Deletion mapping of regulatory elements for GATA3 in T cells reveals a distal enhancer involved in allergic diseases.
Deletion mapping of regulatory elements for GATA3 in T cells reveals a distal enhancer involved in allergic diseases.
复制标题
T 细胞中 GATA3 调控元件的删除图谱揭示了与过敏性疾病有关的远端增强子。
DOI：
10.1016/j.ajhg.2023.03.008
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发表时间：
2023
影响因子：
9.8
通讯作者：
McVicker,Graham
中科院分区：
文献类型：
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作者：
Chen,HsiuyiV;Lorenzini,MichaelH;Lavalle,ShannaN;Sajeev,Karthyayani;Fonseca,Ariana;Fiaux,PatrickC;Sen,Arko;Luthra,Ishika;Ho,AaronJ;Chen,AaronR;Guruvayurappan,Karthik;O'Connor,Carolyn;McVicker,Graham
GATA 3是T细胞分化所必需的，并且被免疫性状的全基因组关联研究（GWAS）命中所包围。这些GWAS命中的解释是具有挑战性的，因为基因表达数量性状基因座（eQTL）研究缺乏检测对特定细胞类型中的基因表达具有小影响的变体的能力，并且包含GATA 3的基因组区域包含数十个潜在的调控序列。为了定位GATA 3的调控序列，我们在Jurkat T细胞中进行了2 Mb基因组区域的高通量平铺缺失筛选。这揭示了23个候选调控序列，除了其中一个之外，所有的都在与GATA 3相同的拓扑关联结构域（topological-associated domain，简称ATRA）内。然后，我们进行了一个低通量的删除屏幕，以精确地映射在原代辅助性T细胞2（Th 2）的调控序列。我们测试了25个序列与100 bp的缺失，并验证了五个最强的命中与独立的删除实验。此外，我们在GATA 3下游1 Mb的远端调控元件中精细定位了过敏性疾病的GWAS命中，并确定了14个候选致病变异体。跨越候选变体rs725861的小缺失降低了Th 2细胞中的GATA 3水平，荧光素酶报告基因测定显示其两个等位基因之间的调节差异，表明该变体在过敏性疾病中的因果机制。我们的研究证明了整合GWAS信号与缺失作图的能力，并确定了GATA 3的关键调控序列。
GATA3is essential for T cell differentiation and is surrounded by genome-wide association study (GWAS) hits for immune traits. Interpretation of these GWAS hits is challenging because gene expression quantitative trait locus (eQTL) studies lack power to detect variants with small effects on gene expression in specific cell types and the genome region containingGATA3contains dozens of potential regulatory sequences. To map regulatory sequences forGATA3, we performed a high-throughput tiling deletion screen of a 2 Mb genome region in Jurkat T cells. This revealed 23 candidate regulatory sequences, all but one of which is within the same topological-associating domain (TAD) asGATA3. We then performed a lower-throughput deletion screen to precisely map regulatory sequences in primary T helper 2 (Th2) cells. We tested 25 sequences with ∼100 bp deletions and validated five of the strongest hits with independent deletion experiments. Additionally, we fine-mapped GWAS hits for allergic diseases in a distal regulatory element, 1 Mb downstream ofGATA3, and identified 14 candidate causal variants. Small deletions spanning the candidate variant rs725861 decreased GATA3 levels in Th2 cells, and luciferase reporter assays showed regulatory differences between its two alleles, suggesting a causal mechanism for this variant in allergic diseases. Our study demonstrates the power of integrating GWAS signals with deletion mapping and identifies critical regulatory sequences forGATA3.