Mapping 5-Hydroxymethylcytosine (5hmC) Modifications in Skeletal Tissues Using High-Throughput Sequencing.
Mapping 5-Hydroxymethylcytosine (5hmC) Modifications in Skeletal Tissues Using High-Throughput Sequencing.
复制标题
使用高通量测序绘制骨骼组织中的 5-羟甲基胞嘧啶 (5hmC) 修饰图谱。
DOI：
10.1007/978-1-0716-0989-7_8
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发表时间：
2021
期刊：
影响因子：
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通讯作者：
Bhutani,Nidhi
中科院分区：
文献类型：
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作者：
Grandi,FiorellaCarla;Bhutani,Nidhi
胞嘧啶修饰可以改变细胞的表观遗传格局，影响转录因子的结合，染色质组织复合体，最终影响基因表达和细胞命运。5-羟甲基胞嘧啶(5hmC)修饰是由Tet-11易位(Tet)家族Tet 1、Tet 2和Tet 3通过氧化甲基化胞嘧啶(5mC)产生的。Tet家族能够进一步将5hmC氧化为5fC和5caC，最终导致DNA去甲基化。然而，5hmC标记也可以稳定存在于DNA中。稳定的5hmC在多个组织中的激活基因的基因体中丰富，并与增强子等调节区相关。现在已经在包括骨关节炎在内的多种疾病中发现了5hmC模式的改变。在这里，我们描述了一种通过使用基于5hmC标记的选择性修饰和丰富的技术通过下一代测序来定位5hmC修饰的方法。此外，我们还提供了生物信息学分析管道来解释结果数据。
Cytosine modifications can alter the epigenetic landscape of a cell, affecting the binding of transcription factors, chromatin organizing complexes, and ultimately affecting gene expression and cell fate. 5-Hydroxymethylcytosine (5hmC) modifications are generated by the Ten-eleven-translocation (TET) family of enzymes, TET 1, 2, and 3, through the oxidation of methylated cytosines (5mC). The TET family is capable of further oxidizing 5hmC to 5fC and 5caC, leading to eventual DNA demethylation. However, 5hmC marks can also exist stably in DNA. Stable 5hmC is enriched in the gene bodies of activated genes in multiple tissues, as well as associated with regulatory regions such as enhancers. Alterations to 5hmC patterns have now been found in multiple diseases including osteoarthritis. Here, we describe a method to map 5hmC modifications by next-generation sequencing using a technique based on the selective modification and enrichment of the 5hmC mark. We additionally provide a bioinformatic analysis pipeline to interpret the resulting data.