Project description:Aim: Identification of long noncoding RNAs using transcriptional analysis of e15.5 mouse embryonic pancreas and adult mouse islets Methods: rRNA-depleted total RNA from e15.5 embryonic mouse pancreata and 12-week-old mouse islets was prepared using the Ribo-Zero rRNA removal kit. Biological replicates indicate that each RNA-seq data set was generated from individual mice (islets) or 3-4 pooled e15.5 embryonic pancreata. Libraries were prepared with Illumina TruSeq RNA sample preparation kit and then sequenced with 60 million, 2 x 100 paired reads on an Illumina HiSeq 2000 V3 instrument. To reconstruct the transcriptomes, we first mapped all reads of total RNAs to the mouse reference genome (mm10) with TopHat v1.3.2 (Trapnell et al., 2012). Cufflinks (v1.2.1) was subsequently applied to assemble the whole transcriptome and to identify all possible transcripts. Significantly differentially expressed genes were calculated using DEseq2.
Project description:Recent studies have uncovered thousands of long non-coding RNAs (lncRNAs) in human pancreatic β cells. β cell lncRNAs are often cell type specific and exhibit dynamic regulation during differentiation or upon changing glucose concentrations. Although these features hint at a role of lncRNAs in β cell gene regulation and diabetes, the function of β cell lncRNAs remains largely unknown. In this study, we investigated the function of β cell-specific lncRNAs and transcription factors using transcript knockdowns and co-expression network analysis. This revealed lncRNAs that function in concert with transcription factors to regulate β cell-specific transcriptional networks. We further demonstrate that the lncRNA PLUTO affects local 3D chromatin structure and transcription of PDX1, encoding a key β cell transcription factor, and that both PLUTO and PDX1 are downregulated in islets from donors with type 2 diabetes or impaired glucose tolerance. These results implicate lncRNAs in the regulation of β cell-specific transcription factor networks.
Project description:Long non-coding RNAs (lncRNAs) are an emerging class of RNA species that may play a critical regulatory role in gene expression. However, the association between lncRNAs and atrial fibrillation (AF) is still not fully understood. In this study, we used RNA sequencing data to identify and quantify the both protein coding genes (PCGs) and lncRNAs. The high enrichment of these up-regulated genes in biological functions concerning response to virus and inflammatory response suggested that chronic viral infection may lead to activated inflammatory pathways, thereby alter the electrophysiology, structure, and autonomic remodeling of the atria. In contrast, the downregulated GO terms were related to the response to saccharides. To identify key lncRNAs involved in AF, we predicted lncRNAs regulating expression of the adjacent PCGs, and characterized biological function of the dysregulated lncRNAs. We found that two lncRNAs, ETF1P2, and AP001053.11, could interact with protein-coding genes (PCGs), which were implicated in AF. In conclusion, we identified key PCGs and lncRNAs, which may be implicated in AF, which not only improves our understanding of the roles of lncRNAs in AF, but also provides potentially functional lncRNAs for AF researchers.
Project description:To explore the potential involvement of lncRNAs in pancreatic ductal adenocarcinoma (PDAC) oncogenesis, we conducted lncRNA profiling in six pairs of human PDAC and adjacent normal tissue by microarray. Our results showed that clusters of lncRNAs were aberrantly expressed in PDAC compared with normal samples, and provided potential targets for future treatment of PDAC and novel insights into PDAC biology.
Project description:Platelets are blood cells who play critical roles in numerous biological and disease processes. This study was designed to identify lncRNAs that may play a role in platelet reactivity. In this study, by using large-scale deep sequencing, we determined the expression profiles of lncRNAs in both hyperreactive and hyporeactive human platelets. To determine the potential link between the expression of lncRNAs and the function of platelets, the expression profiles of hyperreactive and hyporeactive platelets were compared. Compared with hyperreactive platelets, deep sequencing analysis demonstrated that differential lncRNA expression was a remarkable characteristic in hyporeactive platelets.
Project description:Long noncoding RNAs (lncRNAs) have been described in cell lines and various whole tissues, but lncRNA analysis of development in vivo is limited. Here, we comprehensively analyze lncRNA expression for the adult mouse subventricular zone neural stem cell lineage. We utilize complementary genome-wide techniques including RNA-seq, RNA CaptureSeq, and ChIP-seq to associate specific lncRNAs with neural cell types, developmental processes, and human disease states. By integrating data from chromatin state maps, custom microarrays, and FACS purification of the subventricular zone lineage, we stringently identify lncRNAs with potential roles in adult neurogenesis. shRNA-mediated knockdown of two such lncRNAs, Six3os and Dlx1as, indicate roles for lncRNAs in the glial-neuronal lineage specification of multipotent adult stem cells. Our data and workflow thus provide a uniquely coherent in vivo lncRNA analysis and form the foundation of a user-friendly online resource for the study of lncRNAs in development and disease. RNA-seq (both paired end and single) from the adult neurogenic niches- subventricular zone (SVZ), olfactory bulb (OB), dentate gyrus (DG) and control non-neurogenic tissue, striatum (STR). Reads were used to assemble a lncRNA catalogue and determine expression values for both protein-coding and noncoding genes
Project description:Smooth muscle cell (SMC) phenotypic switching from a contractile to a synthetic state is implicated in diverse vascular pathologies, including neointimal formation. This study was designed to identify lncRNAs that may play a role in vascular pathologies. Primary smooth muscle cells cultured from surplus human saphenous vein tissue were treated with inflammatory and proliferative stimuli, IL1α and PDGF, for 72h and RNA extracted for RNA-sequencing. Using edgeR processed data we found expression of many lncRNAs was altered following treatment and could play a role in vascular disease. 4 groups of samples, n= 3/group each replicate using cells cultured from a different venous patient sample. Cells were quiesced in 0.2% serum for 48h followed by addition of 10ng/ml IL1α , 20ng/ml PDGF or both 10ng/ml IL1α and 20ng/ml PDGF together. Cells were collected after 72h and RNA extracted using Qiagen RNeasy kits. RNA-sequencing was carried out by Beckman Coulter Genomics on the r-RNA depleted fraction.