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Liu et al. Cell Biosci (2015) 5:40 DOI 10.1186/s13578-015-0032-zRESEARCHOpen AccessTip110 binding to U6 small nuclear RNA and its participation in pre-mRNA splicingYing Liu1*, Jinfeng Liu1,2, Zenyuan Wang1,3 and Johnny J HeAbstract Background: RNA rotein interactions play important roles in gene expression control. These interactions are mediated by several recurring RNA-binding motifs including a well-known 1-phenyl-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrazole and characterized ribonucleoprotein motif or so-called RNA recognition motif (RRM). Results: In the current study, we set out to identify the RNA ligand(s) of a RRM-containing protein Tip110, also known as p110nrb, SART3, or p110, using a RNA-based yeast three-hybrid cloning strategy. Six putative RNA targets were isolated and found to contain a consensus sequence that was identical to nucleotides 34?6 of U6 small nuclear RNA. Tip110 binding to U6 was confirmed to be specific and RRM-dependent in an electrophoretic mobility shift assay. Both in vitro pre-mRNA splicing assay and in vivo splicing-dependent reporter gene assay showed that the pre-mRNA splicing was correlated PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/12027669 with Tip110 expression. Moreover, Tip110 was found in the spliceosomes containing prespliced pre-mRNA and spliced mRNA products. Nonetheless, the RRM-deleted mutant (RRM) that did not bind to U6 showed promotion in vitro pre-mRNA splicing, whereas the nuclear localization signal (NLS)-deleted mutant NLS that bound to U6 promoted the pre-mRNA splicing both in vitro and in vivo. Lastly, RNA-Seq analysis confirmed that Tip110 regulated a number of gene pre-mRNA splicing including several splicing factors. journal.pone.0167038 Conclusions: Taken together, these results demonstrate that Tip110 is directly involved in constitutive eukaryotic pre-mRNA splicing, likely through its binding to U6 and regulation of other splicing factors, and provide further evidence to support the global roles of Tip110 in regulation of host gene expression. Keywords: Tip110, Small nuclear RNA, U6, RNA binding, Pre-mRNA, Splicing Background In eukaryotic cells, gene expression begins in nucleus with transcription of protein-coding genes to primary RNA transcripts, or so-called pre-messenger RNA (premRNA) or heterogeneous nuclear RNA (hnRNA) [1]. The pre-mRNA are processed to become mature mRNA through a series of post-transcriptional modifications [2]. One of them is the precise excision of noncoding sequences (introns) from pre-mRNA in the spliceosomes [2]. The spliceosomes are formed through assembly of spliceosomal 3-Fluoro-2-(trifluoromethyl)aniline small nuclear ribonucleoprotein (snRNP) and recruitment of numerous splicing factors*Correspondence: ying.liu@unthsc.edu 1 Department of Cell Biology and Immunology, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA Full list of author information is available at the end of the articleto pre-mRNA [1, 2]. Efficient and proper pre-mRNA splicing is a critical step in gene expression control [3, 4]. Dysregulation of splicing elements or splicing regulators and subsequent abnormal pre-mRNA splicing result in expression of aberrant protein products and development of diseases [3, PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/22763976 4]. For example, overexpression of splicing factor SF2/ASF has been shown to trigger malignant transformation [5]. snRNP are important components of the spliceosomes in which.