Placenta specific and ribosomal RNA genes: structure and function

对于PLAC 1，为了确定其非常选择性的组织特异性表达的基础，我们已经表明该基因由两个启动子P1和P2表达，间隔105千碱基，并且是可变剪接的。通过克隆小鼠和人的启动子，确定了最小启动子区。最小启动子区在特定位点结合核受体视黄酸X受体α（RXR-α）、LXR-β和类固醇生成因子1（SF 1）/雌激素相关受体β（ERR-β），并且在它们各自的激动剂存在下，它们的结合具有刺激转录>10倍的积极作用。 在Oncogenesis（2013）的后续出版物中，通过建立癌细胞系的经典方法评估了癌细胞中的Plac 1表达; SV 40介导的原代细胞WI 38和IMR 90细胞的转化。我们发现，在SV 40介导的转化后，原代细胞诱导Plac 1和一系列步骤由SV 40早期区域编码的大T抗原催化，该抗原改变了通常与启动子区域结合的Tp 53阻遏物的性质，使其失去其阻遏能力，导致染色质从封闭状态变为开放状态，从而促进Plac 1的转录。然后在核受体存在下进一步刺激转录，并且如果存在额外的共激活因子NCOA 2（核受体共激活因子2），则其招募RB，导致基因的额外上调。因此，我们已经确定了基因在癌细胞中被激活的主要方式，从而提供了抑制基因活性的途径。 目前，我们已经在生化水平上证明了Plac 1与桥粒相互作用。桥粒功能本身是复杂的，我们继续研究与膜细胞器的特定成分的关联。 在FOXL 2基因调控的相关工作中，我们已经证明FOXL 2介导Col 1a 2基因调控。 对于rDNA结构分析，克隆和分析问题与其他2个NIH小组合作解决。 J.H. NCI的Kim和弗拉基米尔Larionov创建了一种先进的克隆方法，提供了具有多达2个rDNA重复单位的稳定克隆; NHGRI的Adam Phillipy和Alex Dilthey采用了先进的长读段测序技术（PacBio和Nanopore），以促进序列恢复和组装; Ramaiah Nagaraja和我为分析提供了注释和背景。迄今为止的主要发现是，核糖体DNA有许多变体，其中一小部分深深扎根于人类进化中。 13个克隆，约0.32倍的覆盖率（0.82 Mb）的染色体21 rDNA互补，揭示了以前错过了2 kb的道，几个回文结构，和超过300个变种，85个变种落在成熟的18 S/28 S rRNA序列。在独立的全基因组或RNA-Seq数据中也发现了回文断点和>80%的45 S变异等位基因，表明许多变异在人类群体中长期存在。我们已经开发了一个更新的44，838 bp rDNA参考序列注释检测到的变异，这表明了一个可能的路线，以完成分析的rDNA组成的人类基因组。大量的变异揭示了人类核糖体DNA中比以前认为的更多的、更普遍的异质性，从而打开了核糖体动力学中相应变异的可能性。

For PLAC1, to determine the basis for its extraordinarily selective tissue-specific expression, we have shown that the gene is expressed from two promoters, P1 and P2, spaced 105 Kilobases apart and is alternatively spliced. By cloning both promoters from mouse and human, defined the minimal promoter regions. The minimal promoter region binds nuclear receptors Retinoic Acid X Receptor alpha (RXR-alpha), LXR-beta, and Steroidogenic factor 1 (SF1)/ Estrogen related receptor beta (ERR-beta) at specific sites and their binding has a positive effect stimulating transcription >10 fold, in the presence of their respective agonists. In a follow up publication, in Oncogenesis (2013), Plac1 expression in cancer cells was evaluated by a classical approach establishing cancer cell lines; SV40 mediated transformation of primary cells WI38 and IMR90 cells. We found that following SV40 mediated transformation the primary cells induced PLAC1 and a series of steps are catalyzed by Large T antigen encoded by SV40 early regions that modify Tp53 repressor properties normally bound to the promoter region such that it loses its repressive ability, bring about changes in chromatin from closed to open status facilitating Plac1 transcription. The transcription is then further stimulated in the presence of nuclear receptors and if an additional coactivator NCOA2 (nuclear receptor co-activator2) is present, it recruits RB, leading to additional up-regulation of the gene. Thus, we have defined a major way in which the gene is activated in cancer cells, which thereby provides a route to repress the gene activity. Currently, we have shown at the biochemical level that Plac1interacts with desmosomes. Desmosome function is itself complex, and we have continued to study the association with specific components of the membrane organelle. In related work on the regulation of FOXL2 gene, we have shown that FOXL2 mediates Col1a2 gene regulation. For rDNA structure analysis the cloning and analysis problems were resolved with collaborations with 2 other NIH groups. J.H. Kim and Vladimir Larionov at NCI created an advanced approach to cloning that provided stable clones with up to 2 repeat units of rDNA; Adam Phillipy and Alex Dilthey at NHGRI adapted advanced long-read sequencing techniques (PacBio and Nanopore) to facilitate sequence recovery and assembly; and Ramaiah Nagaraja and I supplied annotation and context for the analyses. The major findings thus far are that ribosomal DNA has many variants, with a fraction of them deeply seated in human evolution. Thirteen clones, about 0.32-fold coverage (0.82 Mb) of the chromosome 21 rDNA complement, revealed a previously missed 2 kb tract, several palindromic structures, and over 300 variants; 85 variants fall in mature 18S/28S rRNA sequences. Palindromic breakpoints and >80% of 45S variant alleles were also found in independent whole-genome or RNA-Seq data, indicating that many variants are long established in human populations. We have developed an updated 44,838 bp rDNA reference sequence annotated with detected variants, suggesting a possible route to complete analysis of the rDNA component of the human genome. The large number of variants reveal more - and more universal - heterogeneity in human ribosomal DNA than previously considered, opening the possibility of corresponding variations in ribosome dynamics.