baerhunter: an R package for the discovery and anal-ysis of expressed non-coding regions in bacterial RNA-seq data

Summary: Standard bioinformatics pipelines for the analysis of bacterial transcriptomic data com-monly ignore non-coding but functional elements e.g. small RNAs, long antisense RNAs or untrans-lated regions (UTRs) of mRNA transcripts. The root of this problem is the use of incomplete genome annotation files. Here, we present baerhunter, a coverage-based method implemented in R, that au-tomates the discovery of expressed non-coding RNAs and UTRs from RNA-seq reads mapped to a reference genome. The core algorithm is part of a pipeline that facilitates downstream analysis of both coding and non-coding features. The method is simple, easy to extend and customize and, in limited tests with simulated and real data, compares favourably against the currently most popular alternative. Availability: The baerhunter R package is available from: https://github.com/irilenia/baerhunter Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online

Using a whole genome co-expression network to inform the functional characterisation of predicted genomic elements from Mycobacterium tuberculosis transcriptomic data

A whole genome co-expression network was created using Mycobacterium tuberculosis transcriptomic data from publicly available RNA-sequencing experiments covering a wide variety of experimental conditions. The network includes expressed regions with no formal annotation, including putative short RNAs and untranslated regions of expressed transcripts, along with the protein-coding genes. These unannotated expressed transcripts were among the best-connected members of the module sub-networks, making up more than half of the ‘hub’ elements in modules that include protein-coding genes known to be part of regulatory systems involved in stress response and host adaptation. This dataset provides a valuable resource for investigating the role of non-coding RNA, and conserved hypothetical proteins, in transcriptomic remodelling. Based on their connections to genes with known functional groupings and correlations with replicated host conditions, predicted expressed transcripts can be screened as suitable candidates for further experimental validation

Induced Metastable Memory in Heat Shock Response

We studied the dynamics of the Heat Shock Response (HSR) mechanism, and the persistence of a injury-protected state in the cell following the shocks, known as thermotolerance. A series of double shock experiments were performed on Chinese Hamster Ovary (CHO) cells, tracking the dynamics of some components of HSR pathway (the Hsp70 protein level and Hsp70 mRNA transcription rate). The main features of HSR dynamics were well reproduced by a simplified model of the chemical reaction pathways governing the HSR. In particular, the thermotolerance phenomenon could be well characterized by introducing a shock-dependent switch in mRNA halflife, that can be interpreted as a sort of primitive memory at the mRNA level