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Applied Genomics Technology Center DNA transcription DNA isolation DNA sequencing Genotyping Gene linkage mapping mRNA translation RNA isolation Expression analysis Microarrays QRT-PCR www.AGTC.med.wayne.edu Protein Protein purification Enzymology Immunohistochemistry Western Blot analysis Protein microarrays Ab microarrays Yeast 2 hybrid analysis IPAR 2 - 4TB Illumina GAII 3x R900 64GB RAM Backup Mirror (C&IT) 48TB NAS Primary Server Illumina Pipeline Failover & Reanalysis Server 30TB Direct Attached Storage 30TB Direct Attached Storage Testbed Server 10TB Direct Attached Storage User Data Delivery & Downstream Analysis eg Genomatix Whole Genome Maps from the base pair Ruden Lab, IEHS to the chromosome Coverage/deletion maps Synonymous/Non-synonymous polymorphism Krawetz Lab Histone Locations Relative to All Promoters Histone Locations Relative to Alu/B1 Repeats Permuted Control 2kbase Downstream (Genic) Full ALU Repeat Length Small RNA Digital Gene Expression Most of the reads don’t correspond to known sncRNAs Library AS062 AS064 AS066 Alignments ≤10 Unique ≤10 Unique ≤10 Unique # Sequences 625582 552332 225563 110805 528475 285078 Peak of intergenic location found with high representation in all 3 libraries and showing miRNA potential (hairpin) 4 manuscripts in preparation using Solexa data • At the end of spermatogenesis the DNA is not methylated small RNAs may transfer the information for methylation • Discovery of a new class of small, non-coding RNAs of unknown function Krawetz Lab Ruden Bee Project Genetics and Genomics of Social Behavior Phase I funding for a Glue Grant PI: Gene Robinson (UIUC) 27 Co-PIs Pilot Project: Genome sequencing and bisulfite sequencing of European honey bees and Africanized killer bees (funded by WSU OVPR and Ob/Gyn) Progress: 4 Libraries have been established and about 50% of the sequencing is complete 3 lanes of Sequencing and 1 lane of BS-Seq have been analyzed for each strain Results: 9 Loci on chromosome 1 have >5:1 mC ratios (Eur:Afr) 43 loci on chromosome 1 have >5:1 mC ratios (Afr:Eur) Ruden Bee Project Preliminary Results FMRFamide Receptor •neuropepetide receptor •Methylated in Africanized bees in three regions •Involved in agression in mice (PMID: 7630503) defense behavior in snails (PMID: 2067975) Kainate Glutamate Receptor •Methylated in Euopean bees in two regions •Kainate induces aggression in mice (PMID: 15123017) GAT1 •Methylated in African bees •Deletion of GAT1 in mice causes “reduced agression” (PMID 17183588) Ruden Bee Project Future Experiments How much DNA methylation is Genetic and how much is Environmentally induced? Next step Cross Fostering Experiment Killer bee soldiers in European hives European bee soldiers in Killer bee hives NIH Pioneer Award PI: Gene Robinson Human DBS DNA Methylation DBS from 28 children with varying Pb levels was obtained from MDCH (3 to 16 ug/dL) PB levels (CDC) High:10 ug/dL Low: 3 ug/dL Illumina Whole Genome Methylation Arrays (27,576 CpG islands) Results: Several loci have mC with significant correlations to Pb exposure 5 genes involved in myelination (Mbp, Edg2, Mag, Pmp22, and Ugt8) 6 genes involved in growth factor signaling (FGfr1, Gzd3, Erbb3, Mag, Pmp22 and Ugt 8) All of these genes have prior evidence of differential expression in human postmortem brains from mood disorder subjects (Le-Niculescu et al., 2009) Human DBS DNA Methylation CpG Corr P-value 1 -0.52 0.005 2 -0.54 0.003 overall 0.000015