While in bacteria, TA-like signals are identified at around 12 bp upstream to the TIS, and have a consensus of TANNNT, which resembles the -10 box of σ70 factor binding site "TAtaaT" in E. coli [ 17].
After Weber et al. (2007), we extracted regions from 700 bp upstream to 200 bp downstream around transcription start sites of the genes.
As putative promoters we defined the sequences located from 2000 bp upstream to 2000 bp downstream around ENSEMBL predicted transcription start sites (TSSs) of genes (according to ENSEMBL database, version 42).
GC content and phastCons score: For each gene, we retrieved a genomic region with a length of 8-kb DNA sequence spanning from 4-kb upstream to 4-kb downstream around 5′TSS.
In archaea, it has been discussed that TA-like signals at around 30 bp upstream to the TIS mean leaderless genes, which use leaderless initiation.
We found that deletion of 9 kb of the Xist upstream region (Δ5') leads to around 20% loss of methylation in both region 1 and region 2.
However, because the distal enhancers are juxtaposed to sequences upstream and around the MYC transcription start site, perhaps a more detailed analysis of Wnt responsive elements within the proximal promoter is warranted.
"Luckily they are safe, but the water level has risen covering all the houses up to around a kilometre upstream of the landslide," Bam said.
It also retrieves all values inside each annotation, scale them to the same length, and add the half of values computed around TSS upstream and around TES downstream the annotation to obtain profiles as shown in Figure 2C.
We found that autosomal genes predicted to be subject to inactivation were depleted of Alus upstream of and around the transcription start site (TSS) in addition to within the gene body, but that Alus were enriched in the large domains of multiple escape genes.
