Ribo-depleted RNA-Seq Libraries From Huntington's Disease Brain. Ribo-depleted RNA-Seq Libraries From Huntington's Disease Brain

Transcriptional dysregulation is well documented in Huntington’s disease (HD) post-mortem brain. We previously identified gene expression profiles from both symptomatic and asymptomatic HD prefrontal cortex which characterize the effects of degeneration in disease versus normal brains. Transcriptional dysregulation in HD brain is well documented by these studies and others, but the extent and causes of this dysregulation remain unknown. Here, we present a large ribo-depleted RNA sequencing (rdRNA-Seq) dataset and novel bioinformatic methodology to further characterize transcriptional dysregulation in HD brain as it relates to disease variables, including CAG repeat size, age of symptom onset, and rate of neurodegeneration. Overall design: rdRNA-Seq was performed in 98 post-mortem HD prefrontal cortex samples previously characterized for CAG repeat size and extent of striatal and cortical involvement. rdRNA-Seq data, in contrast to poly-A selected RNA-Seq, allows the assessment of transcribed non-coding genomic regions that may correspond to large-scale regulatory mechanisms as well as individual genes. Unlike traditional RNA-Seq analysis, which focuses almost exclusively on annotated regions of the genome, we developed a novel bioinformatic method that divides the genome into bins and identifies genomic loci of arbitrary length associated with variables of interest.

转录失调在亨廷顿舞蹈症（Huntington’s disease, HD）患者的死后脑组织中已有充分报道。此前我们已从有症状及无症状HD患者的前额叶皮层中鉴定出基因表达谱，该谱可表征疾病状态下的退行性变相较于正常脑组织的特征。尽管本研究及其他多项研究均已充分证实HD脑组织中的转录失调现象，但该失调的波及范围与潜在诱因仍不明确。本研究构建了大规模核糖体去除RNA测序（ribo-depleted RNA sequencing, rdRNA-Seq）数据集，并提出全新的生物信息学方法，以进一步解析HD脑组织中转录失调与疾病相关变量（包括CAG重复序列长度、症状发病年龄及神经退行性变速率）的关联特征。总实验设计如下：我们对98例已完成CAG重复序列长度、纹状体及皮层受累程度表征的死后HD患者前额叶皮层样本开展rdRNA-Seq检测。与聚腺苷酸选择性RNA测序（poly-A selected RNA-Seq）不同，rdRNA-Seq可实现对转录得到的非编码基因组区域的分析，这类区域既可能对应大规模调控机制，也可对应单个基因。相较于传统RNA测序分析几乎仅聚焦于基因组的注释区域，我们开发了一种全新的生物信息学方法：该方法将基因组划分为多个区间，并可识别与目标研究变量相关的任意长度基因组位点。