Choudalakis Michel, Bashtrykov Pavel, Jeltsch Albert
Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany.
Mob DNA. 2024 Apr 3;15(1):6. doi: 10.1186/s13100-024-00315-y.
Repeat elements (REs) play important roles for cell function in health and disease. However, RE enrichment analysis in short-read high-throughput sequencing (HTS) data, such as ChIP-seq, is a challenging task.
Here, we present RepEnTools, a software package for genome-wide RE enrichment analysis of ChIP-seq and similar chromatin pulldown experiments. Our analysis package bundles together various software with carefully chosen and validated settings to provide a complete solution for RE analysis, starting from raw input files to tabular and graphical outputs. RepEnTools implementations are easily accessible even with minimal IT skills (Galaxy/UNIX). To demonstrate the performance of RepEnTools, we analysed chromatin pulldown data by the human UHRF1 TTD protein domain and discovered enrichment of TTD binding on young primate and hominid specific polymorphic repeats (SVA, L1PA1/L1HS) overlapping known enhancers and decorated with H3K4me1-K9me2/3 modifications. We corroborated these new bioinformatic findings with experimental data by qPCR assays using newly developed primate and hominid specific qPCR assays which complement similar research tools. Finally, we analysed mouse UHRF1 ChIP-seq data with RepEnTools and showed that the endogenous mUHRF1 protein colocalizes with H3K4me1-H3K9me3 on promoters of REs which were silenced by UHRF1. These new data suggest a functional role for UHRF1 in silencing of REs that is mediated by TTD binding to the H3K4me1-K9me3 double mark and conserved in two mammalian species.
RepEnTools improves the previously available programmes for RE enrichment analysis in chromatin pulldown studies by leveraging new tools, enhancing accessibility and adding some key functions. RepEnTools can analyse RE enrichment rapidly, efficiently, and accurately, providing the community with an up-to-date, reliable and accessible tool for this important type of analysis.
重复元件（REs）在细胞健康与疾病功能中发挥着重要作用。然而，在短读高通量测序（HTS）数据（如ChIP-seq）中进行RE富集分析是一项具有挑战性的任务。
在此，我们展示了RepEnTools，这是一个用于对ChIP-seq和类似染色质下拉实验进行全基因组RE富集分析的软件包。我们的分析包将各种软件与精心挑选和验证的设置捆绑在一起，为RE分析提供了一个完整的解决方案，从原始输入文件到表格和图形输出。即使是具备最少IT技能（Galaxy/UNIX）的人员也能轻松使用RepEnTools。为了证明RepEnTools的性能，我们分析了人类UHRF1 TTD蛋白结构域的染色质下拉数据，并发现TTD在与已知增强子重叠且带有H3K4me1-K9me2/3修饰的年轻灵长类和人科特异性多态重复序列（SVA、L1PA1/L1HS）上的结合富集。我们通过使用新开发的灵长类和人科特异性qPCR检测方法进行qPCR检测，用实验数据证实了这些新的生物信息学发现，这些检测方法补充了类似的研究工具。最后，我们用RepEnTools分析了小鼠UHRF1 ChIP-seq数据，结果表明内源性mUHRF1蛋白与H3K4me1-H3K9me3在被UHRF1沉默的RE启动子上共定位。这些新数据表明UHRF1在RE沉默中具有功能作用，该作用由TTD与H3K4me1-K9me3双标记的结合介导，并且在两种哺乳动物物种中保守。
RepEnTools通过利用新工具、提高可及性并添加一些关键功能，改进了染色质下拉研究中先前可用的RE富集分析程序。RepEnTools可以快速、高效且准确地分析RE富集，为该重要类型的分析为学界提供了一个最新、可靠且易于使用的工具。
