Figure 1.
Properties of novel lncRNAs and protein-coding transcripts with and without antisense transcription.
A. Size distribution of lncRNAs, B. size distribution, C. number of exons, and D. position of introns in annotated transcripts with (black bars) and without (white bars) antisense transcription.
Figure 2.
Genomic distribution of annotated and lncRNA transcripts.
Annotated genes from the BROAD database are depicted in blue and those that are expressed above a threshold of > = 50 reads in our combined datasets are depicted in black. The distribution of all lncRNAs is shown in green and antisense transcripts are shown in red. Large gaps in the gene annotation indicate centromeric regions.
Table 1.
List of lncRNAs differentially expressed in response to light.
Figure 3.
Examples of sense/antisense transcript pairs annotated from RNA sequencing data and validated by qPCR.
Panels display the locations and distribution of RNAseq reads of sense protein-coding (black) and antisense lncRNA (pink) transcripts. RNAseq reads from the WT dark (D), light pulse (L) and temperature pulse (T) samples mapping to each locus are shown; read count scales differ. Below each panel, arrows represent sense (black) and antisense (pink) transcripts. Thick lines represent exons and thin lines introns. Grey boxes indicate the approximate region of each transcript amplified by qRTPCR. Reads are shown for the following sense transcripts and their complementary antisense RNAs: NCU04182 (coding for splicing factor 3 b subunit 4), NCU07268 (coding for a hypothetical protein with PAS domain), NCU02607 (coding for hypothetical protein), NCU07915 (coding for integral membrane protein), NCU09135 (coding for phosphatidylinositol phospholipase C) and NCU09136 (coding for a hypothetical protein. A single antisense transcript overlaps both NCU09135 and NCU09136. The two transcripts antisense to NCU09136 are separated by more than 200 nts.
Figure 4.
qPCR verification of expression of selected sense/antisense pairs.
Expression of both the sense and antisense transcript for NCU04182, NCU07268, NCU02607, NCU07915, NCU09135 and NCU09136 in the WT is shown, after growth in the dark, and exposure to light and temperature pulses. Black bars indicate the protein-coding sense transcript and white bars indicate its antisense transcript. Error bars represent standard deviation. Statistical significance between light vs dark and temperature vs dark was determined using Student t test, * indicates p-value <0.05 and ** indicates p-value < = 0.005. n = 3.