PDF(Pubmed)
Abstract：
BACKGROUND: Cis-regulatory mutations often underlie phenotypic evolution. However, because identifying the locations of promoters and enhancers in non-coding regions is challenging, we have fewer examples of identified causative cis-regulatory mutations that underlie naturally occurring phenotypic variations than of causative amino acid-altering mutations. Because cis-regulatory elements have epigenetic marks of specific histone modifications, we can detect cis-regulatory elements by mapping and analyzing them. Here, we investigated histone modifications and chromatin accessibility with cleavage under targets and tagmentation (CUT&Tag) and assay for transposase-accessible chromatin-sequencing (ATAC-seq).
RESULTS: Using the threespine stickleback (Gasterosteus aculeatus) as a model, we confirmed that the genes for which nearby regions showed active marks, such as H3K4me1, H3K4me3, and high chromatin accessibility, were highly expressed. In contrast, the expression levels of genes for which nearby regions showed repressive marks, such as H3K27me3, were reduced, suggesting that our chromatin analysis protocols overall worked well. Genomic regions with peaks of histone modifications showed higher nucleotide diversity within and between populations. By comparing gene expression in the gills of the marine and stream ecotypes, we identified several insertions and deletions (indels) with transposable element fragments in the candidate cis-regulatory regions.
CONCLUSIONS: Thus, mapping and analyzing histone modifications can help identify cis-regulatory elements and accelerate the identification of causative mutations in the non-coding regions underlying naturally occurring phenotypic variations.
RESULTS: Using the threespine stickleback (Gasterosteus aculeatus) as a model, we confirmed that the genes for which nearby regions showed active marks, such as H3K4me1, H3K4me3, and high chromatin accessibility, were highly expressed. In contrast, the expression levels of genes for which nearby regions showed repressive marks, such as H3K27me3, were reduced, suggesting that our chromatin analysis protocols overall worked well. Genomic regions with peaks of histone modifications showed higher nucleotide diversity within and between populations. By comparing gene expression in the gills of the marine and stream ecotypes, we identified several insertions and deletions (indels) with transposable element fragments in the candidate cis-regulatory regions.
CONCLUSIONS: Thus, mapping and analyzing histone modifications can help identify cis-regulatory elements and accelerate the identification of causative mutations in the non-coding regions underlying naturally occurring phenotypic variations.
摘要：
背景：顺式调节突变通常是表型进化的基础。然而,因为识别启动子和增强子在非编码区的位置是具有挑战性的，与改变氨基酸的致病突变相比,我们发现的自然表型变异背后的致病顺式调节突变的例子较少.因为顺式调控元件具有特定组蛋白修饰的表观遗传标记，我们可以通过作图和分析来检测顺式调控元件。这里,我们研究了组蛋白修饰和染色质可及性,包括靶标下的裂解和标签化(CUT&Tag)以及转座酶可及的染色质测序测定(ATAC-seq).
结果：使用三松棘鱼（Gasterosteusaculeatus）作为模型，我们证实了附近区域显示有活性标记的基因，如H3K4me1，H3K4me3和高染色质可及性，高度表达。相比之下,附近区域显示抑制标记的基因的表达水平，如H3K27me3，减少，表明我们的染色质分析方案总体运行良好。具有组蛋白修饰峰的基因组区域在种群内部和种群之间显示出更高的核苷酸多样性。通过比较海洋和河流生态型的g中的基因表达，我们在候选顺式调控区中鉴定了几个带有转座元件片段的插入和缺失(indel)。
结论：因此，定位和分析组蛋白修饰可以帮助识别顺式调控元件，并加速识别天然存在的表型变异的非编码区中的致病突变。
结果：使用三松棘鱼（Gasterosteusaculeatus）作为模型，我们证实了附近区域显示有活性标记的基因，如H3K4me1，H3K4me3和高染色质可及性，高度表达。相比之下,附近区域显示抑制标记的基因的表达水平，如H3K27me3，减少，表明我们的染色质分析方案总体运行良好。具有组蛋白修饰峰的基因组区域在种群内部和种群之间显示出更高的核苷酸多样性。通过比较海洋和河流生态型的g中的基因表达，我们在候选顺式调控区中鉴定了几个带有转座元件片段的插入和缺失(indel)。
结论：因此，定位和分析组蛋白修饰可以帮助识别顺式调控元件，并加速识别天然存在的表型变异的非编码区中的致病突变。
