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RNA-seq of tame and aggressive foxes

RNA-seq of tame and aggressive foxes. Laboratory workshop. Dr A. V. Kukekova. Project was supported by FTP grant №8474. ICG SB RAS 26.06.2013. RNA- seq profiling. Brains of 12 tame and 12 aggressive foxes were dissected in Novosibirsk, flash frozen (Prof. L.N. Trut).

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RNA-seq of tame and aggressive foxes

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  1. RNA-seq of tame and aggressive foxes Laboratory workshop Dr A. V. Kukekova Project was supported by FTP grant №8474 ICG SB RAS 26.06.2013

  2. RNA-seq profiling • Brains of 12 tame and 12 aggressive foxes were dissected in Novosibirsk, flash frozen (Prof. L.N. Trut). • Got prefrontal cortex and amygdala from each. • High-throughput RNA sequencing of these 48 samples. • Per sample coverage of 30 million reads. • EdgeR for normalization and statistical testing.

  3. 1.8 Billion RNA-seq reads from 24 individuals x 2 tissues De novo assembly of fox transcriptome • Remove adapters • Quality filter (>Q20) • Remove Poly A/T • Remove mtDNA, rRNA • Convert to fasta ~1.4 Billion RNA-seq reads Inchworm Run time: 100 hours Chrysalis Run time: 400 hours Quantify Graph & Butterfly Run time: 250 hours N50 > 1182 bp Grabherr et al. 2011. Nat Biotech. 29:644-652.

  4. Annotation of the fox transcriptome (using dog) • blastx of the fox transcripts to known dog transcripts HTR5A (Serotonin Receptor 5A) Spady and Ostrander 2007

  5. Principal Components Analysis: amygdala vs. prefrontal cortex clustering Tame Prefrontal Cortex Aggressive Prefrontal Cortex Tame Amygdala Aggressive Amygdala

  6. Up and down-regulated transcripts Prefrontal cortex

  7. Up and down-regulated transcripts Amygdala

  8. Differences in gene expression in serotonergic receptors

  9. Changes in genes in the serotonin pathway Tame Aggressive HTR5A (Serotonin Receptor 5A) • HTR5a polymorphisms have been • associated with a large number of difference in human and mouse behaviors. log(CPM) Amygdala Prefrontal Cortex

  10. Changes in Monoamine Oxidases Tame Aggressive MAO-B • Monoamine oxidases play an important role in the metabolism • of monoamine neurotransmitters, • including serotonin and dopamine. log(CPM) Amygdala Prefrontal Cortex Synapse

  11. NMDA (glutamate) receptors and long term potentiation ADCY1 = adenylate cyclase 1 ITPR3 = inositol 1,4,5-triphosphate receptor, type 3 GRIN2A = glutamate receptor, ionotropic, N-methyl D-aspartate 2A GRIN2B = glutamate receptor, ionotropic, N-methyl D-aspartate 2B CACNA1C = voltage dependent Ca channel a1c

  12. NMDA (glutamate) receptors and long term potentiation Tame Aggressive Adenylate cyclase 1 log(CPM) Amygdala Prefrontal Cortex

  13. NMDA (glutamate) receptors and long term potentiation Tame Aggressive GRIN2A GRIN2B log(CPM) Prefrontal Cortex

  14. NMDA (glutamate) receptors and long term potentiation Tame Aggressive CACNA1S log(CPM) Amygdala Prefrontal Cortex

  15. Dopaminergic receptor pathway did respond to selection for tameness

  16. Dopaminergic receptor pathway did respond to selection for tameness Tame Aggressive DRD1 log(CPM) Amygdala Prefrontal Cortex

  17. Expression of DMBX1 in Aggressive Foxes Tame Aggressive Tame Aggressive Amygdala log(CPM) Prefrontal Cortex log(CPM)

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