TATA and paused promoters active in differentiated tissues have distinct expression characteristics

Core promoter types differ in the extent to which RNA polymerase II (Pol II) pauses after initiation, but how this affects their tissue‐specific gene expression characteristics is not well understood. While promoters with Pol II pausing elements are active throughout development, TATA promoters are highly active in differentiated tissues. We therefore used a genomics approach on late‐stage Drosophila embryos to analyze the properties of promoter types. Using tissue‐specific Pol II ChIP‐seq, we found that paused promoters have high levels of paused Pol II throughout the embryo, even in tissues where the gene is not expressed, while TATA promoters only show Pol II occupancy when the gene is active. The promoter types are associated with different chromatin accessibility in ATAC‐seq data and have different expression characteristics in single‐cell RNA‐seq data. The two promoter types may therefore be optimized for different properties: paused promoters show more consistent expression when active, while TATA promoters have lower background expression when inactive. We propose that tissue‐specific genes have evolved to use two different strategies for their differential expression across tissues.     

Characterisation of sequences required for RNA initiation from the PGK promoter of Saccharomyces cerevisiae.

In the phosphoglycerate kinase (PGK) gene of yeast, as in other highly expressed yeast genes, the sequences surrounding the site of RNA initiation have a loosely conserved structure of a CT rich stretch followed by the tetranucleotide CAAG. Using internal deletions and insertions we have identified the elements in the PGK promoter which are required for correct RNA initiation at the CAAG sequence at -39. The results indicate that two different components of the PGK promoter contribute to correct RNA initiation, the TATA homologies, located at -152 and -113, and the sequences at the site of initiation. Both TATA elements can function in RNA initiation. Deletion of the upstream TATA element, TATAI, results in slightly heterogeneous RNA initiation, but the majority of the RNA initiates correctly. Deletion of both the PGK TATA elements results in the majority of the RNA initiating at sites downstream from the wild-type I site, within the structural gene between +40 to +80. The CT rich box is not essential for correct mRNA initiation as shown by deletion analysis. The site of RNA initiation in the PGK promoter appears to be determined by sequences located immediately 5' of the CAAG sequence motif. This short sequence, ACAGATC, when located the correct distance from the TATA elements may be sufficient to determine a discrete initiation site.     

Organization and expression of the two homologous genes encoding the NADP-malate dehydrogenase in Sorghum vulgare leaves

Summary We previously described the isolation and the nucleotide sequence of a nuclear gene from sorghum (NMDHI; 4.6 kb) encoding the NADP-malate dehydrogenase. Further analysis led us to identify a second homologous gene (NMDH II; 4.8 kb) located within the same 12.3 kb genomic clone (LM17); these two genes are tandemly organized, in direct orientation. This second gene was entirely sequenced and comparison with the first gene showed that the positions on the 14 exons and 13 introns are conserved in both genes. The analysis of the genomic organization and copy number in the Sorghum vulgare genome revealed that there are no additional homologues and there is only one copy each of NMDH I and NMDH II. The isolation of two different cDNA clones in a previous work suggested that both genes were probably expressed. Analysis of specific mRNA accumulation during the greening process using synthetic oligonucleotide probes showed that the NMDH I gene is induced in the presence of light while the NMDH II gene seems to be constitutively expressed at low level.Abbreviations Cab chlorophyll a/b binding protein - CTAB N-cetyl-N,N,N-trimethyl-ammonium bromide - NADP-MDH NADP-dependent dehydrogenase - RbcS ribulose-1,5-bisphosphate carboxylase small subunit - SSC 0.15 M NaCl, 0.015 M sodium citrate pH 7.6     

Transcriptome analysis of the endometrium from Chinese Erhualian sows that differ in calcium ion concentration and litter size

Embryonic survival rate, an important factor in the fecundity of sows, is affected by endometrium‐secreting histotroph. A higher concentration of calcium ion has been observed in the uterus of highly prolific Erhualian sows (EH) compared with those of less prolific (EL) sows. This suggests that EH sows have better establishment and maintenance of pregnancies, thus increasing embryonic survival rate during the peri‐implantation period. To understand the mechanisms of how the endometrium‐secreting histotroph affects embryonic survival rate during the Erhualian peri‐implantation period, the expression patterns of endometrial mRNA in the EH and EL sows on day 12 of gestation were analyzed using RNA sequencing technology. A total of 164 differentially expressed genes (DEGs) were identified (P_adj < 0.05, |log₂(FC)| ≥ 1), including 46 upregulated and 118 downregulated genes in EH compared to EL. Gene Ontology enrichment indicated that a subset of DEGs was involved in calcium ion binding and cell adhesion. Solute carrier family 8 member A3 and solute carrier family 24 member 4, identified as upregulated genes (P_adj < 0.05) in EH, were considered key candidate genes expressed in the endometrium affecting embryonic survival rate during the peri‐implantation period. The results improve understanding of the genetic mechanism underlying the variation in litter size of Erhualian pigs during the peri‐implantation period.     

Codon usage and gene expression pattern of Stenotrophomonas maltophilia R551-3 for pathogenic mode of living

Stenotrophomonas maltophilia strain R551-3 is a multiple-antibiotic-resistant opportunistic human pathogen involved in nosocomial infections. It has a widely distributed GC-rich (>66%) genome. Analysis of differential expression of the genes of this genome reveals that majority of genes belonging to highly expressed category are mostly present on lagging strand without showing any strand specific codon usage bias. Relatively small number of lowly expressed genes is equally distributed on both leading and lagging strands with a difference in codon usage pattern between them. Among several multi drug resistance genes of S. maltophilia involving lowly expressed category some are predicted as horizontally transferred. It can be inferred that horizontally transferred genes may have been imported into this genome for their pathogenic mode of living. Our study may help to modify the expression level of the target genes of this human pathogen in order to control its infection.     

Evolution of Chilean colonizing populations of <Emphasis Type="Italic">Drosophila subobscura</Emphasis>: lethal genes and chromosomal arrangements

Knowledge of the frequency, distribution, and fate of lethal genes in chromosomal inversions helps to illuminate the evolution of recently founded populations. We analyze the relationship between lethal genes and inversions in two colonizing populations of D. subobscura in Chile. In the ancestral Palearctic populations of this species, lethal genes seem distributed at random on chromosomes. But in colonizing American populations, some lethal genes are associated with specific chromosomal arrangements. Some of these associated lethals were detected only during the first stages of the colonization (O ₃₊₄₊₂ ), and never thereafter, whereas others have persisted (O ₃₊₄₊₇ and O₅). However, most lethal genes in American populations have been observed only once: they have arisen by novel mutation and soon disappear. Finally, recombination between different inversions has been observed in America. However, the persistence of lethal genes associated with the heterotic inversions O ₃₊₄₊₇ and O₅ could indicate that recombination inside these inversions is rare. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.