Project description:Vaccinia-related kinase 1 (VRK1) is a nuclear serine/threonine kinase that contributes to genome stability through the phosphorylation of diverse substrates. This study investigated whether VRK1 regulates pre-messenger RNA splicing through serine/arginine repetitive matrix protein 2 (SRRM2), a nuclear speckle-associated splicing scaffold. Messenger RNA sequencing was performed in control HEK293T cells, VRK1-knockout HEK293T cells, and SRRM2-depleted HEK293T cells. Alternative splicing events were analyzed using replicate Multivariate Analysis of Transcript Splicing. Most differential alternative splicing events detected following VRK1 knockout or SRRM2 depletion were skipped-exon events. A subset of skipped-exon events was shared between VRK1-knockout and SRRM2-depleted cells, and the corresponding genes were enriched in DNA repair-related pathways. These data support a role for the VRK1-SRRM2 regulatory axis in maintaining the efficient alternative splicing of DNA damage response-related transcripts.
Project description:To examine the effects of SRp20 on genome-wide RNA splicing in tumor cells, we utilized Exonhit SpliceArray to compare genome-wide changes of RNA splicing and transcription in U2OS cells with or without knockdown of SRp20 by RNAi. U2OS cells were treated by SRp20 siRNA or non-specific siRNA, each performed in triplicate. A human genome-wide splice-array assay was performed by using a service provider ExonHit Therapeutics, Inc (Gaithersburg, MD). Fifty ng of total RNA isolated from U2OS cells with or without knockdown of SRp20 was quality controlled and analyzed by using Affymetrix GeneChip platform to profile the expression of 20,649 genes and splicing events of 19,066 genes.
Project description:Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB (HJAY)
Project description:Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB (Exon array)