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Human brain origin and the evolution of -boxes of protein-coding genes expressed in brain K.V. Gunbin, M.P. Ponomarenko,
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia, genkvg@bionet.nsc.ru, pon@bionet.nsc.ru

D.A. Afonnikov
Institute of Cytology and Genetics SB RAS, Novosibirsk State University, Novosibirsk, Russia, ada@bionet.nsc.ru

The great enigma of contemporary evo lut ionary bio logy is how tiny changes o f ho minid genes could result in the unique human brain. In order to answer this quest ion we performed a co mplex evo lut ionary analysis o f ho minid (H. sapiens, P. troglodytes, G. gorilla, P. pygmaeus) genes whose human orthologs are expressed in the brain and other organs. We extracted mult iple alignments of upstream regions of protein coding genes fro m the EnsEmbl Rel. 70. We took human transcript ion start sites (TSS) from GENCODE rel. 15 (only validated and manually annotated mRNA starts were used). For each alignment, ancestral nucleotide sequences were reconstructed in each internal node of the Ho minidae tree using the Maximum likelihood approach implemented in the PAML 4.7 program package. That was done in order to focus on only those posit ions, whose evo lution could be reconstructed at a probabilit y higher than 99%. To predict TATA-box activit y we implement our algorithm described in [1], which used an empirical equilibrium equat ion for three -step for TBP/TATA binding: TBP slides alo ng DNA, TBP stops in the TATA box, the TBP/TATA-co mplex is stabilized due to deformat ions in DNA. Then, mRNAs wit h biochemically significant changes in TATA-box activit y (negat ive or posit ive) were chose n for each Ho minidae tree branch. Annotation of mRNAs with biochemically significant changes in the act ivit y of their TATA boxes was performed based on the informat ion contained in the 3 sources of gene expressio n data: the Allen Human Brain At las, Human Brain Transcriptome fro m Sestan laboratory and t he Gene Expressio n Barcode 2.0. Only statistically significant gene


expressio n values co mpared with the background were included in the analys is. For the statist ical evaluat ion of the contribut ion of mRNAs with evo lving TATA-boxes to tissue funct ioning we used the fo llowing randomization test. On the basis o f the full se t of mRNAs for each t issue/structure, 105 random samples o f mRNAs were generated, the size o f each o f these samples was equal to the size o f the "evolving" set of mRNAs; than for each of the rando m samples, the sum o f mRNA expressio n values was calculated ; the amount (Q) of such sums equal to or greater than the sum o f the expressio n values for mRNA targets belo nging to the "evolving" set (A) was calculated. Thus, the probabilit y of observing A by rando m chance is p=Q/105. Two global evo lut ionary trends for ho minid genes whose human orthologs are expressed in brain were found: (1) changes in TATA-box act ivit y most characterist ic for ho minid genes whose human orthologs are highly expressed in brain cortex regions (especially in prefrontal cortex); (2) the relat ive conservation of the ancestral TATA-bo x organizat ion (20-90 b.p. upstream TSS) and act ivit y in human genes co mpared wit h intensive negat ive changes in TATA-box act ivit y in primate orthologs. It is of interest that the first trend elucidates the evo lving of prefrontal cortex in ho minids, while the second describes the potential mechanism of brains specializat ions. The work supported by RFBR 13-04-00359 and 13-04-01008, SciSh-5278.2012.4, RAS Programs "Mo lecular and cellular bio logy", RAS program .II.6.8, SB RAS Integratio n projects 39 and 130. 1. Ponomarenko PM, Savinkova LK, Drachkova IA, Lysova MV, Arshino va TV, Ponomarenko MP, Ko lchanov NA. (2008) A step-by-step model o f TBP/TATA box binding allows predict ing hu man hereditary diseases by single nucleotide polymorphism, Dokl Biochem Biophys. 419:88-92.