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. 2021 Feb 3;11:627007. doi: 10.3389/fgene.2020.627007

Figure 5.

Figure 5

Characterization of FAM247A/C/D and linc-UR-B1 molecules. (A) Analysis of FAM247 transcripts in liver. Right gel, 3’ of cDNA Ends (3’RACE). Complementary DNA (cDNA) was obtained by oligo-dT reverse transcription (RT) of polyA+ liver RNA. PCR was performed on this cDNA using the forward (A_FW1) and reverse (AUAP_RV) primers indicated on the schematic above. Several bands were obtained, including the expected 666 bp. Left gel, specific RT-PCR (spRT-PCR). cDNA was obtained from polyA+ liver RNA using a primer designed on the USP18 3’UTR (3UTR_GSP1). PCR was then performed using the forward primer (A_FW1 or A_FW2) and a reverse primer designed on the 3’UTR (3UTR_RV) and internal to 3UTR_GSP1. The length in nt is indicated above each amplified product. (B) Analysis of linc-UR-B1 transcripts in testis. The strategies described in (A) were used on testis poly A+ RNA. Primers are indicated on the schematic above. The length in nt is indicated above each amplified band. (C) Study of linc-UR-B1 transcript extending on the 5’ end. Three forward primers were designed on the annotated intergenic region (B_FW3-4-5). One primer (B_FW6) was designed on the sequence further upstream, corresponding to exon 6 of the annotated NR_135922 transcript. Right panel, 3’RACE on testis RNA. The 537 nt product obtained using the B_FW6 primer corresponds to the annotated NR_135922. Longer products indicated by arrowheads were obtained when using the three primers designed in the intergenic region. Left panel, spRT-PCR was performed on testis RNA using the indicated forward primers and the 3UTR_RV primer. PCR products of the expected lengths were obtained for all primers tested. Panels (A–C): the PCR products of the size expected from the annotations were sequenced. The additional 3’RACE PCR products likely result from the amplification of other transcripts containing sequences identical to the exon upstream of USP18 exon11 (Supplementary Table S1). (D) Schematic of the 3’ end of the two NR_135922 isoforms identified here. Top, the NR_135922 transcript terminating with exon 6, as in the annotation. Bottom, longer isoform of NR_135922 terminating with the USP18 3’UTR, here called linc-UR-B1. The sequences of FAM247A/C/D and linc-UR-B1 are provided as Supplementary Information.