There is increasing evidence to suggest that splicing decisions are largely made when the nascent RNA is still associated with chromatin. Here we demonstrate that activity of histone deacetylases (HDACs) influences splice site selection. Using splicing-sensitive microarrays, we identified ∼700 genes whose splicing was altered after HDAC inhibition. We provided evidence that HDAC inhibition induced histone H4 acetylation and increased RNA Polymerase II (Pol II) processivity along an alternatively ...[more]
Project description:We analyzed a role of histone deacetylases in alternative splicing regulation. Using human exon arrays we identified a list of 683 genes whose splicing changes after HDAC inhibition with sodium butyrate. 6 samples (3 nontreated controls and 3 sodium butyrate treated cells)
Project description:We analyzed a role of histone deacetylases in alternative splicing regulation. Using human exon arrays we identified a list of 683 genes whose splicing changes after HDAC inhibition with sodium butyrate. Overall design: 6 samples (3 nontreated controls and 3 sodium butyrate treated cells)
Project description:Gene expression profiles for ~20,000 genes using Illumina Homo sapiensRef-8 v2 Overall design: Cell lines were picked to match cell lines that were assayed in a complimentary set of transient transfection promoter activity assays. Gene identifiers on the BeadArrays were matched to promoter predictions from SwitchGear Genomics (www.switchdb.com; score>20) for transcripts that were not associated with alternative promoters. The eight cell lines are: Ags, HeLa, HepG2, HT1080, HCT116, T98G, U87MG, and G402.
Project description:In this study, we produced full-length RNA-seq data of 45 single HeLa S3 cells, 8 replicates of 10 pg total RNA and one 5 ng total RNA from HeLa S3 cell population. Using this data, we investigated the heterogeneity of HeLa S3 cells in gene expression, alternative splicing, fusion and HPV-host fusion and expression. This study provides comprehensive transcriptomic characters of HeLa S3 cells at the single cell level.
Project description:We performed EGF treatment and hnRNP A1 knockdown in HeLa cells and analyzed alternative splicing patterns by high-throughput RNA sequencing. Overall design: The mRNA profiles of control/EGF-treated/hnRNP A1-knockdown HeLa cells were generated by deep sequencing using Illumina HiSeq2000.
Project description:Gene expression profiling of immortalized human mesenchymal stem cells with hTERT/E6/E7 transfected MSCs. hTERT may change gene expression in MSCs. Goal was to determine the gene expressions of immortalized MSCs. Overall design: One-condition experment, gene expression of 3A6
Project description:Purpose: The goal of this study is to investigate the role of DDX39B in RNA splicing Methods: RNA-Seq splicing analysis of HeLa cells with experimentally induced DDX39B expression knockdown Overall design: DDX39B expression is reduced in HeLa cells by siRNAs. Effects on alternative RNA splicing are compared between knockdown and control cells.