Turnover of aRNAs is influenced by CPT.

<p>Cells where firstly stimulated for antisense accumulation by a 4 hours treatment with CPT (time 0). Successively CPT was removed (black lines) or maintained (red lines) in the medium. In addition, FLV was added to block transcription in absence (green lines) and in presence (blue lines) of CPT, and antisense transcript levels determined by rtqPCR after additional 20, 40 and 60 minutes. PCR determinations were normalized to β-actine mRNA and to aRNAs levels at time 0. A representative experiment is here reported.</p

R-loops are transiently stabilized and extended by Top1 inhibition by CPT.

<p>R-loop levels as determined by DRIVE at selected genomic regions and active promoters. DNA enrichment of each sample is subtracted of the enrichment value of the same sample treated with RNaseH1 before DRIVE precipitation. Then the enrichment value is normalized against the maximum enrichment value (2-min CPT sample of the RPL13A amplicon) obtained in the same experiment. Values are means ±SEM of two to four independent experiments. (A) R-loop levels at active promoters (on the left) and mitochondrial regions (on the right) after 2 min, 10 min and 4 hours of treatment with 10μM CPT. Control cells are as reported in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0147053#pone.0147053.g001" target="_blank">Fig 1A and 1B</a> to better appreciate variation after drug treatment. (B) R-loop formation at sites close to transcription start site of TAF4 and PCIF1 genes in a time course experiment of CPT treatments. Genome browser views show the genomic localization of the analyzed regions (right panel). DNA digestion with a cocktail of restriction enzymes guarantee the studied regions are properly separated. One representative experiment for each locus is here reported.</p

CPT modulates sense transcription in a particular subset of genes.

<p>Sense tags distribution along non-overlapping Refseq genes of HCT116 cells and HCT116-shRNATop1 cells, were analyzed in a region from 2000 bases upstream the TSS to 2000 bases downstream the TES using NGSplot software. Here, genes have been divided in two groups based on their FPKM. These genes have been selected for an accumulation of sense reads in the 5’ region (CPT-reads minus Control-reads: 10 ≥ 100) and a reduction of sense reads at the 3’ region (CPT-reads minus Control-reads: ≤ 5). Furthermore, genes selected have a fold change above 2 and a minimum number of sense reads above 5 in the 5’ region of CPT treated sample. Reads were normalized to the length of each region (1000 bp). Control reads are reported in gray dotted line and CPT reads in black line. Black arrows indicate an accumulation or not of reads at 5’ level after CPT treatment (10 μM for 4 hours).</p

CPT interferes with sense transcription at 5’-end of genes.

<p>Sense tags distribution along non-overlapping Refseq genes of HCT116 and HCT116-shRNATop1 cells, were analyzed in a region from 2000 bases upstream the TSS to 2000 bases downstream the TES using NGSplot software. Here are reported genes whose FPKM value is below 0,3 up to 500 divided in four groups. Control reads are reported in black lines and CPT reads in red lines.</p

Antisense transcript levels in HCT116 cells overexpressing wt or mutated RNaseH1.

<p>Promoter-associated antisense transcripts were evaluated by rtqPCR after 4 hours CPT treatment at 10μM in cells overexpressing a wt or a mutated RNaseH1. PCR determinations were normalized to cytochrome b mRNA and to untreated cells (dotted line). Values are means +/− SEM of two determinations from at least two independent experiments.</p

Antisense transcript levels induced by CPT in replicating HCT116 and WI38, and in quiescent WI38 cells.

<p>Promoter-associated antisense transcripts were determined by rtqPCR after 4 hours of CPT treatment at 10 μM. PCR determinations were normalized to cytochrome b mRNA and to untreated cells (dotted line). Values are means +/− SEM of two determinations from at least two independent experiments (* <i>P</i> <0.05).</p

R-loop formation at the studied genomic and mitochondrial regions in untreated control N-TERA-2 cells.

<p>DNA enrichment of each sample is subtracted of the enrichment value of the same sample treated with RNase H1 before DRIVE precipitation. Then the enrichment value is normalized against the 2-min CPT sample (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0147053#pone.0147053.g002" target="_blank">Fig 2</a>) of the RPL13A amplicon of the same experiment. Values are means ±SEM of two to four independent experiments. The data show a higher SEM than commonly published as we report median values of several experiments and not a single representative one. (A) DRIVE assay was performed to determine R-loop levels downstream TSS (white bars) and upstream TSS (black bars). Three negative loci for R-loop formation are also reported (SNRPN, a-SAT, TNIK). (B) Mitochondrial DNA was analyzed with DRIVE assay. Three regions of interest were selected: red for the r-loop forming region (RB31-R3), green for the D-loop region (1A-1B) and blue for the non-D-loop region (4A-4B). Map on the right of the panel shows the heavy (H) and the light (L) strands of mitochondrial DNA, with the three Conserved Sequence Blocks (CSB) and the studied regions (in red, green and blue respectively). (C) Antisense transcription after CPT treatment in N-TERA-2 cells. Promoter-associated antisense transcripts were evaluated by rtqPCR after 4 hours CPT treatment at 10 μM. PCR determinations were normalized to cytochrome b mRNA and to untreated cells (dotted line). Values are means +/− SEM of two determinations from at least two independent experiments.</p

Closing the gap: An empirical evidence on firm&#039;s innovation, productivity, and export

It is well known that exporters are productive firms. But the source of their productivity is left unexplained. This paper aims to endogenize the productivity heterogeneity of exporting firms by incorporating innovation in a structural model framework. In doing so, we close the gap between the innovation-productivity and productivity-export literature. Two waves of Swedish Community Innovation Survey (CIS) are merged. This allows for a dynamic setup that takes into account the proper lags from innovation input to innovation output and also from innovation output to productivity and export. The applied framework corrects for selectivity, simultaneity, and potential endogeneity biases. The main findings highlight that exporters are productive firms with innovation output in the past, which in turn was driven by prior R&amp;D and other innovation activity investments

Additional file 6: of Transcriptional profiling of human bronchial epithelial cell BEAS-2B exposed to diesel and biomass ultrafine particles

Table S3. FC and p-value of the genes differentially expressed after exposure to UFP from biomass combustion (as compared to controls) at the different time points. (XLS 3855 kb

Additional file 5: of Transcriptional profiling of human bronchial epithelial cell BEAS-2B exposed to diesel and biomass ultrafine particles

Table S2. FC and p-value of the genes differentially expressed after exposure to UFP from diesel combustion (as compared to controls) at the different time points. (XLS 3855 kb