TAF15 is important for cellular proliferation and regulates the expression of a subset of cell cycle genes through miRNAs

Abstract

1TAF15 (formerly TAFII68) is a member of the FET (FUS, EWS, TAF15) family of RNA-and DNA-binding proteins whose genes are frequently translocated in sarcomas. By performing global gene expression profiling, we found that TAF15 knockdown affects the expression of a large subset of genes, of which a significant percentage is involved in cell cycle and cell death. In agreement, TAF15 depletion had a growth-inhibitory effect and resulted in increased apoptosis. Among the TAF15-regulated genes, targets of microRNAs (miRNAs) generated from the onco-miR-17 locus were overrepresented, with CDKN1A/p21 being the top miRNAstargeted gene. Interestingly, the levels of onco-miR-17 locus coded miRNAs (miR-17-5p and miR-20a) were decreased upon TAF15 depletion and shown to affect the post-transcriptional regulation of TAF15-dependent genes, such as CDKN1A/p21. Thus, our results demonstrate that TAF15 is required to regulate gene expression of cell cycle regulatory genes post-transcriptionally through a pathway involving miRNAs. The findings that high TAF15 levels are needed for rapid cellular proliferation and that endogenous TAF15 levels decrease during differentiation strongly suggest that TAF15 is a key regulator of maintaining a highly proliferative rate of cellular homeostasis.Oncogene ( Keywords: FUS/EWS/TAF15 (FET) proteins; miRNAs; transcription; proliferation; neuronal differentiation; neuroblastoma INTRODUCTION TAF15 (formerly TAF II 68) is a nuclear protein known to associate with a distinct subpopulation of transcription factor IID (TFIID), a multi-subunit complex that nucleates the pre-initiation complex on the promoters of on protein-coding genes.1,2 As TAF15 was not found to be associated with all human TFIID complexes and has no ortholog in other non-vertebrate species, TAF15 is not considered a canonical TAF.3 TAF15 harbors a transcriptional activation domain, a RNA recognition motif and many Arg-Gly-Gly (RGG) repeats known to participate in RNA binding.1 TAF15 together with the related FUS and EWS constitutes the FET (FUS/EWS/TAF15) protein family whose genes are frequently translocated in sarcomas and rare hematopoietic and epithelial cancers. 4 In each case, the N-terminus of the proteins, containing a potent transcriptional activation domain, 5 is fused to the DNA-binding domain of a transcription factor to form oncogenic chimeras.

The apoptotic and genomic studies on A549 cell line induced by silver nitrate

“…25 The downregulated TAF15 has been identified as an inhibitor of cell proliferation and caused apoptosis. 26 The overexpression of leptin (LEP) induced cell proliferation in hepatocellular liver cancer (HepG2) cells. 27 The overexpression of PCBP2 leads to production of oncogenic protein in human gastric cancer.…”

SimiRa: A tool to identify coregulation between microRNAs and RNA-binding proteins

“…From this starting point, simiRa provides useful candidates for functional cooperation partners which might act in concert to carry out a biological function. For example, Ballarino et al 41 identified candidate miRNAs for combined activity with TAF15 by manually screening the small set of validated binding sites from miRTarBase. 59 Using our largescale approach, we are able to identify a lot more potential partners that might function in the same fashion as miR-17-5p and miR-20a-5p.…”

“…While direct targets have not been validated outside of CLIP-Seq studies, it has recently been reported that TAF15 cooperates indirectly with miR-17-5p and miR-20a-5p to repress the cell-cycle gene CDKN1A/p21 by increasing expression levels of the mature miRNAs, which subsequently downregulate CDKN1A/p21. 41 Upon depletion of TAF15, the levels of the miRNAs decrease, CDKN1A/p21 increases and proliferation is impaired. Again, we found that TAF15 and both miRNAs are similar in terms of enriched categories (»0.22, rank 94%) and less similar in terms of targets (»0.15, rank 83%).…”

“…Ballarino et al 41 found candidate miRNAs for an interaction with TAF15 by manually screening the small set of validated binding sites from miRTarBase. 59 Functionally similar miRNAs identified by our large-scale approach are interesting candidates to extend the TAF15/ miRNA interaction network by direct and indirect cooperation.…”

“…To our knowledge there is currently no experimental evidence for indirect interaction on the same gene while experimental evidence supports functional regulation of miRNAs by RBPs. 41 Identification of interaction via functional similarity of miRNA and RBP targets While some functional interactions might be identified by comparing target sets, most will be difficult to identify due to incomplete targeting data. Even though recent CLIP methods perform better than computational methods, it has been shown that target detection depends on target mRNA expression and binding affinity of the used antibody.…”