Bioinformatics Pipelines for Identification of Super-Enhancers and 3D Chromatin Contacts.
Bioinformatics Pipelines for Identification of Super-Enhancers and 3D Chromatin Contacts.
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用于识别超级增强子和 3D 染色质接触的生物信息学流程。
DOI：
10.1007/978-1-0716-2724-2_9
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发表时间：
2023
期刊：
影响因子：
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通讯作者：
Namekawa,SatoshiH
中科院分区：
文献类型：
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作者：
Sakashita,Akihiko;Takeuchi,Chikara;Maezawa,So;Namekawa,SatoshiH
基因表达的精确调节是发育中不可或缺的一部分。新兴的研究已经强调，超级增强子（SE），这是多个增强子的集群，在通过3D染色质调节细胞类型特异性基因表达中发挥关键作用，从而定义给定细胞的细胞身份。在这里，我们提供优化的生物信息学管道来识别SE和3D染色质接触。我们的管道包括染色质免疫沉淀测序（ChIP-seq）数据的处理，以识别SE和全基因组染色体构象捕获（Hi-C）数据的处理。然后，我们可以推断SE和其他基因组区域之间的长距离染色质接触。这种综合计算方法可以应用于CUT&RUN和CUT&Tag，ChIP-seq的替代技术，使我们能够识别SE的基因组位置及其3D基因组构型，从而使多个SE协同作用。我们显示了小鼠精子发生的分析作为这种应用的一个例子。
Precise regulation of gene expression is integral in development. Emerging studies have highlighted that super-enhancers (SEs), which are clusters of multiple enhancers, play critical roles in regulating cell type-specific gene expression via 3D chromatin, thereby defining the cellular identities of given cells. Here we provide optimized bioinformatics pipelines to identify SEs and 3D chromatin contacts. Our pipelines encompass the processing of chromatin immunoprecipitation sequencing (ChIP-seq) data to identify SEs and the processing of genome-wide chromosome conformation capture (Hi-C) data. We can then infer long-range chromatin contacts between SEs and other genomic regions. This integrative computational approach, which can be applied to CUT&RUN and CUT&Tag, alternative technologies to ChIP-seq, allows us to identify genomic locations of SEs and their 3D genome configuration, whereby multiple SEs act in concert. We show an analysis of mouse spermatogenesis as an example of this application.