Hello everyone! RepEnTools, our new program, is now published in Mobile DNA.
RepEnTools takes raw ChIP-seq (& input) data and reports genome-wide enrichments and depletions on repeat elements (REs). We use experimental and simulated data to show that it is fast, efficient, and accurate. It is also easily accessible to all users, thanks to Galaxy workflows or the UNIX auto-installer, and the step-by-step instructions for both!
Validated files are available for the human chm13v2.0 and mouse mm39 assemblies on GitHub and figshare. We have seen that RepEnTools and the scripts that come with it can be very versatile and we expect the package to also be of interest beyond the narrow field of RE analysis. In the future, we aim to keep RepEnTools alive and continue development with additional modules to extend functionality. So, we look forward to your feedback!
In the paper, to demonstrate the use of RepEnTools, we analyse literature data to show that hUHRF1-TTD in human hepatoblastoma HepG2 cells and endogenous mUHRF1 in mouse preimplantation ESCs colocalise with H3K4me1-K9me3 on promoters of species-specific REs which are silenced by UHRF1.
Moreover, we carefully developed ChIP-seq qPCR assays that are specific for entire subfamilies of REs, most notably for the young primate/human-specific L1PA1/L1HS and SVA-F. We applied these to fully validate the bioinformatic findings from the human cells.
Together, the data from human and mouse cells suggest a functional role for UHRF1 in silencing of REs that is mediated by TTD binding to the H3K4me1-K9me3 double mark and is conserved in two mammalian species.
Paper
GitHub - github.com/PavelBashtrykov/RepEnTools
Figshare
RepEnTools takes raw ChIP-seq (& input) data and reports genome-wide enrichments and depletions on repeat elements (REs). We use experimental and simulated data to show that it is fast, efficient, and accurate. It is also easily accessible to all users, thanks to Galaxy workflows or the UNIX auto-installer, and the step-by-step instructions for both!
Validated files are available for the human chm13v2.0 and mouse mm39 assemblies on GitHub and figshare. We have seen that RepEnTools and the scripts that come with it can be very versatile and we expect the package to also be of interest beyond the narrow field of RE analysis. In the future, we aim to keep RepEnTools alive and continue development with additional modules to extend functionality. So, we look forward to your feedback!
In the paper, to demonstrate the use of RepEnTools, we analyse literature data to show that hUHRF1-TTD in human hepatoblastoma HepG2 cells and endogenous mUHRF1 in mouse preimplantation ESCs colocalise with H3K4me1-K9me3 on promoters of species-specific REs which are silenced by UHRF1.
Moreover, we carefully developed ChIP-seq qPCR assays that are specific for entire subfamilies of REs, most notably for the young primate/human-specific L1PA1/L1HS and SVA-F. We applied these to fully validate the bioinformatic findings from the human cells.
Together, the data from human and mouse cells suggest a functional role for UHRF1 in silencing of REs that is mediated by TTD binding to the H3K4me1-K9me3 double mark and is conserved in two mammalian species.
Paper
GitHub - github.com/PavelBashtrykov/RepEnTools
Figshare