RepEnTools: An automated repeat enrichment analysis package for ChIP-seq data reveals hUHRF1 Tandem-Tudor domain enrichment in young repeats

Background: Repeat elements (REs) play important roles in cell function in health and disease. However, RE enrichment analysis within short-read high-throughput sequencing (HTS) data, such as ChIP-seq, is a challenging task. 

Results: 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, starting from raw input files to tabular and graphical outputs. This is done in implementations that are easily accessible, even with minimal IT skills (Galaxy/UNIX). To demonstrate the performance of our programme, we analysed chromatin pulldown data by the human UHRF1 TTD protein domain and discovered TTD enrichment on young primate and hominid specific polymorphic repeats (SVA, L1PA1/L1HS) overlapping known enhancers. Finally, we corroborated the bioinformatic findings with new experimental data, using validated qPCR assays. Our primate and hominid specific qPCR assays complement similar research tools.

Conclusions: 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.