Fig. 7: Molecular interaction involving BASP1-AS1, BASP1 genomic locus, and transcription factor TCF12. | Cell Death Discovery

Fig. 7: Molecular interaction involving BASP1-AS1, BASP1 genomic locus, and transcription factor TCF12.

From: Temporal transcriptome analysis of neuronal commitment reveals the preeminent role of the divergent lncRNA biotype and a critical candidate gene during differentiation

Fig. 7

a Bar graph showing BASP1-AS1 retrieval after ChIRP followed by qPCR showed that ChIRP retrieved about 80% of BASP1-AS1 RNA, while GAPDH was almost undetectable. b Pulldown of different genomic regions of BASP1. Regions of the BASP1 gene corresponding to R3, R11, and R14 were enriched maximally. R3 that is located at the 5′ end and R11 and R14 at the 3′ end of the 58-kb BASP1 gene showed the maximum pulldown. R1, R2, R4–R10, and R12 and R13 had undetectable levels of the target (n = 3 biological replicates, mean ± SD). c Hi-C data of GM12878 represent loop formation at the genomic locus of BASP1. This image was generated using Juicebox package. The GM12878 cells Hi-C data set was used to visualize the contact domain within the BASP1 gene locus. The matrix with a resolution of 0.5 kb is shown, indicating genomic locations of BASP1 and LOC285696 (BASP1-AS1—chr5: 172717224-17219214), CTCF sequence orientation (red represents “reverse”—chr5: 17216900 and green represents “forward” orientation—chr5: 17283500), and CTCF-binding track. The presence of a chromatin loop is indicated in the track with annotated peaks (cyan, peak1—chr5: 17220001-17230000 and peak2—chr5: 17270001-17280000). Chromatin loops are frequently anchored with the convergent CTCF motifs; here at BASP1 genomic locus, both the CTCF sequences read in a convergent fashion as shown in panels 2 and 3. d Image adopted from UCSC browser showing proximity of DYX1C1 and TCF12, both genes being components of the DYX1 locus. e Enrichment of the R11 region of the BASP1 gene after ChIP analysis following TCF12 pulldown, indicating binding of TCF12 to the specific region (n = 3 biological replicates, mean ± SD). f The E-box-binding domain on the R11 fragment (red) that has been earlier predicted to bind to TCF12. g A regulatory model showing the interaction of BASP1-AS1 RNA, BASP1, and TCF12 and possible other transcription factors, to form a looped structure.

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