Targeted, High-Resolution RNA Sequencing of Non-coding Genomic Regions Associated With Neuropsychiatric Functions
Targeted, High-Resolution RNA Sequencing of Non-coding Genomic Regions Associated With Neuropsychiatric Functions
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DOI：
10.3389/fgene.2019.00309
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发表时间：
2019-04-12
影响因子：
3.7
通讯作者：
Mattick, John S.
中科院分区：
文献类型：
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作者：
Hardwick, Simon A.;Bassett, Samuel D.;Mattick, John S.
人脑是生物医学研究的最后前沿之一。全基因组关联研究(GWAS)已经成功地识别了数千个与一系列神经精神特征相关的单倍型块，包括精神分裂症、阿尔茨海默氏症和帕金森氏症等疾病。然而，标记这些单倍型区块的大多数单核苷酸多态(SNPs)落在基因组的非编码区，阻碍了它们的功能验证。虽然这些GWAS基因座中的一些可能包含顺式作用的调控DNA元件，如增强子，但我们假设许多也被转录成非编码RNA，这些RNA在公开可用的转录组注释中缺失。在这里，我们使用靶向RNA捕获(‘RNA CaptureSeq’)和纳米孔长读cDNA测序相结合的方法，使用来自三个神经学健康捐赠者的死后人脑组织，在基因组中转录分析1,023个单倍型块，其中包含与神经精神特征相关的非编码GWASNP。我们发现，大多数(62%)的目标单倍型块，包括13%的基因间隔块，被转录成新的、多外显子RNA，其中大多数还没有在GENCODE注释中记录。我们用短读RNA-SEQ验证了我们的发现，为新的剪接连接提供了正交确认，并使长读组件的定量评估成为可能。许多新的转录本都得到了独立的转录证据的支持，包括基因表达的帽分析(CAGE)数据和表观遗传标记，有些转录本显示出潜在功能作用的迹象。我们将这些转录本作为人脑中非编码转录的初步图谱，可以用来连接神经表型和基因表达。
The human brain is one of the last frontiers of biomedical research. Genome-wide association studies (GWAS) have succeeded in identifying thousands of haplotype blocks associated with a range of neuropsychiatric traits, including disorders such as schizophrenia, Alzheimer's and Parkinson's disease. However, the majority of single nucleotide polymorphisms (SNPs) that mark these haplotype blocks fall within non-coding regions of the genome, hindering their functional validation. While some of these GWAS loci may contain cis-acting regulatory DNA elements such as enhancers, we hypothesized that many are also transcribed into non-coding RNAs that are missing from publicly available transcriptome annotations. Here, we use targeted RNA capture ('RNA CaptureSeq') in combination with nanopore long-read cDNA sequencing to transcriptionally profile 1,023 haplotype blocks across the genome containing non-coding GWAS SNPs associated with neuropsychiatric traits, using post-mortem human brain tissue from three neurologically healthy donors. We find that the majority (62%) of targeted haplotype blocks, including 13% of intergenic blocks, are transcribed into novel, multi-exonic RNAs, most of which are not yet recorded in GENCODE annotations. We validated our findings with short-read RNA-seq, providing orthogonal confirmation of novel splice junctions and enabling a quantitative assessment of the long-read assemblies. Many novel transcripts are supported by independent evidence of transcription including cap analysis of gene expression (CAGE) data and epigenetic marks, and some show signs of potential functional roles. We present these transcriptomes as a preliminary atlas of non-coding transcription in human brain that can be used to connect neurological phenotypes with gene expression.