Fig. 3: Identification and functional characterization of novel lncRNA loc285696 (BASP1-AS1). | Cell Death Discovery

Fig. 3: Identification and functional characterization of novel lncRNA loc285696 (BASP1-AS1).

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

Fig. 3

a Schematic diagram of the BASP1-AS1 lncRNA and its coding partner BASP1. Fickett score and ORF coverage of 50 coding and noncoding transcripts, and comparison of these scores with the BASP1-AS1 transcript, indicates that it is a noncoding transcript. b Table showing BASP1-AS1 coding potential values and its cutoff using different coding potential calculators. For PhyloCSF, a score lower than 41 represents that the transcript is noncoding; a score above the cutoff is likely to be coding. PhyloCSF value was taken from LNCpedia with ID: lnc-BASP1–9, location (hg19): chr5:17202383-17203254. In the same manner for CPC, a score equal to or lower than zero cutoff means that the transcript is noncoding. Same is the cutoff for CPAT, where a score near zero indicates that it is noncoding. By all the three indications, BASP1-AS1 is a noncoding transcript. c Nuclear and cytosolic fractionation followed by RT-qPCR for indicated mRNAs and for BASP1-AS1 (represented as log2 expression values). The result indicates nuclear localization of the BASP1-AS1 as a feature of lncRNAs. As expected, control GAPDH was cytoplasmic, while unspliced GAPDH and U6 were predominantly nuclear (n = 3, mean ± SD of three independent experiments). d Localization of BASP1-AS1. Reads per kilobase per million (RPKM) values for BASP1-AS1 transcript (AC091878.1) in indicated tissue samples, as obtained from the GTEx RNA-seq database indicated that it was mainly expressed in the CNS and whole blood. e ISH for BASP1-AS1 in human SVZ fetal brain sections, indicating its expression in human fetal brain.

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