsequent studies have focused on the roles of TDP-43 in mRNA splicing and stability (2). Interest in TDP-43, however, increased exponentially after the discovery in 2006 that aberrantly truncated, phosphorylated, and mislocalized TDP-43 was present in the intracellular ubiquitinated inclusions in the brains of patients with frontotemporal lobar degeneration with ubiquitin-positive inclusions, amyotrophic lateral sclerosis, and Alzheimer disease (3). Although a large number of reports have since confirmed the link between TDP-43 and human neurodegenerative disorders, it is not yet clear how TDP-43 contributes to disease. This is due to the fact that very little is known about the normal nuclear function of TDP-43 (4). Understanding TDP-43 nuclear function is important to determine the contribution of loss-of-function to TDP proteinopathies. The evolutionarily conserved TDP-43 must play a fundamental role in biological processes because knock-out ...

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“…TDP-43 was initially discovered as a regulator of HIV transcription 33 but since then it was implicated in multiple nuclear and cytoplasmic functions ranging from alternative splicing, 7,34 miRNA biogenesis, 35 mRNA translation, 36 mRNA stability, 30,31 to TDP-43 mRNA levels autoregulation, 16,29 Recently, it was demonstrated its involvement in 3 0 end processing of its own pre-mRNA. High levels of TDP-43 block the recognition of the first PAS present on its transcript by competing with the polyadenylation factor CstF-64 for DSE binding.…”

Section: Discussionmentioning

confidence: 99%

TDP-43 regulatesβ-adducin(Add2) transcript stability

et al. 2014

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Keywords: Add2, DSE, mRNA stability, TDP-43, 3 0 end processing, 3 0 UTR Abbreviations: RBP, RNA binding protein, DSE, downstream element, PAS, polyadenylation site, ActD, actinomycin D.TDP-43 is an RNA-binding protein involved in several steps of mRNA metabolism including transcription, splicing and stability. It is also involved in ALS and FTD, neurodegenerative diseases characterized by TDP-43 nuclear depletion. We previously identified TDP-43 as a binder of the downstream element (DSE) of the b-Adducin (Add2) brain-specific polyadenylation site (A4 PAS), suggesting its involvement in pre-mRNA 3 0 end processing. Here, by using chimeric minigenes, we showed that TDP-43 depletion in HeLa and HEK293 cells resulted in down-regulation of both the chimeric and endogenous Add2 transcripts. Despite having confirmed TDP-43-DSE in vitro interaction, we demonstrated that the in vivo effect was not mediated by the TDP-43-DSE interaction. In fact, substitution of the Add2 DSE with viral E-SV40 and L-SV40 DSEs, which are not TDP-43 targets, still resulted in decreased Add2 mRNA levels after TDP-43 downregulation. In addition, we failed to show interaction between TDP-43 and key polyadenylation factors, such as CstF-64 and CPSF160 and excluded TDP-43 involvement in pre-mRNA cleavage and regulation of polyA tail length. These evidences allowed us to exclude the pre-hypothesized role of TDP43 in modulating 3 0 end processing of Add2 pre-mRNA. Finally, we showed that TDP-43 regulates Add2 gene expression levels by increasing Add2 mRNA stability. Considering that Add2 in brain participates in synapse assembly, synaptic plasticity and their stability, and its genetic inactivation in mice leads to LTP, LTD, learning and motor-coordination deficits, we hypothesize that a possible loss of Add2 function by TDP-43 depletion may contribute to ALS and FTD disease states.

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Nuclear factor TDP‐43 can affect selected microRNA levels

Cited by 208 publications

References 64 publications

TDP-43 promotes microRNA biogenesis as a component of the Drosha and Dicer complexes

TDP-43 promotes microRNA biogenesis as a component of the Drosha and Dicer complexes

TDP-43 Is a Transcriptional Repressor

TDP-43 regulatesβ-adducin(Add2) transcript stability

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