Positive natural selection of N6-methyladenosine on the RNAs of processed pseudogenes

Background Canonical nonsense-mediated decay (NMD) is an important splicing-dependent process for mRNA surveillance in mammals. However, processed pseudogenes are not able to trigger NMD due to their lack of introns. It is largely unknown whether they have evolved other surveillance mechanisms. Results Here, we find that the RNAs of pseudogenes, especially processed pseudogenes, have dramatically higher m6A levels than their cognate protein-coding genes, associated with de novo m6A peaks and motifs in human cells. Furthermore, pseudogenes have rapidly accumulated m6A motifs during evolution. The m6A sites of pseudogenes are evolutionarily younger than neutral sites and their m6A levels are increasing, supporting the idea that m6A on the RNAs of pseudogenes is under positive selection. We then find that the m6A RNA modification of processed, rather than unprocessed, pseudogenes promotes cytosolic RNA degradation and attenuates interference with the RNAs of their cognate protein-coding genes. We experimentally validate the m6A RNA modification of two processed pseudogenes, DSTNP2 and NAP1L4P1, which promotes the RNA degradation of both pseudogenes and their cognate protein-coding genes DSTN and NAP1L4. In addition, the m6A of DSTNP2 regulation of DSTN is partially dependent on the miRNA miR-362-5p. Conclusions Our discovery reveals a novel evolutionary role of m6A RNA modification in cleaning up the unnecessary processed pseudogene transcripts to attenuate their interference with the regulatory network of protein-coding genes.

Higher Rates of Processed Pseudogene Acquisition in Humans and Three Great Apes Revealed by Long-Read Assemblies

LINE-1-mediated retrotransposition of protein-coding mRNAs is an active process in modern humans for both germline and somatic genomes. Prior works that surveyed human data mostly relied on detecting discordant mappings of paired-end short reads, or exon junctions contained in short reads. Moreover, there have been few genome-wide comparisons between gene retrocopies in great apes and humans. In this study, we introduced a more sensitive and accurate method to identify processed pseudogenes. Our method utilizes long-read assemblies, and more importantly, is able to provide full-length retrocopy sequences as well as flanking regions which are missed by short-read based methods. From 22 human individuals, we pinpointed 40 processed pseudogenes that are not present in the human reference genome GRCh38 and identified 17 pseudogenes that are in GRCh38 but absent from some input individuals. This represents a significantly higher discovery rate than previous reports (39 pseudogenes not in the reference genome out of 939 individuals). We also provided an overview of lineage-specific retrocopies in chimpanzee, gorilla, and orangutan genomes.

Poxviruses capture host genes by LINE-1 retrotransposition

Horizontal gene transfer (HGT) provides a major source of genetic variation. Many viruses, including poxviruses, encode genes with crucial functions directly gained by gene transfer from hosts. The mechanism of transfer to poxvirus genomes is unknown. Using genome analysis and experimental screens of infected cells, we discovered a central role for Long Interspersed Nuclear Element-1 (LINE-1) retrotransposition in HGT to virus genomes. The process recapitulates processed pseudogene generation, but with host messenger RNA directed into virus genomes. Intriguingly, hallmark features of retrotransposition appear to favor virus adaption through rapid duplication of captured host genes on arrival. Our study reveals a previously unrecognized conduit of genetic traffic with fundamental implications for the evolution of many virus classes and their hosts.SummaryActive selfish genetic elements in infected cells aid virus adaptation by catalyzing transfer of host genes to virus genomes.

Structural characterization of the DRF1 gene of Aegilops speltoides and comparison of its sequence with those of B and other Triticeae genomes

The genus Aegilops L. has been intensively investigated due to its close relationship with wheat (Triticum L.) as contributor of B and D subgenomes. Because of their vast genetic diversity, Aegilops species represent a rich source of alleles of agronomic interest, which could be used to widen the wheat gene pool and improve tolerance to diseases, pests, drought, cold and other environmental stresses. We report the isolation and characterization of the Dehydration Responsive Factor 1 (DRF1) gene in three accessions of Ae. speltoides coming from different regions of the Fertile Crescent. The DRF1 gene belongs to the DREB gene family and encodes transcription factors which play a key role in plant response to water stress. As in other cereals, the DRF1 gene in Aegilops speltoides consists of four exons and three introns and undergoes alternative splicing. A processed pseudogene was also identified and compared with the sequence of an actual mRNA transcript, breaking new ground in the understanding of the complex regulation mechanism of this gene. The genetic diversity was evaluated by comparison of inter- and intra-species variation among some Aegilops and Triticeae, by considering both the whole gene and exon 4 sequences. The phylogenetic analyses were able to cluster the sequences in well-supported clades attributable to the genomes analysed. The overall results suggest that there is a high similarity between the B and S genome copies of the DRF1 gene but also features indicating that the two genomes have evolved independently.

Higher rates of processed pseudogene acquisition in humans and three great apes revealed by long read assemblies

LINE-1 mediated retrotransposition of protein-coding mRNAs is an active process in modern humans for both germline and somatic genomes. Prior works that surveyed human data or human cohorts mostly relied on detecting discordant mappings of paired-end short reads, or assumed L1 hallmarks such as polyA tails and target site duplications. Moreover, there has been few genome-wide comparison between gene retrocopies in great apes and humans. In this study, we introduced a more sensitive and accurate approach to the discovery of processed pseudogene. Our method utilizes long read assemblies, and more importantly, is able to provide full retrocopy sequences as well as the neighboring sequences which are missed by short-read based methods reads. We provided an overview of novel gene retrocopies of 40 events (38 parent genes) in 20 human assemblies, a significantly higher discovery rate than previous reports (39 events of 36 parent genes out of 939 individuals). We also performed comprehensive analysis of lineage specific retrocopies in chimpanzee, gorilla and orangutan genomes.