hMTR4 plays a central role in creating balanced nuclear RNA pools for degradation and export III

To eliminate the possibility that for a particular gene the increased RNA level is an effect of enhanced transcription. We carried out ChIP-seq for RNAPII to compare transcription of mRNAs and lncRNAs in control, hRRP40 and hMTR4 knockdown cells. Among 15000 RNAPII binding peaks identified in these samples, only less than 50 peaks was significantly increased in hRRP40 or hMTR4 knockdown cells. Overall design: DNAs isolated from input and IP sample in control, hRRP40 or hMTR4 knockdown HeLa cells were generated by deep sequencing, using Illumina HiSeq 2000.