Pseudogenes

The accurate identification and description of the genes in the human and mouse genomes is a fundamental requirement for high quality analysis of data informing both genome biology and clinical genomics. Over the last 15 years, the GENCODE consortium has been producing reference quality gene annotations to provide this foundational resource. The GENCODE consortium includes both experimental and computational biology groups who work together to improve and extend the GENCODE gene annotation. Specifically, we generate primary data, create bioinformatics tools and provide analysis to support the work of expert manual gene annotators and automated gene annotation pipelines. In addition, manual and computational annotation workflows use any and all publicly available data and analysis, along with the research literature to identify and characterise gene loci to the highest standard. GENCODE gene annotations are accessible via the Ensembl and UCSC Genome Browsers, the Ensembl FTP site, Ensembl Biomart, Ensembl Perl and REST APIs as well as https://www.gencodegenes.org.

BackgroundPseudogenes have long been considered as nonfunctional genomic sequences. However, recent evidence suggests that many of them might have some form of biological activity, and the possibility of functionality has increased interest in their accurate annotation and integration with functional genomics data.ResultsAs part of the GENCODE annotation of the human genome, we present the first genome-wide pseudogene assignment for protein-coding genes, based on both large-scale manual annotation and in silico pipelines. A key aspect of this coupled approach is that it allows us to identify pseudogenes in an unbiased fashion as well as untangle complex events through manual evaluation. We integrate the pseudogene annotations with the extensive ENCODE functional genomics information. In particular, we determine the expression level, transcription-factor and RNA polymerase II binding, and chromatin marks associated with each pseudogene. Based on their distribution, we develop simple statistical models for each type of activity, which we validate with large-scale RT-PCR-Seq experiments. Finally, we compare our pseudogenes with conservation and variation data from primate alignments and the 1000 Genomes project, producing lists of pseudogenes potentially under selection.ConclusionsAt one extreme, some pseudogenes possess conventional characteristics of functionality; these may represent genes that have recently died. On the other hand, we find interesting patterns of partial activity, which may suggest that dead genes are being resurrected as functioning non-coding RNAs. The activity data of each pseudogene are stored in an associated resource, psiDR, which will be useful for the initial identification of potentially functional pseudogenes.

The concept of competitive endogenous RNA (ceRNA) was first proposed by Salmena and colleagues. Evidence suggests that pseudogene RNAs can act as a 'sponge' through competitive binding of common miRNA, releasing or attenuating repression through sequestering miRNAs away from parental mRNA. In theory, ceRNAs refer to all transcripts such as mRNA, tRNA, rRNA, long non-coding RNA, pseudogene RNA and circular RNA, because all of them may become the targets of miRNA depending on spatiotemporal situation. As binding of miRNA to the target RNA is not 100% complementary, it is possible that one miRNA can bind to multiple target RNAs and vice versa. All RNAs crosstalk through competitively binding to miRNAvia miRNA response elements (MREs) contained within the RNA sequences, thus forming a complex regulatory network. The ratio of a subset of miRNAs to the corresponding number of MREs determines repression strength on a given mRNA translation or stability. An increase in pseudogene RNA level can sequester miRNA and release repression on the parental gene, leading to an increase in parental gene expression. A massive number of transcripts constitute a complicated network that regulates each other through this proposed mechanism, though some regulatory significance may be mild or even undetectable. It is possible that the regulation of gene and pseudogene expression occurring in this manor involves all RNAs bearing common MREs. In this review, we will primarily discuss how pseudogene transcripts regulate expression of parental genes via ceRNA network and biological significance of regulation.

Pseudogenes have been regarded as nonfunctional byproducts of evolutionary processes. However, emerging evidence indicates that pseudogenes perform diverse biological roles in human physiology and pathology. We identified the BRCA1 pseudogene (BRCA1P1), a fusion pseudogene derived from the BRCA1 tumor suppressor and RPLP1 ribosomal protein genes, as an immunoregulatory RNA in breast cancer. In this study, we show that BRCA1P1 expression varies across multiple cancer cell types, with no significant association with BRCA1 or BRCA2 somatic mutations in breast and ovarian tumors. Interestingly, BRCA1P1 inhibition elicits antitumor effects in multiple cancer cell types and preclinical tumor models through an antiviral defense mechanism. Loss of BRCA1P1 induces antiviral gene expression, promotes apoptosis, and increases sensitivity to chemotherapy in various cancer cells, without inducing apoptosis in nonmalignant cells. This antiviral response also enhances macrophage-mediated phagocytosis of BRCA1P1-deficient cancer cells. Mechanistically, the majority of BRCA1P1 transcripts are circular RNAs and regulate NF-κB-driven antiviral gene expression. Furthermore, intratumoral expression of BRCA1P1 is elevated in tumor cells, compared to normal breast tissue, and its depletion significantly inhibits the growth of both primary and metastatic breast tumor organoids. Finally, in a humanized mouse model of breast cancer, BRCA1P1 loss stimulates antiviral gene expression and increases T cell infiltration into tumors. These findings support a critical role for BRCA1P1 in regulating innate immune defense and antitumor responses across cancer types, suggesting that targeting pseudogene-derived RNAs may offer innovative therapeutic strategies to enhance antitumor immunity in breast and other cancers.