ALT lncRNA knockdown in BCBL1 cells

ALT is an KSHV immediately early transcript that expresses at high abundance in the nucleus. This lncRNA has an extreme long length, around 12,400 nt and coded from the KSHV latency-associated region on the opposite strand of the KSHV latency genes, including clusters of miRNAs, LANA,v-Flip, v-Cyclin and co-terminates with K14. It is identified to interact with multiple splicing proteins. In order to study the alternative splicing change upon ALT KD, RNAseq was conducted on ALT knockdown PEL cells. BCBL1 cells are induced with TPA for24 hours and transfected with 4 different GapmeRs targeting ALT or negative control gameR.

ALT是卡波西肉瘤相关疱疹病毒（KSHV）的即刻早期转录本，在细胞核内呈高丰度表达。该长链非编码RNA（lncRNA, long non-coding RNA）长度极长，约12400个核苷酸（nt, nucleotide），由KSHV潜伏相关区域的反义链编码，该区域涵盖miRNA簇、LANA、v-Flip、v-Cyclin等KSHV潜伏基因，且与K14共终止。研究证实该转录本可与多种剪接蛋白发生相互作用。为探究ALT敲低（KD, knockdown）后发生的可变剪接变化，研究人员对ALT敲低的原发性渗出性淋巴瘤（PEL, primary effusion lymphoma）细胞开展了RNA测序（RNA sequencing, RNAseq）。实验中，将BCBL1细胞经佛波醇12-十四酸酯13-乙酸酯（TPA, 12-O-Tetradecanoylphorbol-13-acetate）诱导24小时后，转染4种靶向ALT的GapmeR及阴性对照GapmeR。