Multidimensional chromatin profiling of zebrafish and human pancreas to uncover and validate disease-related enhancers

The pancreas is a central organ for human diseases. Most disease-associated alleles overlap with non-coding cis-regulatory elements of DNA, suggesting that alterations in regulatory sequences contribute to pancreatic diseases. However, the interspecies identification of equivalent cis-regulatory elements required for in vivo testing face fundamental challenges, including lack of sequence conservation. In this work, we performed a combined analysis of ATAC-seq, ChIP-seq, 4C-seq and HiChIP-seq data from zebrafish and human pancreatic cells to identify interspecies functionally equivalent cis-regulatory elements, regardless of sequence conservation. To link cis-regulation with the expression of target genes in the pancreas, we additionally integrated in our analysis own and public RNA-seq data from zebrafish pancreatic cell-types. Among several disease-associated sequences, we identified a zebrafish ptf1a distal enhancer whose deletion generates pancreatic agenesis, demonstrating the causality of this condition in humans. Our results further demonstrate that this phenotype is a consequence of loss of pancreas progenitor cells. Overall, we show that chromatin profiling can uncover interspecies functional equivalency of cis-regulatory elements, contributing to the prediction of new disease-causative enhancers and their role in human disease.

胰腺是人类疾病相关的核心器官。多数疾病相关等位基因与DNA的非编码顺式调控元件（cis-regulatory elements）存在重叠，这提示调控序列的改变可导致胰腺疾病的发生。然而，用于体内验证的跨物种等效顺式调控元件的识别面临根本性挑战，其中包括序列保守性的缺失。本研究中，我们对斑马鱼和人类胰腺细胞的ATAC-seq、ChIP-seq、4C-seq及HiChIP-seq数据进行整合分析，以识别跨物种功能等效的顺式调控元件，无需考虑序列保守性。为将顺式调控与胰腺靶基因的表达建立关联，我们还在分析中整合了自身及公开的斑马鱼胰腺细胞类型的RNA-seq数据。在多个疾病相关序列中，我们鉴定出一个斑马鱼ptf1a远端增强子，敲除该增强子可导致胰腺发育不全，证实了该致病表型在人类中的因果关系。我们的研究结果进一步表明，该表型是胰腺祖细胞丢失的结果。综上，本研究证明染色质谱分析可揭示顺式调控元件的跨物种功能等效性，有助于预测新的致病增强子及其在人类疾病中的作用。