The objective of this study was to observe the differences in alternative splicing between human and nonhuman primate brains, and in particular to analyse the lineage-specific changes in splicing during the evolution of humans diverging from chimpanzees. It was also contemplated if factors such as genetics, environment and sex biased splicing affected the outcome of splicing evolution. However, the aim was comparison of variations between species rather than focusing on these factors.
During the study tissue samples of humans, chimpanzees and rhesus macaques were taken and a microarray analysis of alternative splicing, including RT-PCR tests of brain transcriptomes was performed (Lin, L. et al 2010).
The analysis of splicing patterns in the primate brain was studied by high-density exon junction array profiling of brain transcriptomes of the three species. When comparing human and nonhuman primate transcriptomes changes in transcript levels during human evolution had been observed. These changes can account for the phenotypical and splicing variability between species.
During the examination of the brain transcriptomes, splicing differences were discovered in 509 genes between the three species. RT-PCR analysis indicated that from 40 exons, there was a confirmed splicing evolution of 33 exons. It was confirmed that 13 of the 33 human-specific exons had an increase or decrease in transcript levels and revealed widespread changes of the alternative splicing of brain transcriptomes during human and primate evolution.
The results included a significant increase in the rate of silent substitutions within exon, coupled and accelerated sequence divergence in flanking introns. Indicating that evolution of cis-regulatory signals had helped contribute to human-specific splicing patterns (Lin, L. et al. 2010).
In a similar study there is conflicting evidence regarding exon usage and how it can vary between species due to genetic variations in cis-regulatory regions. They found that when comparing transcriptomes of several human subjects there had been several erroneous splicing in low abundance isoforms. This gave a prominent difference in splicing between close species like humans and chimpanzees. Also, they found after analyzing transcriptomes of physiologically similar organs of mammalian and vertebrate species, splicing variation between these species exceeds the within-species variation across tissues which contradicts the previous studies analysis that gene expression levels in which patterns show strong conversation (Reyes, A. et al. 2013).
Another study in variation in splicing between species showed higher frequencies in alternative splicing in primates than vertebrates. In this particular study it was concluded that organ splicing reflected the identity of species more than organ type and that it had more of a widespread role in separating the differences between species than changes in mRNA expression. It was said that re-assortment of splicing code can explain the differences between vertebrate species. Due to these alternative splicing changes affecting trans-acting factors involved in gene regulation, there can be an explanation for the difference in diversification in alternative splicing and changes within phenotypic change between species (Barbosa-Morais, N. et al. 2012).
In these studies the different methods of comparisons between mammalian transcriptomes appeared limited to closely related primates. The microarrays required hybridization for specie specific probes making the study of specie specific transcripts difficult. In the future the development of RNA sequencing that can be an effective way of assessing expression levels could be a way for more extensive studies of the variations in species.