Transcriptome analysis upon Nipbl, Brd2 and Brd4 knockdown in P19 cells

Mutations in NIPBL are the major cause of Cornelia de Lange Syndrome (CdLS). NIPBL is the cohesin loading factor and has recently been associated with the BET (Bromodomains and Extra Terminal (ET) domain) proteins BRD2 and BRD4. Related to this, a CdLS-like phenotype has been described associated to BRD4 mutations. To understand the relationship between NIPBL and BET proteins, we have performed RNA-Seq expression analysis following depletion of the different proteins in mouse P19 teratocarcinoma cells. Results indicate that genes regulated by NIPBL largely overlap with those regulated by BRD4 but not with those regulated by BRD2. mRNA profiles of P19 mouse teratocarcinoma cells treated with siControl, siNipbl, esiBrd2 or esiBrd4 were generated by deep sequencing, in duplicates, using Illumina Nexseq.

NIPBL基因突变是科妮莉亚·德·朗格综合征（Cornelia de Lange Syndrome, CdLS）的主要致病原因。NIPBL作为黏连蛋白加载因子，近期被发现与BET（溴结构域与额外末端（Extra Terminal, ET）结构域）蛋白BRD2和BRD4存在关联。与此相关，已有研究报道存在与BRD4突变相关的类CdLS表型。为明确NIPBL与BET蛋白之间的调控关系，本研究在小鼠P19畸胎瘤细胞中分别敲低各靶蛋白后开展了RNA测序（RNA-Seq）表达谱分析。结果显示，受NIPBL调控的基因与受BRD4调控的基因存在大量重叠，但与受BRD2调控的基因无显著重叠。本研究采用Illumina Nexseq测序平台，对经阴性对照小干扰RNA（siControl）、靶向Nipbl的小干扰RNA（siNipbl）、靶向Brd2的esiBrd2或靶向Brd4的esiBrd4处理的小鼠P19畸胎瘤细胞进行了双重复深度测序，获取了其mRNA表达谱。