acal is a Long Non-coding RNA in JNK Signaling in Epithelial Shape Changes during Drosophila Dorsal Closure
Figure 3
acal is a processed long non-coding RNA.
(A) acal full-length transcript sequence conservation plot compared to other dipterans, and pairwise alignments between acal in D. melanogaster and its homologs (adapted from the UCSC genome browser). Location of molecular lesions in acal1 (1) and acal2(2) are marked within brackets after an ‘X’ in the transcript (gray arrow). Above the plot is the location of the probes used for small RNA Northern blots in (E) and in S3 Fig. (B) Protein coding potential of acal and other well known coding (white) and non-coding (black) RNAs. pipsqueak (psq) is a transcription factor and basket (bsk) codes for JNK. polished rice (pri) and pncr003 are polycistronic and code for small peptides. roX1 (RNA on the X1), iab-4 (infra-abdominal 4), and Heat shock RNA ω (Hsrω) are long non-coding RNAs. bereft (bft) is a microRNA precursor. Negative values correspond to non-coding scores, and positive values are for protein coding RNAs. Asterisks denote significantly coding or non-coding scores. (C) Semi-quantitative RT-PCR of total [T], cytoplasmic [C], and nuclear [N] RNA against acal, Rp49 (protein coding gene), and bantam microRNA precursor (pre-ban). [G] is the genomic control. (D) Band intensity of acal cytoplasmic and nuclear amplification, compared to total RNA amplification. Means of 5 independent experiments +/− SEM. Significance was assessed using Student’s t test. (E) Small RNA Northern blots for acal A and B probes, using wild type embryos [E] and pupae [P] RNA. Sizes were estimated from 4 independent experiments.
