The CIGENE journal club reviews and discuss new and old scientific papers within genetics, genomics, comparative omic’s, bioinformatics, and computational biology. Basically all the good stuff. Feel free to get inspired and read small comments on past club-papers. We meet at H249 (meeting room, 2nd floor IHA over the canteen) at 11 every other Wednesday.
Paper 3 – 2018: Dag Inge – 14th February
di Julio et al, The Human noncoding genome defined by genetic diversity.
Very interesting paper that Analyse reseq datasets from 10,000 humans, using a k-mer approach (7-mere), to detect non-coding regions under purifying selection in the human genome. Absolutely worth a read.
Paper 2 – 2018: Simen – 28th of Feb.
Alexandre et al. Complex Relationships between Chromatin Accessibility, Sequence Divergence, and Gene Expression in Arabidopsis thaliana. An extremely detailed analyses of the link between ecotype chromatin regulation and transcriptional regulation. Some really good lessons. Comparative chromatin analyses using one reference genome might lead to large biases in results. And, there was little correlation between divergence in chromatin accessibility and divergence in transcriptional regulation of nearby genes between the ecotypes.
Paper 1 – 2018: Marian – 24th of Jan. Gordon et al. Nature Com. Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure. A thorough analyses of the variation in genome content across a diverse set of Brachypodium distachyon lines. Massive variation in gene content of genes involved in NON-essential processes – linked environmental adaptations but surely also lots of non adaptive variation.
Paper 5: Presented by Line (6th of Dec)
Parallel epigenomic changes induced by hatchery conditions in pacific salmon compare DNA-methylation profiles of hatchery reared and wild pacific salmon (all samples caught in the wild during sea migration). The analyses show that hatchery rearing results in reproducible DNA-methylation patterns in muscle tissue. Some of the differentially methylated genomic regions are in close vicinity to genes linked to ion regulation, and the authors argue that its plausible that these changes affect the fish ability to regulate ion concentration when they go to sea. This papers finding is interesting in that it demonstrates that wild stock hatcheries can potentially induce epigenetic changes that render the fish less fit. However, this paper does not link the DNA-methylation to any functional changes (e.g. gene expression changes), nor does the paper present a mechanistic explanation for what factor in the hatchery that induces the observed effect on methylation. Lastly, the link the authors make between muscle cell DNA methylation and the potential to osmo-regulate efficiently after sea migration remains unclear and somewhat speculative.
Paper 4: Presented by Jing (22nd Nov)
Boyle et al. ( From polygenic to omnigenic (Cell, 2017).) presents a really nice perspective on the genetic architecture of complex traits as we understand it from GWAS and functional genomic data. This paper propose a mechanistic explanation of the “missing heritability” – the “omnigenic model”. A must-read for anyone with the slightest interest in genetics.
Paper 3: Presented by Simen (8th Nov)
Crawford et al. presents a GWAS study of skin pigmentation in 1500 Africans. They find four major regions explaining 30% of the phenotypic variation in skin pigmentation (using the top 8 associated SNPs). The nice thing about this paper is how they then integrate population genomics, extensive functional omics data (RNAseq, ChIPseq, chromatin structure), and functional experimental validation studies to predict causative variation in non-coding regions and shed light on the evolution of skin pigmentation in African (and non African) populations. For example, the results support the idea that the modern human lineage evolved darker pigmentation in Africa several hundred thousands of years ago, and that dark skin colouration in south-east Asian are encoded by the same alleles as exists in Africa populations (and not attributed to convergent evolution).
Paper 2: Presented by Dag Inge
Jachowicz et al. have produced an extremely method dense paper, telling a compelling a story about how TEs are important and integral part of embryonic development in mice (and most likely in other mammals). The authors show how LINE1 expression (retro-transposable elements) play an important role in regulating global chromatin accessibility in the early mouse embryo, from 2 cell stage to blastocyte stage. The results clearly demonstrate the non-junkness of “junk DNA”. Creative molecular biology and omic’s approaches! For example, TALEs for targeted manipulation of global LINE1 expression to evaluate the effects on post-zygotic development.
Paper 1: Presented by Torgeir.
Guschanski et al. (Genome Research. 2017) have made a comprehensive analyses of gene regulatory evolution of mammalian gene duplicates. This is a super interesting read for those of you with an interest in comparative transcriptomics and genome evolution.