Biology subjects

Torres-Mendez, A.

Publications and source records attributed to Torres-Mendez, A..

8 recordsLinked to original sources

bioRxiv2026

Alternative splicing and gene expression repurpose ancestral genes through distinct evolutionary routes

Specialized tissues often evolve by repurposing ancestral genes. Tissue-specific alternative splicing (TS-AS) and tissue-specific gene expression (TS-GE) have been proposed as complementary mechanisms contributing to tissue specialization, but whether they provide broadly interchangeable solutions or instead follow distinct, constrained evolutionary routes remains unknown. To address this question, here we compare TS-AS and TS-GE across eight homologous tissues, 20 bilaterian species and 7,178 ancestral gene families spanning 700 million years. The two mechanisms were similarly prevalent and, together, they affected nearly three-quarters of ancestral gene families across our dataset. However, they targeted largely non-overlapping gene sets within species, with contrasting architectures and functions. TS-AS usually acts on longer, exon-rich genes and modulates intracellular machinery shared across tissues, whereas TS-GE preferentially evolves in duplicated genes and impacts tissue-defining extracellular and nuclear processes. Unexpectedly, although TS-GE was globally more conserved, neural-specific splicing gains outnumbered expression gains at the origins of vertebrates and insects, revealing a prominent contribution of TS-AS to early nervous system transcriptome diversification. Exon-level orthology reconstructions further uncovered extensive recurrent evolution of neural-specific exons in the same ancestral genes across the phylogeny. Importantly, deletion of two such microexons in Drosophila negatively impacted overall fitness and led to neurological-associated phenotypes such as reduced climbing or hyperactivity. Altogether, our findings reveal distinct but complementary evolutionary routes by which gene expression and alternative splicing repurpose ancestral genes, and highlight recurrent neural exon evolution as a functionally important contributor to nervous systems.

evolutionary biology↗

bioRxiv2023

The V-ATPase/ATG16L1 axis is controlled by the V1H subunit

Defects in organellar acidification indicate compromised or infected compartments. Recruitment of the autophagy-related ATG16L1 complex to pathologically de-acidified compartments targets ubiquitin-like ATG8 molecules to perturbed membranes. How this process is coupled to pH gradient disruption is unclear. Here, we reveal a direct role for the V1H subunit of the V-ATPase proton pump in recruiting ATG16L1. The interaction between V1H and ATG16L1 occurs within assembled V-ATPases, but not dissociated V1 complexes. This selectivity allows recruitment to be coupled to changes in V-ATPase assembly that follow pH dissipation. Cells lacking V1H undergo canonical macroautophagy but are unable to recruit ATG16L1 in response to influenza infection or ionophore drugs. We identify a loop within V1H that mediates ATG16L1 binding, which is absent in a neuronal isoform of V1H. Thus, V1H controls ATG16L1 recruitment in response to proton gradient dissipation, suggesting that the V-ATPase acts autonomously as a cell-intrinsic damage sensor.

molecular biology↗

bioRxiv2022

Pervasive evolution of tissue-specificity of ancestral genes differentially shaped vertebrates and insects

Regulation of gene expression is arguably the main mechanism contributing to tissue phenotypic diversity within and between species. Here, we assembled an extensive transcriptomic dataset covering twenty bilaterian species and eight tissues, selecting a specular phylogeny that allowed both the combined and parallel investigation of gene expression evolution between vertebrates and insects. We specifically focused on widely conserved ancestral genes, identifying strong cores of pan-bilaterian tissue-specific genes and even larger groups that diverged to define vertebrate and insect tissues. Systematic inferences of tissue-specificity gains and losses show that nearly half of all ancestral genes have been recruited into tissue-specific transcriptomes. This occurred during both ancient and, especially, recent bilaterian evolution, with several gains being associated with the emergence of unique phenotypes. Such pervasive evolution of tissue-specificity was linked to gene duplication coupled with specialization, including an unappreciated prolonged effect of whole genome duplications during recent vertebrate evolution.

genomics↗

bioRxiv2022

Insplico: Effective computational tool for studying intron splicing order genome-wide with short and long RNA-seq reads

Although splicing occurs largely co-transcriptionally, the order by which introns are removed does not necessarily follow the order in which they are transcribed. Whereas several genomic features are known to influence whether or not an intron is spliced before its downstream neighbour, multiple questions related to intron splicing order (ISO) remain unanswered. Here, we present Insplico, the first standalone tool to quantify ISO that works with both short and long read sequencing technologies. We first demonstrate its applicability and effectiveness recapitulating previously reported patterns, while unveiling overlooked biases associated with long read sequencing. We next show that ISO around individual exons is remarkably constant across cell and tissue types and even upon major spliceosomal disruption, and it is evolutionarily conserved between human and mouse brains. We also establish a set of universal features associated with ISO patterns across various animal and plant species. Finally, we used Insplico to investigate ISO in the context of tissue-specific exons, particularly focusing on SRRM4-dependent microexons. We found that the majority of such microexons have non-canonical ISO, in which the downstream intron is spliced first, and we revealed two potential modes of SRRM4 regulation of microexons related to their ISO and various splicing-related features. Insplico is available on gitlab.com/aghr/insplico.

molecular biology↗

bioRxiv2021

Parallel evolution of a splicing program controlling neuronal excitability in flies and mammals

Neurons draw on alternative splicing for their increased transcriptomic complexity throughout animal phylogeny. To delve into the mechanisms controlling the assembly and evolution of this regulatory layer, we characterized the neuronal microexon program in Drosophila and compared it with that of mammals. We found that in Drosophila, this splicing program is restricted to neurons by the post-transcriptional processing of the enhancer of microexons (eMIC) domain in Srrm234 by Elav and Fne. eMIC deficiency or misexpression leads to widespread neurological alterations largely emerging from impaired neuronal activity, as revealed by a combination of neuronal imaging experiments and cell-type-specific rescues. These defects are associated with the genome-wide skipping of short neural exons, which are strongly enriched in ion channels. Remarkably, we found no overlap of eMIC-regulated exons between flies and mice, illustrating how ancient post-transcriptional programs can evolve independently in different phyla to impact distinct cellular modules while maintaining cell-type specificity.

molecular biology↗

bioRxiv2020

Hypersilencing of SRRM4 suppresses basal microexon inclusion and promotes tumor growth across cancers

RNA splicing is widely dysregulated in cancer, frequently due to altered expression or activity of splicing factors. Microexons are extremely small exons (3-27 nucleotides long) that are highly evolutionarily conserved and play critical roles in promoting neuronal differentiation and development. Inclusion of microexons in mRNA transcripts is mediated by the splicing factor SRRM4, whose expression is largely restricted to neural tissues. However, microexons have been largely overlooked in prior analyses of splicing in cancer, as their small size necessitates specialized computational approaches for their detection. Here we demonstrate that despite having low expression in normal non-neural tissues, SRRM4 is hypersilenced in tumors, resulting in the suppression of basal microexon inclusion. Remarkably, SRRM4 is the most consistently silenced splicing factor across all tumor types analyzed, implying a general advantage of microexon downregulation in cancer independent of its tissue of origin. We show that this silencing is favorable for tumor growth, as decreased SRRM4 expression in tumors is correlated with an increase in mitotic gene expression, and upregulation of SRRM4 in cancer cell lines dose-dependently inhibits proliferation in vitro and in a mouse xenograft model. Further, this proliferation inhibition is accompanied by induction of neural-like expression and splicing patterns in cancer cells, suggesting that SRRM4 expression shifts the cell state away from proliferation and towards differentiation. We therefore conclude that SRRM4 acts as a proliferation brake, and tumors gain a selective advantage by cutting off this brake. SignificanceMicroexons are extremely small exons enriched in the brain that play important roles in neural development. Their inclusion is mediated by the splicing factor SRRM4, also predominantly expressed in the brain. Surprisingly, we find that low expression of SRRM4 outside of the brain is further decreased in tumors, and in fact SRRM4 is the most consistently silenced splicing factor in tumors across tissue types. We demonstrate that SRRM4 inhibits cancer cell proliferation in vitro and in vivo by inducing a neuronal differentiation program. Our findings add a new element to the overall picture of splicing dysregulation in cancer, reveal an antiproliferative function for SRRM4 and microexons outside of the brain, and may present a common therapeutic intervention point across cancer types.

cancer biology↗

bioRxiv2019

Srrm234, but not canonical SR and hnRNP proteins drive inclusion of Dscam exon 9 variable exons

Alternative splicing of pre-mRNA is a major mechanism to diversify protein functionality in metazoans from a limited number of genes. In the Drosophila melanogaster Down Syndrome Cell Adhesion Molecule (Dscam) important for neuronal wiring up to 38,016 isoforms can be generated by mutually exclusive alternative splicing in four clusters of variable exons. However, it is not understood how a specific exon is chosen from the many variables and how variable exons are prevented from being spliced together. A main role in the regulation of Dscam alternative splicing has been attributed to RNA binding proteins, but how they impact on exon selection is not well understood. Serine-arginine-rich (SR) proteins and hnRNP proteins are the two main types of RNA binding proteins with major roles in exon definition and splice site selection. Here, we analyzed the role of SR and hnRNP proteins in Dscam exon 9 alternative splicing in mutant Drosophila melanogaster embryos because of their essential function for development. Strikingly, loss or overexpression of canonical SR and hnRNP proteins even when multiple proteins are depleted together, does not affect Dscam alternative exon selection very dramatically. Conversely, non-canonical SR protein Serine-arginine repetitive matrix 2/3/4 (Srrm234) is a main determinant of exon inclusion in Dscam exon 9 cluster. Since long-range base-pairings are absent in the exon 9 cluster, our data argue for a small complement of regulatory factors as main determinants of exon inclusion in the Dscam exon 9 cluster.

molecular biology↗

bioRxiv2017

A rhamnose-inducible system for precise and temporal control of gene expression in cyanobacteria

Cyanobacteria are important for fundamental studies of photosynthesis and have great biotechnological potential. In order to better study and fully exploit these organisms, the limited repertoire of genetic tools and parts must be expanded. A small number of inducible promoters have been used in cyanobacteria, allowing dynamic external control of gene expression through the addition of specific inducer molecules. However, the inducible promoters used to date suffer from various drawbacks including toxicity of inducers, leaky expression in the absence of inducer and inducer photolability, the latter being particularly relevant to cyanobacteria which, as photoautotrophs, are grown under light. Here we introduce the rhamnose-inducible rhaBAD promoter of Escherichia coli into the model freshwater cyanobacterium Synechocystis sp. PCC 6803 and demonstrate it has superior properties to previously reported cyanobacterial inducible promoter systems, such as a non-toxic, photostable, non-metabolizable inducer, a linear response to inducer concentration and crucially no basal transcription in the absence of inducer.

synthetic biology↗