Biology subjects

Tress, M. L.

Publications and source records attributed to Tress, M. L..

7 recordsLinked to original sources

bioRxiv2026

More than 100 dual coding regions have evidence for selection constraints in both reading frames

Alternative splicing can generate multiple differently spliced transcripts from a single pre-mRNA. A striking number of genes have alternative splice events that ccan hange the downstream reading frame leading to exons that code from distinct reading frames. In fact, more than a third of the coding genes in the human gene set are annotated with dual coding exons derived from alternative splicing events. Here we analysed a set of 537 dual coding regions that have evidence to support their functional importance. These dual coding regions produce protein isoforms with completely different C-terminals and have reading frames that are supported by either peptide or conservation evidence. More than a quarter of the alternative reading frames are preserved across all mammals, and many can be traced back to the earliest jawed vertebrates. Most of these ancient dual coding regions appear to be under selective constraints. We find support for purifying selection on both frames in 105 pairs of transcripts and two genes, CCSER2 and SH2B1, have triple coding regions that are under clear selection pressure in all three frames. We found evidence to suggest that many ancient dual coding regions may have played important roles in the evolution of the vertebrate central nervous system. Most ancient dual coding regions with evidence for protein level tissue specificity were brain specific and we showed that genes with ancient dual coding regions are highly enriched in brain tissues. Most remarkably, we found that more than 80% of the genes with these ancient dual coding regions are implicated in neuron development, synapses and neural cell projections.

genomics↗

bioRxiv2024

More than 2,500 coding genes in the human reference gene set still have unsettled status

In 2018 we analysed the three main repositories for the human proteome, Ensembl/GENCODE, RefSeq and UniProtKB. They disagreed on the coding status of one of every eight annotated coding genes. The analysis inspired bilateral collaborations between annotation groups. Here we have repeated our analysis with updated versions of the three reference coding gene sets. Superficially, little appears to have changed. Although there are slightly fewer genes predicted as coding overall, the three groups still disagree on the status of 2,606 annotated genes. However, a comparison without read-through genes and immunoglobulin fragments shows that the three reference sets have merged or reclassified more than 700 genes since the last analysis and that just 0.6% of Ensembl/GENCODE coding genes are not also annotated by the other two reference sets. We used eight features indicative of non-coding genes to examine the 21,873 coding genes annotated across the three reference sets. We found that more than 2,000 had one or more potential non-coding features. While some of these genes will be protein coding, we believe that most are likely to be non-coding genes or pseudogenes. Our results suggest that annotators still vastly overestimate the number of true coding genes.

genomics↗

bioRxiv2024

The rapid degradation of translated upstream regions points to an inefficient translation initiation process

Large-scale experimental analyses find ever more abundant evidence of translation from start codons upstream of the canonical start site. This translation either generates entirely new proteins (from novel upstream open reading frames) or produces isoforms with extended N-terminals when the novel start codon is in frame Most extended N-terminals are likely to just add a disordered region to the canonical protein isoform, but some may also block the recognition of the signal peptide causing the isoform to accumulate in the incorrect cellular compartment. This analysis finds evidence that upstream translations that would interfere with signal peptides are detected in expected quantities in ribosome profiling experiments, but that the equivalent N-terminally extended protein isoforms are significantly reduced in multiple proteomics experiments. This suggests that these isoforms are likely to be degraded shortly after translation by the ubiquitination pathway, thus preventing the build up of potentially harmful proteins with hydrophobic regions in the cytoplasm. In addition, this is further evidence that most of the transcripts translated from upstream start sites are the result of an inefficient translation initiation process. This has implications for the annotation of proteins given the huge numbers of upstream translations that are being detected in large-scale experiments.

genomics↗

bioRxiv2024

A deep audit of the PeptideAtlas database uncovers evidence for unannotated coding genes and aberrant translation

The human genome has been the subject of intense scrutiny by experimental and manual curation projects for more than two decades. Novel coding genes have been proposed from large-scale RNASeq, ribosome profiling and proteomics experiments. Here we carry out an in-depth analysis of an entire proteomics database. We analysed the proteins, peptides and spectra housed in the human build of the PeptideAtlas proteomics database to identify coding regions that are not yet annotated in the GENCODE reference gene set. We find support for hundreds of missing alternative protein isoforms and unannotated upstream translations, and evidence of cross-contamination from other species. There was reliable peptide evidence for 34 novel unannotated open reading frames (ORFs) in PeptideAtlas. We find that almost half belong to coding genes that are missing from GENCODE and other reference sets. Most of the remaining ORFs were not conserved beyond human, however, and their peptide confirmation was restricted to cancer cell lines. We show that this is strong evidence for aberrant translation, raising important questions about the extent of aberrant translation and how these ORFs should be annotated in reference genomes.

genomics↗

bioRxiv2023

Lost in the WASH. The functional human WASH complex 1 gene is on chromosome 20

The WASH1 gene produces a protein that forms part of the developmentally important WASH complex. The WASH complex activates the Arp2/3 complex to initiate branched actin networks at the surface of endosomes. As a curiosity, the human reference gene set includes nine WASH1 genes. How many of these are pseudogenes and how many are bona fide coding genes is not clear. Eight of the nine WASH1 genes reside in rearrangement and duplication-prone subtelomeric regions. Many of these subtelomeric regions had gaps in the GRCh38 human genome assembly, but the recently published T2T-CHM13 assembly from the Telomere to Telomere (T2T) Consortium has filled in the gaps. As a result, the T2T Consortium has added four new WASH1 paralogues in previously unannotated subtelomeric regions. Here we show that one of these four novel WASH1 genes, LOC124908094, is the gene most likely to produce the functional WASH1 protein. We also demonstrate that the other twelve WASH1 genes derived from a single WASH8P pseudogene on chromosome 12. These 12 genes include WASHC1, the gene currently annotated as the functional WASH1 gene. We propose LOC124908094 should be annotated as a coding gene and all functional information relating to the WASHC1 gene on chromosome 9 should be transferred to LOC124908094. The remaining WASH1 genes, including WASHC1, should be annotated as pseudogenes. This work confirms that the T2T assembly has added at least one functionally relevant coding gene to the human reference set. It remains to be seen whether other important coding genes are missing from the GRCh38 reference assembly.

molecular biology↗

bioRxiv2021

APPRIS principal isoforms and MANE Select transcripts in clinical variant interpretation

Most coding genes are able to generate multiple alternatively spliced transcripts. Determining which of these transcript variants produces the main protein isoform, and which of a genes multiple splice variants are functionally important, is crucial in comparative genomics and essential for clinical variant interpretation. Here we show that the principal isoforms chosen by APPRIS and the MANE Select variants provide the best approximations of the main cellular protein isoforms. Principal isoforms are predicted from conservation and from protein features, and MANE transcripts are chosen from the consensus between teams of expert manual curators. APPRIS principal isoforms coincide in over 94% of coding genes with MANE Select transcripts and the two methods are particularly discriminating when they agree on the main splice variant. Where the two methods agree, the splice variants coincide with the main isoform detected in proteomics experiments in 98.2% of genes with multiple protein isoforms. We also find that almost all ClinVar pathogenic mutations map to MANE Select or APPRIS principal isoforms. Where APPRIS and MANE agree on the main isoform, 99.93% of validated pathogenic variants map to principal rather than alternative exons. MANE Plus Clinical transcripts cover most validated pathogenic mutations in alternative coding exons. TRIFID functional importance scores are particularly useful for distinguishing clinically important alternative isoforms: the highest scoring TRIFID isoforms are more than 300 times more likely to have validated pathogenic mutations. We find that APPRIS, MANE and TRIFID are important for determining the biological relevance of splice isoforms and should be an essential part of clinical variant interpretation.

genomics↗

bioRxiv2018

Nearly all new protein-coding predictions in the CHESS database are not protein-coding

In a 2018 paper posted to bioRxiv, Pertea et al. presented the CHESS database, a new catalog of human gene annotations that includes 1,178 new protein-coding predictions. These are based on evidence of transcription in human tissues and homology to earlier annotations in human and other mammals. Here, we reanalyze the evidence used by CHESS, and find that nearly all protein-coding predictions are false positives. We find that 86% overlap transposons marked by RepeatMasker that are known to frequently result in false positive protein-coding predictions. More than half are homologous to only nine Alu-derived primate sequences corresponding to an erroneous and previously withdrawn Pfam protein domain. The entire set shows poor evolutionary conservation and PhyloCSF protein-coding evolutionary signatures indistinguishable from noncoding RNAs, indicating lack of protein-coding constraint. Only four predictions are supported by mass spectrometry evidence, and even those matches are inconclusive. Overall, the new protein-coding predictions are unsupported by any credible experimental or evolutionary evidence of function, result primarily from homology to genes incorrectly classified as protein-coding, and are unlikely to encode functional proteins.

genomics↗