Evolutionary and Environmental Genomics with yeast and its hybrids

1. Analysing the relationships between genotype, phenotype and fitness to assess whether gross genomic rearrangements have adaptive value in asexually propagated yeast populations, and to establish their contribution as reproductive isolation barrier between species. Investigate the environmental specificity of genetic interactions, the dispensability and the robustness of biological systems.
2. Investigate the nature of genomes and protein networks in yeast hybrids of biotechnological and industrial importance. Determine the evolutionary role of chimeric protein complexes and shed light on the possible molecular mechanisms of hybrid vigour. Investigate the role of mitochondrial DNA on the genome evolution of hybrids.
3. Use of yeast mutant collections in genome profiling and large-scale functional analysis to assess the contribution of individual genes to the organism fitness under different environmental challenges, in the presence of chemical compounds (such as drugs of pharmaceutical relevance) and in different genetic backgrounds.
4. Large-scale functional analysis of non coding RNA (ncRNA) mutants in yeast, including bar-seq fitness profiles in different environments and Synthetic Genetic Analysis (SGA) to uncover higher order of ncRNA-ncRNA interactions.

Grant Support

BBSRC Responsive Mode, Wellcome Biomedical Resource and Technology Development Grant, NERC Advanced Fellowship, Royal Society, BBSRC CASE studentship.

Lab Members

Dr Samina Naseeb (Post-doctoral Research Associate); Dr Marcin Fraczek (Post-doctoral Research Associate); Mr Steven Parker (Technician and PhD student); Mrs Qamar Almutawa (PhD student); Mr Kobchai Dungranalatter (PhD student); Miss Haya Alsammar (PhD student); Miss Alkisti Manousaki (BBSRC-DTP PhD student).

Selected Publications

1. Hooks KB, Naseeb S, Parker S, Griffiths-Jones S, and Delneri D (2016)Novel intronic RNA structures contributes to maintenance of phenotype in Saccharomyces cerevisiae. Genetics 203: 1469-1481

2. Naseeb S, Carter Z, Minnis D, Donaldson I, Zeef L, and Delneri D (2016)Widespread impact of chromosomal inversions on gene expression uncovers network robustness via phenotypic buffering. Molecular Biology and Evolution 33: 1679-1696.

3. Paget CM, Schwartz JM, Delneri D (2014) Environmental systems biology of cold-tolerant phenotype in Saccharomyces species adapted to grow at different temperatures. Molecular Ecology 23: 5241-5257.

4. Hewitt SK, Donaldson IJ, Lovell SC, Delneri D. (2014) Sequencing and characterisation of rearrangements in three S. pastorianus strains reveals the presence of chimeric genes and gives evidence of breakpoint reuse. PLoS One 9: e92203.

5. Piatkowska EM, Naseeb S, Knight D and Delneri D (2013) Chimeric protein complexes in hybrid species generate novel evolutionary phenotypes, PLoS Genetics 9: e1003836 (Highlights in Nature Reviews Genetics: 14,822).

6. Norris M, Lovell S, and Delneri D (2013), Characterisation and prediction of haploinsufficiency using systems-level gene properties in yeast, G3, 3: 1965-1977

7. Naseeb S. and Delneri D (2012) “Impact of chromosomal inversions on the yeast DAL cluster”, PLoS One, 7: e42022

8. Delneri D "Competition experiments coupled with high-throughput analyses for functional genomics studies in yeast" (2010), Methods in Molecular Biology, 759: 271-282.

9. Bivi N, Romanello M, Harrison R, Clarke I, Hoyle DC, Moro L, Ortolani F, Bonetti A, Quadrifoglio F, Tell G, Delneri D (2009) Identification of secondary targets of N-containing bisphosphonates in mammalian cells via parallel competition analysis of the barcoded yeast deletion collection. Genome Biol. 10:R93

10. Delneri D, Hoyle DC, Gkargkas K, CrossEJM, Rash B, Zeef L, LeongH-S, DaveyH, Hayes A, KellDB, Griffith GW, and Oliver SG  (2009). Identification and characterisation of high flux control (HFC) genes of Saccharomyces cerevisiae through competition analyses in continuous cultures. Nature Genetics, 40: 113-117.

11. Harrison R, Papp B, Pal C, Oliver SG and Delneri D (2007) Plasticity of genetic interactions in metabolic networks of yeast, Proc Natl Acad Sci U S A.  104: 2307-2312.

12. Colson I*, Delneri D* and Oliver S.G. (2004) The impact of chromosomal rearrangements on the fitness of Saccharomyces cerevisiae, (*equal contribution), EMBO rep, 5: 392-398.

13. Delneri D, Colson I, Grammenoudi S, Roberts I N, Louis E J, and Oliver S G, (2003) Engineering evolution to study speciation in yeasts. Nature, 422: 68-72 (News and Views, Nature, 422, 25-26).