| Element name | Description | Source | Total count | Method | Cell line |
|---|---|---|---|---|---|
| cCRE (Candidate cis-Regulatory Elements) | Genomic regions with biochemical signatures of regulatory activity (e.g., open chromatin, characteristic histone marks), nominated by ENCODE as putative promoters, enhancers, or insulators. In the lncRNA context they help distinguish whether a phenotype stems from the RNA transcript or an underlying DNA regulatory element. | Moore, Jill E., et al. "Expanded encyclopaedias of DNA elements in the human and mouse genomes." Nature 583.7818 (2020): 699-710. | 926,535 | DNase-seq, ATAC-seq, ChIP-seq (H3K4me3, H3K27ac, CTCF) | Multiple cell and tissue types, refer to the ENCODE data website |
| CpG Islands | Stretches of DNA with high frequency of CG dinucleotides, typically unmethylated and often located at gene promoters/transcription start sites, where they regulate transcription initiation. | Kent, W. James, et al. "The human genome browser at UCSC." Genome research 12.6 (2002): 996-1006. | 31,144 (masked), 55,149 (unmasked) | Computational screening | NA |
| CRS (Conserved RNA Structures) | RNA secondary/tertiary structures whose folding is evolutionarily conserved across species, indicating structurally constrained (and likely functional) regions of a transcript. | Seemann, Stefan E., et al. "The identification and functional annotation of RNA structures conserved in vertebrates." Genome research 27.8 (2017): 1371-1383. | 773,850 | Computational screening | NA |
| MREs/encori (MicroRNA Response Elements) | Short sequence motifs, usually complementary to a miRNA seed, where microRNAs bind; lncRNAs can act as sponges/competing endogenous RNAs by harbouring MREs that sequester miRNAs. | Zhou KR, Liu S, Cai L, Bin L, et al. ENCORI: The Encyclopedia of RNA Interactomes. | 58,538 | CLIP-seq of AGO protein | Multiple cell and tissue types, refer to the ENCORI data website |
| MREs/mircode (MicroRNA Response Elements) | Jeggari, Ashwini, Debora S. Marks, and Erik Larsson. "miRcode: a map of putative microRNA target sites in the long non-coding transcriptome." Bioinformatics 28.15 (2012): 2062-2063. | 1,328,768 (highcons), 1,146,722 (mediumcons) | Computational screening | NA | |
| phastCons | Conserved sequences based on multiple-species genome alignments. | Siepel, A., et al. "Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes." Genome Research 15.8 (2005): 1034-1050. | 1,234,990 (7way), 2,244,053 (20way), 2,949,865 (30way), 10,350,729 (100way) | Computational screening | NA |
| RBP (RNA Binding Protein sites) | Positions where proteins attach to an RNA, marking sequences that mediate RNA–protein interactions and complex assembly. | Please refer to the experiment table | 59,763,508 | eCLIP | HepG2, K562 |
| repeats | Repetitive sequences. | Smit, A., Hubley, R., & Green, P. (2013, 2015). RepeatMasker Open-4.0. http://www.repeatmasker.org | 5,607,738 | Computational screening | NA |
| RIDLS (Repeat Insertion Domains of LncRNA) | Transposable/repetitive elements embedded in lncRNAs that have been exapted to serve as functional domains, contributing roles such as protein binding or subcellular localization. | Carlevaro-Fita, Joana, et al. "Ancient exapted transposable elements promote nuclear enrichment of human long noncoding RNAs." Genome research 29.2 (2019): 208-222. | 5,374 | Computational screening | NA |
| RNA:DNA/R-Loop | A three-stranded nucleic acid structure where an RNA hybridises with one strand of duplex DNA, displacing the other strand as single-stranded DNA. | Sanz, Lionel A., et al. "Prevalent, dynamic, and conserved R-loop structures associate with specific epigenomic signatures in mammals." Molecular cell 63.1 (2016): 167-178. | 88,088 | DRIPc-seq | Ntera2 |
| RNA:DNA/TriplexRNA | A structure where a single-stranded RNA binds within the major groove of double-stranded DNA via Hoogsteen base-pairing. | Sentürk Cetin, Nevcin, et al. "Isolation and genome-wide characterization of cellular DNA: RNA triplex structures." Nucleic acids research 47.5 (2019): 2306-2321. | 12,063 | DNA-IP | HeLaS3, U2OS |
| TFBS | Transcription Factor Binding Sites | Pachkov, Mikhail, et al. "SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates." Nucleic acids research 41.D1 (2012): D214-D220. | 1,322,194 | Computational screening based on deepCAGE, ChIP-chip and ChIP-seq data | NA |
| UCSC literature | DNA sequences extracted from biomedical articles. | Haeussler, Maximilian, Martin Gerner, and Casey M. Bergman. "Annotating genes and genomes with DNA sequences extracted from biomedical articles." Bioinformatics 27.7 (2011): 980-986. | 955,080 | Text-mining | NA |
This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska Curie grant agreement No 884178 (RNADOMAIN)