Isoform Evolution in Primates through Independent Combination of Alternative RNA Processing Events.

Recent RNA-seq technology revealed thousands of splicing events that are under rapid evolution in primates, whereas the reliability of these events, as well as their combination on the isoform level, have not been adequately addressed due to its limited sequencing length. Here, we performed comparative transcriptome analyses in human and rhesus macaque cerebellum using single molecule long-read sequencing (Iso-seq) and matched RNA-seq. Besides 359 million RNA-seq reads, 4,165,527 Iso-seq reads were generated with a mean length of 14,875 bp, covering 11,466 human genes, and 10,159 macaque genes.

Selectively Constrained RNA Editing Regulation Crosstalks with piRNA Biogenesis in Primates.

Although millions of RNA editing events have been reported to modify hereditary information across the primate transcriptome, evidence for their functional significance remains largely elusive, particularly for the vast majority of editing sites in noncoding regions. Here, we report a new mechanism for the functionality of RNA editing-a crosstalk with PIWI-interacting RNA (piRNA) biogenesis. Exploiting rhesus macaque as an emerging model organism closely related to human, in combination with extensive genome and transcriptome sequencing in seven tissues of the same animal, we deciphered accurate RNA editome across both long transcripts and the piRNA species.

Evolutionary interrogation of human biology in well-annotated genomic framework of rhesus macaque.

With genome sequence and composition highly analogous to human, rhesus macaque represents a unique reference for evolutionary studies of human biology. Here, we developed a comprehensive genomic framework of rhesus macaque, the RhesusBase2, for evolutionary interrogation of human genes and the associated regulations. A total of 1,667 next-generation sequencing (NGS) data sets were processed, integrated, and evaluated, generating 51.

Topological properties of the drug targets regulated by microRNA in human protein-protein interaction network.

The investigation of topological properties of proteins in protein-protein interaction network (PPIN) has great potentials to identify basic protein functions and mechanisms of action. Based on human PPIN, previous study has shown that the topological properties of drug targets are significantly distinguished from those of proteins that are not targeted by drugs (non-drug-targets). MicroRNAs (miRNAs) are known to regulate gene expression at the post-transcriptional level.