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← Back to eRNAkit

Core

The Core is the foundational framework of eRNAkit, providing a unified platform for studying human enhancer RNAs (eRNAs) as functional regulatory molecules. It integrates multiple orthogonal genomic and transcriptomic resources into eRNAkitDB, a harmonised annotation database centred on experimentally defined enhancer coordinates. The database combines complementary evidence spanning expression, subcellular localisation, RNA–RNA interactions, translation, RNA stability and regulatory context to support systems-level, RNA-centric investigation of eRNA biology. Alongside eRNAkitDB, the Core module includes the interactive eRNAkitApp for data exploration and a comprehensive collection of analytical Workflows supporting bioinformatic analysis, data extraction and wet-lab experimental design.

Although several annotations are provided as harmonised reference resources, the accompanying workflows expose the intermediate datasets and processing steps used to generate them. This allows users to reproduce, customise or extend individual analyses to meet the requirements of specific biological questions or analytical pipelines.

📦 eRNAkitDB

The eRNAkitDB object eRNAkitDB.rds contains harmonized eRNA annotations and interaction datasets to support integrative regulatory analysis. It includes post-transcriptional regulatory information across human cell types, experimental techniques and molecules. You can download the eRNAkitDB.rds from the root of the repository.

Below is a summary of each slot.

Foundation

Slot Name Description
core Consensus eRNA annotation (hg38), with genomic coordinates and identifiers. Serves as the central reference set.
E BED formatted companion for the core annotation.
G Gene-level BED formatted annotation for potential mRNA targets.
EOC Tissue- and organ-level eRNA expression quantification and specificty.
loc Sub cellular localisation expression and index (cytoplasm, nucleus, fractions) for eRNAs across cell types.
PAcy Polysome and Ribosome profile infromation for eRNAs.
w100bp_n25 ±100bp window expression of eRNAs across 25 samples of polyA+/-. Serves as valuable resource for designing siRNAs, primers and cloning constructs.
E_sequence FASTA-format eRNA sequences for oligo designs and motif/structure analysis.

Interaction Data

Slot Name Description
R2R RNA–RNA interactions between eRNAs and mRNAs (from KARR-Seq, RIC-seq and PARIS).
R2R_location Exact location of the R2R interactions for feature mapping and motif/structure analysis.
D2D 3D genome interactions linking eRNAs to genes (via Hi-C, derives from TADS).
eRNA2TF eRNA–TF associations from ChIP-seq overlaps (via remap2022).
eRNA2RBP eRNA-RNA-binding protein interactions from eCLIP (via Encode datasets).

Decay and Translation

Slot Name Description
eDecay eRNA RNA decay kinetics from time-resolved transcriptions (via Actinomycin D, set92).
eDecay2mRNA Impact of eRNA half-lives on target mRNA stability (derives from eDecay and R2R).
TE2mRNA Impact of eRNA expression on target mRNA translation efficiency (via RPFdb).

Sequence and Genomic Context

Slot Name Description
TADS Genome wide topologically associating domains (TADS, via Encode). Serves as template for upstream regulations.
Regulome Genome wide regulatory element status across multiple cell types (via Ensemble regulatory build).

A column mapping for the information in these slots can be found inside eRNAkitDB.meta

🔁 Workflows

Several upstream and downstream processing functions are available in the eRNAkit package to support common eRNA analysis workflows. Examples include:

Function Description
R2R() Call RNA-RNA interactions in STAR alignment junction files.
fit_decay2() Model decay kinetics of RNA expression in decay experiments.
eRNkitApp() Launch the interactive eRNAkit Shiny app.
Wet lab support Utility functions to extract information for desiging wet lab experiments such as siRNA, primers and cloning.
DB operations Utility functions to extract standard bioinformatics formats including, gtf, BED4, windows etc

...and many more.

📘 Full documentation and usage examples is available through the standard R manual files.

🖥️ eRNAkitApp

The eRNAkit Shiny app provides an interactive dashboard for exploring the eRNAkitDB. The UI provides multiple search options, including by eRNA, gene and coordinates.

Main programms

The dashboard features buttons to switch views and analyses, including:

Label Content
LOCALISATION eRNA localisation information.
TARGET eRNA-target interactions.
EXPRESSION eRNA expression across primary cells and major tissues.
RIBOSOME Ribosome and polysome association.

Notes

We will add new UI features as we develop the resource. Please, get in touch if you will want to see something implemented. Currently, the UI is most suitable for exploring high confidence interactions for a few eRNAs. For large scale analysis, we recommend using the eRNAkitDB directly which contains extended datasets and annotations.

Citation

For the Foundation components of the package, please cite:
Benova, N., Kuklinkova, R., Eldahshoury, M.K. and Anene, C.A., 2025. ** eRNAkit: Expanding the Functional Atlas of human
Enhancer RNAs Beyond the Nucleus.** bioRxiv, pp.2025-04.
doi: https://doi.org/10.1101/2025.04.25.650683

For eRNA's link to target mRNA stability and translation efficiency, please cite:
Kuklinkova, R., Benova, N. and Anene, C.A., 2026. eRNAs modulate mRNA stability and translation efficiency to bridge
transcriptional and post-transcriptional gene regulation. RNA, 32(5), pp.704-723.
doi: 10.1261/rna.080681.125