Genomic environments scale the activities of diverse core promoters

One model for how cells integrate cis-regulatory information is that different classes of core promoters respond specifically to certain genomic environments. We tested this model using a genome-integrated massively parallel reporter assay (MPRA) to measure the activity of hundreds of diverse core promoters at four genomic locations and, in a complementary experiment, six core promoters at thousands of genomic locations. While genomic locations had large effects on expression, the relative strengths of core promoters were preserved across locations regardless of promoter class, suggesting that their intrinsic activities are scaled by diverse genomic environments. The extent of scaling depends on the genomic location and the strength of the core promoter, but not on its class. Our results support a modular genome in which genomic environments scale the activities of core promoters.One Sentence SummaryGenomic environments have consistent effects on gene expression that depend on the strength, but not the class of core promoter.

Multiple Alignment of Promoter Sequences from the Human Genome

A new algorithm for multiple alignment of nucleotide sequences of MAHDS has been developed. A statistically significant multiple alignment of promoter sequences from the human genome was first created using this algorithm. Based on the constructed alignments, 25 classes of promoter sequences were created with the volume of each class exceeding 100 sequences. The classes of promoters can be used to search for promoter sequences in eukaryotic genomes. promoter, class, dynamic programming, human genome. The work was partially supported by the Russian Foundation for Basic Research (Grant no. 20-016-00057).

Promoter scanning during transcription initiation in Saccharomyces cerevisiae: Pol II in the “shooting gallery”

ABSTRACTBackgroundThe majority of eukaryotic promoters utilize multiple transcription start sites (TSSs). How multiple TSSs are specified at individual promoters across eukaryotes is not understood for most species. In S. cerevisiae, a preinitiation complex comprised of Pol II and conserved general transcription factors (GTFs) assembles and opens DNA upstream of TSSs. Evidence from model promoters indicates that the preinitiation complex (PIC) scans from upstream to downstream to identify TSSs. Prior results suggest that TSS distributions at promoters where scanning occurs shift in a polar fashion upon alteration in Pol II catalytic activity or GTF function.ResultsTo determine extent of promoter scanning across promoter classes in S. cerevisiae, we perturbed Pol II catalytic activity and GTF function and analyzed their effects on TSS usage genome-wide. We find that alterations to Pol II, TFIIB, or TFIIF function widely alter the initiation landscape consistent with promoter scanning operating at all yeast promoters, regardless of promoter class. Promoter architecture, however, can determine extent of promoter sensitivity to altered Pol II activity in ways that are predicted by a scanning model.ConclusionsOur observations coupled with previous data validate key predictions of the scanning model for Pol II initiation in yeast – which we term the “shooting gallery”. In this model, Pol II catalytic activity, and the rate and processivity of Pol II scanning together with promoter sequence determine the distribution of TSSs and their usage.

Role of tobacco vacuolar invertase regulated by patatin promoter in potato tuber resistance to cold sweetening

To slow down the accumulation of reducing sugar in potato tubers exposed to low-temperature storage, an expression vector, pBICNI, including Nt-VIF (Nicotiana tabacum vacuolar inhibitor of beta fructosidase, a vacuolar invertase inhibitor from Nicotiana tabacum) gene regulated by potato tuber specific promoter class I patatin promoter (CIPP) was constructed and transformed into potato (Solanum tuberosum L.) cultivar E-potato 3 (E3). Detection by polymerase chain reaction (PCR), Northern and Southern hybridizations indicated that the full-length Nt-VIF cDNA was transformed successfully into cv. E3. After storing potato tubers of 14 transgenic lines at 4 or 20°C for 30 days, their activities of vacuolar invertase (VI) and reducing sugar (RS) content were analysed. The results showed that there were no significant differences in RS content between transgenic and untransformed (control) tubers stored at 20°C. However, RS content of transgenic lines was obviously reduced at 4°C compared to the control, from 34.0% (line B-13) to 76.8% reduction (line B-1), implying that VI activity was inhibited by Nt-VIF cDNA expression and RS content was reduced. Further analysis revealed a positive linear relationship between VI activity and RS content (VI=0.308RS+0.067), and lines B-1, B-2, B-6, B-9 and B-14 could meet the requirements of potato chips in terms of their low RS content after cold storage.