Full-length mRNA sequencing uncovers a widespread coupling between transcription initiation and mRNA processing

Background: The multifaceted control of gene expression requires tight coordination of regulatory mechanisms at transcriptional and post-transcriptional level. Here, we studied the interdependence of transcription initiation, splicing and polyadenylation events on single mRNA molecules by full-length mRNA sequencing. Results: In MCF-7 breast cancer cells, we find 2700 genes with interdependent alternative transcription initiation, splicing and polyadenylation events, both in proximal and distant parts of mRNA molecules, including examples of coupling between transcription start sites and polyadenylation sites. The analysis of three human primary tissues (brain, heart and liver) reveals similar patterns of interdependency between transcription initiation and mRNA processing events. We predict thousands of novel open reading frames from full-length mRNA sequences and obtained evidence for their translation by shotgun proteomics. The mapping database rescues 358 previously unassigned peptides and improves the assignment of others. By recognizing sample-specific amino-acid changes and novel splicing patterns, full-length mRNA sequencing improves proteogenomics analysis of MCF-7 cells. Conclusions: Our findings demonstrate that our understanding of transcriptome complexity is far from complete and provides a basis to reveal largely unresolved mechanisms that coordinate transcription initiation and mRNA processing. Electronic supplementary material The online version of this article (10.1186/s13059-018-1418-0) contains supplementary material, which is available to authorized users

Loss of ZNF148 enhances insulin secretion in human pancreatic β cells

Insulin secretion from pancreatic β cells is essential to the maintenance of glucose homeostasis. Defects in this process result in diabetes. Identifying genetic regulators that impair insulin secretion is crucial for the identification of novel therapeutic targets. Here, we show that reduction of ZNF148 in human islets, and its deletion in stem cell-derived β cells (SC-β cells), enhances insulin secretion. Transcriptomics of ZNF148-deficient SC-β cells identifies increased expression of annexin and S100 genes whose proteins form tetrameric complexes involved in regulation of insulin vesicle trafficking and exocytosis. ZNF148 in SC-β cells prevents translocation of annexin A2 from the nucleus to its functional place at the cell membrane via direct repression of S100A16 expression. These findings point to ZNF148 as a regulator of annexin-S100 complexes in human β cells and suggest that suppression of ZNF148 may provide a novel therapeutic strategy to enhance insulin secretion

Additional file 2: of Full-length mRNA sequencing uncovers a widespread coupling between transcription initiation and mRNA processing

Reviewer reports and authors’ response to reviewers. (DOCX 30 kb

Occupational exposure to crystalline silica and risk of lung cancer: a multicenter case-control study in Europe.

BACKGROUND: The role of crystalline silica dust as a possible cause of lung cancer has been controversial. Relatively few large community-based studies have been conducted to investigate the lung cancer risk from exposure to silica at low levels, taking into account potential confounding factors. METHODS: Detailed lifestyle and occupational information were collected from 2852 newly diagnosed cases of lung cancer and 3104 controls between 1998 and 2002 in 7 European countries. For each job held, local experts assessed the probability, intensity, and duration of silica exposure. RESULTS: Occupational exposure to crystalline silica was associated with an increased risk of lung cancer (odds ratio = 1.37; 95% confidence interval = 1.14-1.65). This risk was most apparent for the upper tertile of cumulative exposure (OR = 2.08; 95% CI = 1.49-2.90; P for trend <0.0001), duration of exposure (1.73; 1.26-2.39; P for trend = 0.0001) and weighted duration of exposure (1.88; 1.35-2.61; P for trend <0.0001). We did not observe any interaction beyond a multiplicative model between tobacco smoking and silica exposure. CONCLUSIONS: Our results support the hypothesis that silica is an important risk factor for lung cancer. This risk could not be explained by exposure to other occupational carcinogens or smoking, and it was present for the main histologic types of lung cancer, different sources of silica exposure, and different industrial settings

The number of <i>cis-</i>regulated tags per gene.

<p>The percentages of cis-regulated tags mapping into the same gene are indicated (781 genes overall). For nearly half of the genes (48%) only one tag shows an eQTL effect. If multiple tags map within the same gene, only one eQTL tag should pass the FDR<0.05 significance threshold while the other tag could be less significant. For these eQTLs the allelic direction is shown: same allelic direction (multiple tags within the same gene are cis-regulated by a SNP in the same direction), significantly opposite allelic direction (multiple tags within the same gene are cis-regulated by a SNP but with opposite directions and the difference between the correlation coefficients is significant), or opposite allelic direction but not significant (if the difference between correlation coefficients is not significant).</p

<i>Cis-</i>regulating SNPs significantly^* affecting multiple tags of the same gene in opposite directions.

*<p>Only significant eQTLs with FDR<0.05 for both <i>cis-</i>regulated tags were used.</p

Number of detected <i>cis-</i>eQTLs in transcript-wise analysis of three harmonized RNA NGS datasets.

<p>Number of detected <i>cis-</i>eQTLs in transcript-wise analysis of three harmonized RNA NGS datasets.</p