Monoallelic expression in neurons derived from induced pluripotent stem cells

描述（由申请人提供）：随机和印迹单等位基因表达影响细胞分化和发育。印迹基因以亲本起源的方式表达，而在随机的单等位基因表达中，母亲或父亲的等位基因在细胞中都是活跃的。经典的，印迹被认为在神经精神障碍普拉德-威利综合征和安吉尔曼综合征的发展中起着关键作用。此外，在一些患有精神分裂症（SZ）、自闭症谱系障碍（ASD）和双相情感障碍（BD）的家庭中也发现了原生父母效应。随机单等位基因表达和脑表达基因的印记都有助于解释神经精神疾病的一些有趣的流行病学特征，例如同卵双胞胎的不一致和外显率降低。两种实验工具已经出现，提供了评估单等位基因（也称为等位基因偏倚）基因表达在神经元分化和神经精神疾病中的作用的手段；诱导多能干细胞（iPSC）技术和全转录组测序（RNA-Seq）。为了鉴定单等位基因表达，我们使用Affymetrix Genome-Wide Human SNP Array 6.0对来自iPSC对照系的神经元进行了初步的RNA-Seq分析和基因分型DNA。鉴定杂合snp，并分析其RNA-Seq读数。我们在801个基因中发现了等位基因偏倚表达的证据。此外，SZ和ASD候选基因A2BP1 （RBFOX1）、ERBB4、NLGN4X、NRG1、NRG3、NRXN1和NLGN1的富集也有统计学意义。A2BP1特别有趣，因为作为神经元基因剪接的调节因子，破坏其表达具有影响许多下游靶标的能力。在本研究中，我们将探索等位基因偏表达的机制，并确定这种现象是由顺式作用的遗传因素引起的，还是由导致印迹或随机单等位基因表达的表观遗传过程引起的。通过开展全基因组DNA甲基化和染色质免疫沉淀研究，探索分化人类神经元中等位基因偏表达的表观遗传学基础。在完成这些研究后，我们将能够将大量SZ、ASD和BD候选基因分组到一个共同的功能伞中：通过等位基因偏倚表达调控，这一发现将为基于表观遗传学的治疗策略提供基础。

DESCRIPTION (provided by applicant): Stochastic and imprinted monoallelically expressed genes influence cellular differentiation and development. Imprinted genes are expressed in a parent-of-origin manner, whereas in stochastic monoallelic expression either the maternal or paternal allele is active in a cell. Classically, imprinting is known to play a key role in the development of the neuropsychiatric disorders Prader-Willi Syndrome and Angelman Syndrome. In addition, parent-of-origin effects have also been found in a subset of families with schizophrenia (SZ), autism spectrum disorders (ASD) and bipolar disorder (BD). Both stochastic monoallelic expression and imprinting of brain-expressed genes could help explain some interesting epidemiological features of neuropsychiatric disorders, such as discordance in monozygotic twins and reduced penetrance. Two experimental tools have emerged that provide the means to evaluate the role of monoallelic (also known as allele-biased) gene expression in neuronal differentiation and neuropsychiatric disorders; induced pluripotent stem cell (iPSC) technology, and whole transcriptome sequencing (RNA-Seq). To identify monoallelically expressed genes, we carried out a preliminary RNA-Seq analysis of neurons derived from a control iPSC line and genotyped DNA using the Affymetrix Genome-Wide Human SNP Array 6.0. Heterozygous SNPs were identified and RNA-Seq reads across them were analyzed. We found evidence for allele-biased expression in 801 genes. In addition, a statistically significant enrichment for SZ and ASD candidate genes was found, which included A2BP1 (RBFOX1), ERBB4, NLGN4X, NRG1, NRG3, NRXN1, and NLGN1. A2BP1 is particularly interesting because as a regulator of neuronal gene splicing disrupting its expression has the capacity to influence numerous downstream targets. In this current proposal, we will explore the mechanism of allele-biased expression and determine whether the phenomenon is caused by cis-acting genetic factors, or by an epigenetic process leading to either imprinting or stochastic monoallelic expression. The epigenetic basis underlying allele-biased expression in differentiating human neurons will be explored by carrying out genome-wide DNA methylation and chromatin immunoprecipitation studies. Upon completion of these studies we will be able to group a large number of SZ, ASD and BD candidate genes into a common functional umbrella: regulation by allele-biased expression, a finding that will provide the foundation for epigenetic-based treatment strategies.