Sense-antisense pairs in mammals: functional and evolutionary considerations

Analysis of a catalog of S-AS pairs in the human and mouse genomes revealed several putative roles for natural antisense transcripts and showed that some are artifacts of cDNA library construction

RT-PCR analysis for the internal priming (IP) candidates in fetal liver, colon and lung total RNA

<p><b>Copyright information:</b></p><p>Taken from "Sense-antisense pairs in mammals: functional and evolutionary considerations"</p><p>http://genomebiology.com/2007/8/3/R40</p><p>Genome Biology 2007;8(3):R40-R40.</p><p>Published online 19 Mar 2007</p><p>PMCID:PMC1868933.</p><p></p> RT-PCR was conducted in DNA-free RNA previously treated with (lanes 1 and 2) and in untreated RNA, which was, therefore, contaminated with genomic DNA (gDNA; lanes 3 and 4) for each candidate in the corresponding tissue. As a control, RT-PCR was conducted in the presence (lanes 1 and 3) and absence (lanes 2 and 4) of reverse transcriptase. gDNA was used as a positive control of the PCR reaction (lane 5) and no template as a negative control (lane 6). For fetal liver, in 3 IP candidates (5, 8 and 11) the PCR products (152 bp, 153 bp and 160 bp, respectively) were observed in the treated RNA when RT was added (lane 1) or in untreated RNA independent of the RT (lanes 3 and 4). For colon, in 1 IP candidate (9) the PCR product (158 bp) was observed in the treated RNA when RT was added (lane 1) or in untreated RNA independent of the RT (lanes 3 and 4). For the remaining IP candidates (1, 2, 4, 6, 7, 10 and 12), the PCR products (214 bp, 229 bp, 207 bp, 156 bp, 227 bp, 205 bp and 234 bp, respectively) were observed only in untreated RNA independent of the RT (lanes 3 and 4). The PCR products were analyzed on 8% polyacrylamide gels with silver staining. A 100 bp ladder (M) was used as molecular weight marker. In each gel the lower fragment in lane M correspond to 100 bp

Expression pattern (in a set of 31 tissues covered by MPSS) of genes belonging to all three types of S-AS pairs (3'3', 5'5'and embedded)

<p><b>Copyright information:</b></p><p>Taken from "Sense-antisense pairs in mammals: functional and evolutionary considerations"</p><p>http://genomebiology.com/2007/8/3/R40</p><p>Genome Biology 2007;8(3):R40-R40.</p><p>Published online 19 Mar 2007</p><p>PMCID:PMC1868933.</p><p></p> Categories are as follows: 'no expression', for S-AS pairs whose expression was not detected (see Materials and methods for details); 'single-gene expression', for S-AS pairs in which expression is observed for only one gene in the pair; 'co-expression', for pairs in which expression is seen for both genes in the pair. Rate of differential expression for the set of co-expressed S-AS pairs. Ratio of sense/antisense genes in the pair is shown on the x-axis

A potential role for intragenic miRNAs on their hosts' interactome

<p>Abstract</p> <p>Background</p> <p>miRNAs are small, non-coding RNA molecules that mainly act as negative regulators of target gene messages. Due to their regulatory functions, they have lately been implicated in several diseases, including malignancies. Roughly half of known miRNA genes are located within previously annotated protein-coding regions ("intragenic miRNAs"). Although a role of intragenic miRNAs as negative feedback regulators has been speculated, to the best of our knowledge there have been no conclusive large-scale studies investigating the relationship between intragenic miRNAs and host genes and their pathways.</p> <p>Results</p> <p>miRNA-containing host genes were three times longer, contained more introns and had longer 5' introns compared to a randomly sampled gene cohort. These results are consistent with the observation that more than 60% of intronic miRNAs are found within the first five 5' introns. Host gene 3'-untranslated regions (3'-UTRs) were 40% longer and contained significantly more adenylate/uridylate-rich elements (AREs) compared to a randomly sampled gene cohort. Coincidentally, recent literature suggests that several components of the miRNA biogenesis pathway are required for the rapid decay of mRNAs containing AREs. A high-confidence set of predicted mRNA targets of intragenic miRNAs also shared many of these features with the host genes. Approximately 20% of intragenic miRNAs were predicted to target their host mRNA transcript. Further, KEGG pathway analysis demonstrated that 22 of the 74 pathways in which host genes were associated showed significant overrepresentation of proteins encoded by the mRNA targets of associated intragenic miRNAs.</p> <p>Conclusions</p> <p>Our findings suggest that both host genes and intragenic miRNA targets may potentially be subject to multiple layers of regulation. Tight regulatory control of these genes is likely critical for cellular homeostasis and absence of disease. To this end, we examined the potential for negative feedback loops between intragenic miRNAs, host genes, and miRNA target genes. We describe, how higher-order miRNA feedback on hosts' interactomes may at least in part explain correlation patterns observed between expression of host genes and intragenic miRNA targets in healthy and tumor tissue.</p