Project description:Quantitative analysis of the sequence determinants of transcription and translation regulation is of special relevance for systems and synthetic biology applications. Here, we developed a novel generic approach for the fast and efficient analysis of these determinants in vivo. ELM-seq (expression level monitoring by DNA methylation) uses Dam coupled to high-throughput sequencing) as a reporter that can be detected by DNA-seq. We used the genome-reduced bacterium Mycoplasma pneumoniae to show that it is a quantitative reporter. We showed that the methylase activity correlates with protein expression, does not affect cell viability, and has a large dynamic range (~10,000-fold). We applied ELM-seq to randomized libraries of promoters or 5’ untranslated regions. We found that transcription is greatly influenced by the bases around the +1 of the transcript and the Pribnow box, and we also identified several epistatic interactions (including the +1 and the “extended Pribnow”). Regarding translation initiation, we confirmed that the Shine-Dalgarno motif is not relevant, but instead, that RNA secondary structure is the main governing factor. With this in hand, we developed a predictor to help tailor gene expression in M. pneumoniae. The simple ELM-seq methodology will allow identifying and optimizing key sequence determinants for promoter strength and translation. The ELM-seq methodology allows both researchers and companies to identify and optimize in an easy and comprehensive manner, key sequence determinants for promoter strength and translation.

2017-08-29 | PXD005606 | Pride

High-throughput RNA sequencing on circular RNA profiles of human pancreatic cancer cell lines and gemcitabine resistant pancreatic cancer cell lines.

Project description:High-throughput RNA sequencing on circular RNA profiles of human pancreatic cancer cell lines and gemcitabine resistant pancreatic cancer cell lines.

| PRJNA434013 | ENA

Genome-wide transcripts from X chromosome by high throughput sequencing [RNA-Seq]

Project description:Genome-wide transcripts from X chromosome by high throughput sequencing [RNA-Seq]

| PRJNA661459 | ENA

High-throughput RNA sequencing of six ant transcriptomes

Project description:High-throughput RNA sequencing of six ant transcriptomes

| PRJEB21038 | ENA

RNA high-throughput sequencing for Lupinus micranthus Guss

Project description:RNA high-throughput sequencing for Lupinus micranthus Guss

| PRJNA811775 | ENA

High-throughput profiling of human castration-resistant prostate cancer cell lines

Project description:High-throughput profiling of human castration-resistant prostate cancer cell lines