SON and the MALAT1 locus in chromatin interaction and metastasis gene regulation

描述（申请人提供）：转移是癌症死亡的主要原因，也是癌症治疗的一个障碍。由于基因表达的改变在转移中起着重要作用，因此了解转移相关基因表达的机制对于开发新的治疗方法是必要的。转移相关肺腺癌转录物1 （MALAT1）是一种在许多癌症中高度表达的长链非编码RNA （lncRNA）。MALAT1的上调与预后不良、肿瘤转移增加和细胞周期/转移相关基因表达有关。尽管它与癌症密切相关，但MALAT1的确切细胞功能仍然难以捉摸。最近对人类和小鼠敲除系统研究MALAT1功能缺失表型的努力未能证明全球基因表达的显著变化，这提出了MALAT1基因座介导的基因表达控制可能存在未确定的分子机制的可能性。我们研究了一种新的核斑点蛋白SON，我们最近用SON抗体和测序（ChIP-seq）对染色质免疫沉淀的研究表明，SON与MALAT1基因3'端的直接下游DNA序列强烈相互作用，同时它与许多与细胞周期/转移相关的其他基因的启动子或第一外显子相互作用。此外，根据ENCODE （DNA元件百科全书）数据，靠近MALAT1基因3'端的DNA序列具有远端调控元件的许多特征。我们假设，转移癌细胞中开放/活跃的MALAT1基因座通过位于MALAT1基因下游的DNA序列增强了染色质相互作用，而SON是介导该基因组位点与其他基因的启动子/增强子序列之间染色质相互作用的关键成分，从而共同调控多个转移/癌症相关基因。为了验证这一假设，我们提出以下具体目标：(1)在正常肺上皮细胞和转移性肺癌细胞中鉴定MALAT1基因座的全基因组染色质相互作用；(2)研究SON在转移性肺癌细胞中MALAT1基因座的染色质相互作用和细胞周期/转移基因表达中的作用。我们将使用增强的染色体构象捕获和深度测序（e4C）方法来建立MALAT1染色质相互作用谱，并确定SON在染色质相互作用和细胞周期/转移相关的基因表达中的作用。阐明MALAT1基因座染色质相互作用在控制整体基因表达中的作用将为该基因座在癌症中的作用提供新的见解。此外，调查

DESCRIPTION (provided by applicant): Metastasis is a main cause of cancer death, and a hurdle in cancer therapy. Since altered gene expression significantly contributes to metastasis, understanding the mechanism of metastasis-related gene expression is necessary for developing new therapeutic modalities. The metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is a long non-coding RNA (lncRNA) highly expressed in many cancers. Upregulation of MALAT1 has been linked to poor prognosis, increased tumor metastasis and cell cycle/metastasis-related gene expression. Despite its close association with cancer, exact cellular functions of MALAT1 remain elusive. Recent efforts on human and mouse knockout systems to study the loss-of-function phenotypes of MALAT1 failed to demonstrate noticeable changes in global gene expression, raising a possibility that there may be unidentified molecular mechanisms of MALAT1 locus-mediated gene expression control. We have studied a novel nuclear speckle protein, SON, and our recent effort on chromatin immunoprecipitation with SON antibody and sequencing (ChIP-seq) revealed that SON strongly interacts with the immediate downstream DNA sequence of the MALAT1 gene 3' end, while it interacts with the promoter or the first exon of many other genes associated with cell cycle/metastasis. Moreover, the DNA sequence near the 3' end of the MALAT1 gene possesses many characteristic features of a distal regulatory element, according to ENCODE (Encyclopedia of DNA Elements) data. We hypothesize that the open/active MALAT1 locus in metastatic cancer cells has enhanced chromatin interaction through the DNA sequence located immediately downstream from the MALAT1 gene, and SON is a critical component mediating chromatin interaction between this genomic locus and promoter/enhancer sequences of other genes, resulting in co- regulation of multiple metastasis/cancer-related genes. To test this hypothesis, we propose following specific aims; (1) Identify genome-wide chromatin interactions of the MALAT1 locus in normal lung epithelial cells and metastatic lung cancer cells, (2) Investigate the role of SON in chromatin interaction of the MALAT1 locus and expression of cell cycle/metastasis genes in metastatic lung cancer cells. We will use an enhanced method of chromosome conformation capture and deep sequencing (e4C) to establish the MALAT1 chromatin interaction profile, and to identify the role of SON in chromatin interaction and gene expression related to cell cycle/metastasis. Elucidating the role of MALAT1 locus chromatin interaction in controlling global gene expression will provide novel insights into the action of this locus in cancer. Furthermore, investigating the role of SON in MALAT1-mediated gene regulation will serve as a basis of targeting SON together with the genomic locus of MALAT1 for treatment and prevention of metastatic cancer.