Formation of human long intergenic non-coding RNA genes, pseudogenes, and protein genes: Ancestral sequences are key players

An ancestral genomic sequence that serves as a nucleation site for de novo gene birth

The process of gene birth is of major interest with current excitement concerning de novo gene formation. We report a new and different mechanism of de novo gene birth based on the finding and the characteristics of a short non-coding sequence situated between two protein genes, termed a spacer sequence. This non-coding sequence is present in genomes of Mus musculus, the house mouse and Philippine tarsier, a primitive ancestral primate. The ancestral sequence is highly conserved during primate evolution with certain base pairs totally invariant from mouse to humans. By following the birth of the sequence of human lincRNA BCRP3 (BCR activator of RhoGEF and GTPase 3 pseudogene) during primate evolution, we find diverse genes, long non-coding RNA and protein genes (and sequences that do not appear to encode a gene) that all stem from the 3’ end of the spacer, and all begin with a similar sequence. During primate evolution, part of the BCRP3 sequence initially formed in the Old World Monkeys and developed into different primate genes before evolving into the BCRP3 gene in humans. The gene developmental process consists of the initiation of DNA synthesis at spacer 3’ ends, addition of a complex of tandem transposable elements and the addition of a segment of another gene. The findings support the concept of the spacer sequence as a starting site for DNA synthesis that leads to formation of different genes with the addition of other sequences. These data suggest a new process of de novo gene birth.

Human Ubiquitin-Specific Peptidase 18 Is Regulated by microRNAs via the 3'Untranslated Region, A Sequence Duplicated in Long Intergenic Non-coding RNA Genes Residing in chr22q11.21

Ubiquitin-specific peptidase 18 (USP18) acts as gatekeeper of type I interferon (IFN) responses by binding to the IFN receptor subunit IFNAR2 and preventing activation of the downstream JAK/STAT pathway. In any given cell type, the level of USP18 is a key determinant of the output of IFN-stimulated transcripts. How the baseline level of USP18 is finely tuned in different cell types remains ill defined. Here, we identified microRNAs (miRNAs) that efficiently target USP18 through binding to the 3’untranslated region (3’UTR). Among these, three miRNAs are particularly enriched in circulating monocytes which exhibit low baseline USP18. Intriguingly, the USP18 3’UTR sequence is duplicated in human and chimpanzee genomes. In humans, four USP18 3’UTR copies were previously found to be embedded in long intergenic non-coding (linc) RNA genes residing in chr22q11.21 and known as FAM247A-D. Here, we further characterized their sequence and measured their expression profile in human tissues. Importantly, we describe an additional lincRNA bearing USP18 3’UTR (here linc-UR-B1) that is expressed only in testis. RNA-seq data analyses from testicular cell subsets revealed a positive correlation between linc-UR-B1 and USP18 expression in spermatocytes and spermatids. Overall, our findings uncover a set of miRNAs and lincRNAs, which may be part of a network evolved to fine-tune baseline USP18, particularly in cell types where IFN responsiveness needs to be tightly controlled.

Genesis of Non-Coding RNA Genes in Human Chromosome 22-A Sequence Connection with Protein Genes Separated by Evolutionary Time

A small phylogenetically conserved sequence of 11,231 bp, termed FAM247, is repeated in human chromosome 22 by segmental duplications. This sequence forms part of diverse genes that span evolutionary time, the protein genes being the earliest as they are present in zebrafish and/or mice genomes, and the long noncoding RNA genes and pseudogenes the most recent as they appear to be present only in the human genome. We propose that the conserved sequence provides a nucleation site for new gene development at evolutionarily conserved chromosomal loci where the FAM247 sequences reside. The FAM247 sequence also carries information in its open reading frames that provides protein exon amino acid sequences; one exon plays an integral role in immune system regulation, specifically, the function of ubiquitin-specific protease (USP18) in the regulation of interferon. An analysis of this multifaceted sequence and the genesis of genes that contain it is presented.