a Knuckle-downstream orientation.
Two operational orientations of the lifted pantograph are considered in each position: the knuckle-downstream orientation and the knuckle-upstream orientation, as shown in Fig. 6.
A detailed analysis of genomic architecture allowed us for the first time to demonstrate that lncRNAs in downstream-associated orientations towards protein coding genes tend to correlate negatively with the protein coding genes, while intronic antisense transcripts were equally represented as positively and negatively correlating.
Reminding everyone of what work was done "upstream" and what will need to be done "downstream" provides critical orientation and keeps the conversation focused.
Similarly, spontaneous genetic rearrangements were observed in E. coli when cDNA encoding the 5' fragment of the West Nile virus (WNV) genome was cloned in the direct orientation downstream from bacterial promoters, but not in the opposite orientation, suggesting that the characteristic flavivirus genetic instability was caused by viral gene product toxicity to the bacterial cells [12].
Pairing rescue was also performed, which uses one aligned tag as an anchor and searches for the other tag in a nearby window (of 1.4 3.7 kb, either upstream or downstream, depending on orientation of the anchored tag) with more relaxed criteria.
The PCR product was then purified and cloned in a sense orientation downstream of the T7 promoter of pDrive vector (QIAGEN).
Two 197 bp DNA fragments homologous to the PPV genome were placed in inverted orientation downstream from the 1182 bp DNA fragment containing the promoter of the RolC gene of Agrobacterium rhizogenes strain A4.
Presence of the insert in the correct orientation downstream from the FMV promoter was confirmed by PCR using the FMV-specific primer FMV-F (Additional file 3: Table S3) and the A. thaliana gene-specific reverse primer.
In the opposite orientation, downstream of the 3′ Ds repeat sequences, a short glial fibrillary acidic protein (GFAP) promoter (consisting of 360 bp of upstream sequence and the entire 16 bp 5′UTR) was sub-cloned into the pDs vector, preceding a lox2272 site and EGFP sequences, and followed by an SV40 polyA signal.
