Department of Biotechnology and Biosciences, University of Milano-Bicocca, piazza della Scienza 2, 20126 Milano, Italy.
Institute of Informatics and Telematics (IIT), National Research Council (CNR), 56124 Pisa, Italy.
Int J Mol Sci. 2023 Jan 6;24(2):1164. doi: 10.3390/ijms24021164.
DNA sequence variants (single nucleotide polymorphisms or variants, SNPs/SNVs; copy number variants, CNVs) associated to neurodevelopmental disorders (NDD) and traits often map on putative transcriptional regulatory elements, including, in particular, enhancers. However, the genes controlled by these enhancers remain poorly defined. Traditionally, the activity of a given enhancer, and the effect of its possible alteration associated to the sequence variants, has been thought to influence the nearest gene promoter. However, the obtainment of genome-wide long-range interaction maps in neural cells chromatin challenged this view, showing that a given enhancer is very frequently not connected to the nearest promoter, but to a more distant one, skipping genes in between. In this Perspective, we review some recent papers, who generated long-range interaction maps (by HiC, RNApolII ChIA-PET, Capture-HiC, or PLACseq), and overlapped the identified long-range interacting DNA segments with DNA sequence variants associated to NDD (such as schizophrenia, bipolar disorder and autism) and traits (intelligence). This strategy allowed to attribute the function of enhancers, hosting the NDD-related sequence variants, to a connected gene promoter lying far away on the linear chromosome map. Some of these enhancer-connected genes had indeed been already identified as contributive to the diseases, by the identification of mutations within the gene's protein-coding regions (exons), validating the approach. Significantly, however, the connected genes also include many genes that were not previously found mutated in their exons, pointing to novel candidate contributors to NDD and traits. Thus, long-range interaction maps, in combination with DNA variants detected in association with NDD, can be used as "pointers" to identify novel candidate disease-relevant genes. Functional manipulation of the long-range interaction network involving enhancers and promoters by CRISPR-Cas9-based approaches is beginning to probe for the functional significance of the identified interactions, and the enhancers and the genes involved, improving our understanding of neural development and its pathology.
与神经发育障碍（NDD）和特征相关的 DNA 序列变体（单核苷酸多态性或变体，SNP/SNV；拷贝数变体，CNV）通常映射到假定的转录调控元件上，包括特别是增强子。然而，这些增强子控制的基因仍然定义不明确。传统上，给定增强子的活性及其与序列变体相关的可能改变的影响被认为会影响最近的基因启动子。然而，在神经细胞染色质中获得全基因组长程相互作用图谱挑战了这一观点，表明给定的增强子通常与最近的启动子没有连接，而是与更远的启动子连接，在两者之间跳过基因。在这种观点下，我们回顾了一些最近的论文，这些论文生成了长程相互作用图谱（通过 HiC、RNApolII ChIA-PET、Capture-HiC 或 PLACseq），并将鉴定出的长程相互作用 DNA 片段与与 NDD（如精神分裂症、双相情感障碍和自闭症）和特征（智力）相关的 DNA 序列变体重叠。这种策略允许将 NDD 相关序列变体所在的增强子的功能归因于线性染色体图谱上远处连接的基因启动子。其中一些增强子连接的基因已经通过鉴定基因蛋白编码区域（外显子）内的突变被确定为疾病的贡献者，验证了这种方法。然而，重要的是，连接的基因还包括许多以前在外显子中没有发现突变的基因，这指向了 NDD 和特征的新候选贡献者。因此，长程相互作用图谱与与 NDD 相关的检测到的 DNA 变体结合使用，可以作为识别新的候选疾病相关基因的“指针”。通过基于 CRISPR-Cas9 的方法对涉及增强子和启动子的长程相互作用网络进行功能操作，开始探测鉴定出的相互作用、涉及的增强子和基因的功能意义，从而提高我们对神经发育及其病理学的理解。
