The description of the protein encoded in this ORF: BCL2 protein
The translational frameshift (ribosome slippage) involved: 0
The ribosome read-through involved: no
The alternative forms of this protein occur by the alternative initiation of translation: no
The ORF absolute position (the base range includes START and STOP codons or their equivalents): 1459-2178
The sequence of the BCL2 mRNA (1458b 5'-UTR, 5086b total) corresponds to the sequence in Fig. 3A in Tsujimoto
and Croce, 1986 which has in addition to the GenBank record also the polyA tail stretch. According to Sherrill
et al., 2004, this mRNA sequence corresponds to the so called 5.5 kb variant and should originate from the P1
promoter. The 1458b long 5'-UTR contains an intron, which is only optionally spliced out in vivo.
Excision of the intron does not affect IRES activity (K. Sherrill, personal communication).
BTW, the 3.5kb variant (146b 5'-UTR, 911b total) is stored under GI:179368 and is in Tsujimoto and Croce, 1986
in Fig. 3B.
Back to Sherrill et al., 2004, the transcript integrity was verified by RT-PCR. Cells were transfected by DNA
and also directly by in vitro transcribed mRNA. RNAi targeted against renilla luciferase in the first cistron
was contransfected into the cells to lower background noise by ~80%. Possible promoter presence within part of
the BCL2 5'-UTR studied was examined by use of a promoter-less plasmid (Fig. 3A) and also judged from the
effect of RNAi on levels of Rluc and Fluc (although such result could be biased by the fact aberrant splicing
was detected as pointed above it seems excision of the intron does not affect IRES activity; K. Sherrill,
personal communication). In case of BCL2 and XIAP IRESs it was found that RNAi decreased RLuc luciferase but
not FLuc activity in same scale (Fig. 3B). The Northern blot analysis and RNAi assay confirmed the BCL2 region
studied had a weak promoter activity (should be the P2 promoter described elsewhere?). The experiments have
shown/confirmed that the pRL-BCL2-FL plasmid contains previously known 3' splice acceptor site within the BCL2
region. The presence of the acceptor site resulted in both bicistronic Rluc-BCL2-Fluc mRNA and also Fluc
monocistronic mRNA being produced in vivo. Note: The IRES region studied by Sherrill et al., 2004 was only
1138b upstream the START codon -- instead of 1146b upstream as misreported in the article (K. Sherrill,
personal communication) because longer region could not be amplified by RT-PCR, possibly due to the very high
Additional comments from K. Sherrill:
A key point is that our evidence for BCL-2 IRES activity is based exclusively
upon transfection of mRNA transcripts containing the BCL-2 IRES 5'UTR, and not
DNA transfection. Our RT-PCR results and RNAi work were performed only to
show the dangers inherent with defining an IRES solely by transfecting DNA
alone. The minor BCL-2 promoter that is present within this sequence is not
cryptic, but rather well-defined in the literature. However, it is primarily
active in lymphocytes. There is nothing to be taken "with a grain of salt"
as these data are not the supporting data of the paper. They simply show why
we had to obtain all of our REAL data via direct transfection of capped and
poly-adenylated mRNA, which is to avoid the possibility that promoter and/or
splicing activity might have affected our data.
In addition, I'd like to note that the presence (or absence) of the
alternatively-spliced intron within this BCL-2 5'UTR doesn't appear to
affect IRES activity, as we selectively deleted this intron and saw no
Cammas et al. (2007) used the Bcl2 IRES in their RNAi experiments showing that either the splicing issue or
the promoter make the RNAi-based approach not unsuccessful (Supplemental Figure S2 of their publication).