Computational genome-wide cell- type-specific predictions of dimeric transcription factor complexes

It is estimated that the human genome contains as many as 8 000–15 000 copies of protein coding genes generated by reverse transcription. Although majority of them are in the state of a “relaxed” selection and remain “dormant”, as they are lacking regulatory regions, many become functional. The evolutionary path of these functional retrogenes’ is not uniform. In the course of the evolution they may undergo subfuctionalization and consequently share the function with their parent or develop a brand new function (neofunctionalisation). A good number of studies was recently performed to explore these unique sequences, yet our knowledge about retrogenes evolution and function is exceptionally limited. We performed a comprehensive analysis of 62 animal genomes to identify retrocopies of protein coding genes, study their evolution and decipher putative functions. Our analyses revealed that the fraction of expressed retrocopies is much higher than previously estimated and that retrocopies provide genetic material for new proteins, microRNA genes as well as trans natural antisense transcripts (trans-NAT). In addition, they may srve as microRNA sponges and, in case of nested retrocopies, possibly act as transcriptional interference factor and cause premature termination of host gene transcription. Moreover, our studies demonstrated remarkable differences in retrocopies evolution between placental mammals and other animals. L4.2