Pairing of Homologous Regions in the Mouse Genome Is Associated with Transcription but Not Imprinting Status

This work was funded by the BBSRC, grant BB/H088071/1 (www.bbsrc.ac.uk), MRC, grant G0700760 (www.mrc.ac.uk), Wellcome Trust, grant 095645/Z/11/Z (www.wellcome.ac.uk) and the EU through EpiGeneSys (www.epigenesys.eu) and Blueprint (www.blueprint-epigenome.eu). C.K. was funded by the DFG, personal fellowship KR 3317/2-1 (www.dfg.de) and CTR, personal short term fellowship (www.trophoblast.cam.ac.uk). M.J.H. received funding through grant NCI/NIH 2RO1 CA089426 (www.nih.gov)

From Structure Prediction to Genomic Screens for Novel Non-Coding RNAs

Non-coding RNAs (ncRNAs) are receiving more and more attention not only as an abundant class of genes, but also as regulatory structural elements (some located in mRNAs). A key feature of RNA function is its structure. Computational methods were developed early for folding and prediction of RNA structure with the aim of assisting in functional analysis. With the discovery of more and more ncRNAs, it has become clear that a large fraction of these are highly structured. Interestingly, a large part of the structure is comprised of regular Watson-Crick and GU wobble base pairs. This and the increased amount of available genomes have made it possible to employ structure-based methods for genomic screens. The field has moved from folding prediction of single sequences to computational screens for ncRNAs in genomic sequence using the RNA structure as the main characteristic feature. Whereas early methods focused on energy-directed folding of single sequences, comparative analysis based on structure preserving changes of base pairs has been efficient in improving accuracy, and today this constitutes a key component in genomic screens. Here, we cover the basic principles of RNA folding and touch upon some of the concepts in current methods that have been applied in genomic screens for de novo RNA structures in searches for novel ncRNA genes and regulatory RNA structure on mRNAs. We discuss the strengths and weaknesses of the different strategies and how they can complement each other

Sample Management: Recommendation for best practices and harmonization from the Global Bioanalysis Consortium Harmonization Team

The regulations do not contain much guidance on sample management; however this is a very important aspect in regulatory work. A balanced team was formed to discuss the aspects involved and to put forward recommendations. Sampling conditions should be described in the protocol and in the laboratory manual. Items to be described include volume, anticoagulant, protection from light, labelling. The correct procedures for storing the samples at the clinical site and for shipment of the samples are also very important, along with the accompanying information. The chain of custody for the samples must be maintained throughout the complete lifespan of each sample. Therefore storage location and conditions must also be clearly defined at the analytical lab, pre and post analysis. A transparent way to do this is via a LIMS. The storage temperature of the samples must be traceable and controlled, via freezer monitoring. The team suggests to move away from using temperatures to define the storage condition, but rather move to a standard convention of room temperature, refrigerator, freezer and ultra-freeze