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Genome-wide computational analysis of potential long noncoding RNA mediated DNA:DNA:RNA triplexes in the human genome

Jalali, Saakshi, Singh, Amrita, Maiti, Souvik, Scaria, Vinod·2017·Journal of Translational Medicine
DOI 10.1186/s12967-017-1282-9PMC PMC7670996
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Fig. 1 Proportion of lncRNAs acting as potential third strand of PTS across GENCODE biotypes. a Distribution of 23,898 GENCODE v19 lncRNAs across six subclasses. b Distribution of 286 lncRNAs forming purine motif c 231 lncRNAs forming pyrimidine motif and d 237 lncRNAs forming mixed motif across the six classes including Antisense, LincRNA, Processed Transcript, Retained Intron, Sense intronic and Sense Overlapping
Fig. 1 Proportion of lncRNAs acting as potential third strand of PTS across GENCODE biotypes. a Distribution of 23,898 GENCODE v19 lncRNAs across six subclasses. b Distribution of 286 lncRNAs forming purine motif c 231 lncRNAs forming pyrimidine motif and d 237 lncRNAs forming mixed motif across the six classes including Antisense, LincRNA, Processed Transcript, Retained Intron, Sense intronic and Sense OverlappingCC BY · PubMed Central
Fig. 2 Distribution of PTS frequency across human chromosomes. a Mapping frequency of potential triplex sites (PTS) across forming purine motif b (PTS) across forming pyrimidine motif c (PTS) across forming mixed motif across Human chromosomes
Fig. 2 Distribution of PTS frequency across human chromosomes. a Mapping frequency of potential triplex sites (PTS) across forming purine motif b (PTS) across forming pyrimidine motif c (PTS) across forming mixed motif across Human chromosomesCC BY · PubMed Central
Fig. 3 Distribution of purine motif forming PTS across the transcription start sites (TSS). a and across the Exon–Intron–Exon boundaries (ESS exon start site and EES exon end site) b of RefSeq genes and genomic features associated with RefSeq genes. Distribution of pyrimidine motif forming PTS across TSS (c) and across ESS and EES (d)
Fig. 3 Distribution of purine motif forming PTS across the transcription start sites (TSS). a and across the Exon–Intron–Exon boundaries (ESS exon start site and EES exon end site) b of RefSeq genes and genomic features associated with RefSeq genes. Distribution of pyrimidine motif forming PTS across TSS (c) and across ESS and EES (d)CC BY · PubMed Central
Fig. 4 a Distribution of purine motif PTS across b pyrimidine motif of RefSeq genes and genomic features associated with RefSeq genes c mixed motif. The frequency of PTS was plotted for five distinct genomic features associated with the genes including 1000 bases upstream of TSS (promoter), 5′ Untranslated region (5′UTR), Protein-coding exon (CDS), Intron, 3′ Untranslated region (3′UTR) and 1000 bases downstream of transcription end site (1000 bp down)
Fig. 4 a Distribution of purine motif PTS across b pyrimidine motif of RefSeq genes and genomic features associated with RefSeq genes c mixed motif. The frequency of PTS was plotted for five distinct genomic features associated with the genes including 1000 bases upstream of TSS (promoter), 5′ Untranslated region (5′UTR), Protein-coding exon (CDS), Intron, 3′ Untranslated region (3′UTR) and 1000 bases downstream of transcription end site (1000 bp down)CC BY · PubMed Central
Fig. 5 a Gel Retardation Assay: duplex DNA incubated alone (lane 1) or with increasing concentrations of RNA TFO depicting gel mobility shift with formation of triplex. b UV melting assay: UV spectra of duplex and triplex (1:3::duplex:RNA TFO) representing the biphasic melting transitions for triplex (red) and single melting peak for duplex (blue curve). c CD spectroscopy: CD spectra of duplex and triplex (1:3::duplex:RNA TFO) represented with blue and red curves respectively, indicating the sharp negative peak obtained at 210 nm for the triplex
Fig. 5 a Gel Retardation Assay: duplex DNA incubated alone (lane 1) or with increasing concentrations of RNA TFO depicting gel mobility shift with formation of triplex. b UV melting assay: UV spectra of duplex and triplex (1:3::duplex:RNA TFO) representing the biphasic melting transitions for triplex (red) and single melting peak for duplex (blue curve). c CD spectroscopy: CD spectra of duplex and triplex (1:3::duplex:RNA TFO) represented with blue and red curves respectively, indicating the sharp negative peak obtained at 210 nm for the triplexCC BY · PubMed Central
Fig. 6 Frequency of a purine motif forming PTS and b pyrimidine motifs PTS across regulatory regions including CpG islands, sites of Transcription Factor binding Clustered V2 (TFBS), Transcription Factor Binding Clustered V3 (TFBS V3), Conserved Transcription Factor binding sites (TFBS Conserved), Literature Curated regulatory regions (Open Regulatory Annotations: ORegAnno) and Enhancers
Fig. 6 Frequency of a purine motif forming PTS and b pyrimidine motifs PTS across regulatory regions including CpG islands, sites of Transcription Factor binding Clustered V2 (TFBS), Transcription Factor Binding Clustered V3 (TFBS V3), Conserved Transcription Factor binding sites (TFBS Conserved), Literature Curated regulatory regions (Open Regulatory Annotations: ORegAnno) and EnhancersCC BY · PubMed Central
Fig. 7 Comparative analysis of the association of a purine motif forming PTS and b pyrimidine motifs forming with different histone modification marks H3K4Me1, H3K4me3 and H3K27Ac
Fig. 7 Comparative analysis of the association of a purine motif forming PTS and b pyrimidine motifs forming with different histone modification marks H3K4Me1, H3K4me3 and H3K27AcCC BY · PubMed Central
Fig. 8 Distribution of a purine motif forming PTS and b pyrimidine motifs forming PTS across the ten different classes of repeats which includes DNA repeat elements (DRE), long interspersed nuclear elements (LINE), low complexity repeats (LCR), long terminal repeat elements (LTR), rolling circle (RC), RNA Repeats (RR), Satellite (Sa), short interspersed nuclear elements (SINE), simple repeats (SR), interrupted repeats (IR) and unknown (UC)
Fig. 8 Distribution of a purine motif forming PTS and b pyrimidine motifs forming PTS across the ten different classes of repeats which includes DNA repeat elements (DRE), long interspersed nuclear elements (LINE), low complexity repeats (LCR), long terminal repeat elements (LTR), rolling circle (RC), RNA Repeats (RR), Satellite (Sa), short interspersed nuclear elements (SINE), simple repeats (SR), interrupted repeats (IR) and unknown (UC)CC BY · PubMed Central

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Metadata

Authors
Jalali, S., Singh, A., Maiti, S., & Scaria, V.
ORCID
Scaria, Vinod
Venue
Journal of Translational Medicine
Publisher
Springer Science and Business Media LLC
Published
2017-09-02
Volume
15
Issue
1
ISSN
1479-5876
DOI
10.1186/s12967-017-1282-9
PMC
PMC7670996
Cited by
37
References
0
Language
en
Licence
creativecommons.org/licenses/by/4.0/ (tdm)
Funders
Council of Scientific and Industrial Research (BSC0123)

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