Divergence in alternative polyadenylation contributes to gene regulatory differences between humans and chimpanzees

Abstract

While comparative functional genomic studies have shown that inter-species differences in gene expression can be explained by corresponding inter-species differences in genetic and epigenetic regulatory mechanisms, co-transcriptional mechanisms, such as alternative polyadenylation (APA), have received little attention. We characterized APA in lymphoblastoid cell lines from six humans and six chimpanzees by identifying and estimating usage for 44,432 polyadenylation sites (PAS) in 9,518 genes. Although APA is largely conserved, 1,705 genes showed significantly different PAS usage (FDR 0.05) between species. Genes with divergent APA also tend to be differentially expressed, are enriched among genes showing differences in protein translation, and can explain a subset of observed inter-species protein expression differences that do not differ at the transcript level. Finally, we found that genes with a dominant PAS, which is used more often than other PAS, are particularly enriched for differentially expressed genes.

Genetic Dissection of the RNA Polymerase II Transcription Cycle

“…Allelic differences in termination could be caused by factors that influence the mature mRNA, such as differences in the polyadenylation cleavage site (Mittleman et al, 2021(Mittleman et al, , 2020. To determine whether allelic differences in termination correlate with differences in the composition of the mature mRNA, we sequenced poly-A enriched mRNA from two liver and brain samples.…”

“…Allelic differences in termination may influence the primary structure (i.e., the RNA sequence) of the mature mRNA by affecting polyadenylation cleavage site or splice site use between the two alleles (Mittleman et al, 2021(Mittleman et al, , 2020. To identify allelic differences in mRNA primary structure we sequenced poly-A enriched mRNA from two liver and brain samples.…”

Evolutionary insights into primate skeletal gene regulation using a comparative cell culture model

“…10X cell barcodes were also bioinformatically reassigned to their species of origin using standard Cell Ranger pipelines (Figure S2.1E). As before, reads were aligned to both human (hg38) and chimpanzee (panTro6) genomes, the same curated set of orthologous exons [55] was used. Additional modifications to the assignment protocol were also incorporated (Supplemental Text).…”

“…Sequencing read quality was confirmed using FastQC, and raw scRNA-seq reads were processed using standard 10X Genomics Cell Ranger 3.1.0 pipelines (Cell Ranger) [40] (Figure 2.1D), with the exception that reads were aligned once to the human genome (hg38) and once to the chimpanzee genome (panTro6) and that a curated set of orthologous exons [55] was used for transcriptome alignment (Supplemental Text). Briefly, 10X cell barcodes and UMIs were extracted from reads, and the remaining reads were mapped to genes using the specified reference genomes.…”

Transcriptome innovations in primates revealed by single-molecule long-read sequencing

“…Particularly, the fine-tuning of alternative splicing (AS) is a critical mechanism underlying disease and phenotypic evolution 1,2 . Hence, previous research on the conservation of RNA processing events in human and non-human primates (NHP) has revealed the functional importance of transcriptomic diversity [3][4][5][6][7][8][9][10] . Interestingly, the potential of increasingly complex transcriptomes to produce alternative protein isoforms is under intense debate as most of the predicted proteins remain undetected [11][12][13][14][15][16][17] , and alternative transcripts can carry out other regulatory functions 18 .…”