Evolution of tissue and developmental specificity of transcription start sites in Bos taurus indicus

Mehrnush Forutan,Stephen Moore,Brett Mason,Josie B Garner,Ruidong Xiang,Ben J Hayes,Loan Nguyen,Elizabeth Ross,Amanda J Chamberlain

doi:10.1038/s42003-021-02340-6

Abstract

To further the understanding of the evolution of transcriptional regulation, we profiled genome-wide transcriptional start sites (TSSs) in two sub-species, Bos taurus taurus and Bos taurus indicus, that diverged approximately 500,000 years ago. Evolutionary and developmental-stage differences in TSSs were detected across the sub-species, including translocation of dominant TSS and changes in TSS distribution. The 16% of all SNPs located in significant differentially used TSS clusters across sub-species had significant shifts in allele frequency (472 SNPs), indicating they may have been subject to selection. In spleen and muscle, a higher relative TSS expression was observed in Bos indicus than Bos taurus for all heat shock protein genes, which may be responsible for the tropical adaptation of Bos indicus.

Highlights

To further the understanding of the evolution of transcriptional regulation, we profiled genomewide transcriptional start sites (TSSs) in two sub-species, Bos taurus taurus and Bos taurus indicus, that diverged approximately 500,000 years ago
A minimum technical reproducibility of 73% was obtained when the total sample coverage was less than 0.08 million CAGE tags starting sites (CTSSs) supported by 3 or more Cap Analysis of Gene Expression (CAGE) read 5’-ends for Bos indicus fetal lung and Bos taurus adult liver samples (Supplementary Tables 1-2) The maximum technical reproducibility of 99% between total and half samples was observed in adult Bos indicus lung and liver tissues with more than 0.14 million CTSSs supported by 3 or more CAGE read 5’ends in the total sample
Consistent with above results, the highest (0.96) and lowest (0.80) correlation was achieved in adult and fetal Bos indicus lung, respectively (Supplementary Fig. 1DE)

Summary

Introduction

To further the understanding of the evolution of transcriptional regulation, we profiled genomewide transcriptional start sites (TSSs) in two sub-species, Bos taurus taurus and Bos taurus indicus, that diverged approximately 500,000 years ago. More recent studies[8] have shown that the majority of human and mouse RNA Polymerase II core promoters have an array of closely positioned TSSs instead of the expected single TSS. In agreement with this finding, the FAN-. There is evidence in human genes that different isoforms are produced as a result of the usage of alternative TSSs11,12. These results led to the “adaptive hypothesis”; that alternative TSSs are a widely used, regulated mechanism to expand the transcriptome diversity[9]. For example more than 90,000 TSSs are annotated for

Methods

Results

Conclusion