Biology subjects

Hernandez-Corchado, A.

Publications and source records attributed to Hernandez-Corchado, A..

10 recordsLinked to original sources

bioRxiv2026

A high-resolution protein-RNA binding atlas for structure-aware interaction prediction and post-transcriptional regulatory modeling

RNA-binding proteins (RBPs) control post-transcriptional gene expression by regulating RNA processing, localization, stability, and translation. However, our understanding of RNA regulation remains limited by the resolution, scale, and uniformity of available RBP binding maps. Here we introduce eclair CLIP (ecCLIP), a high-throughput CLIP-seq platform that combines endogenous protein tagging for uniform affinity capture with ligation-free library preparation to generate high-resolution RNA-protein binding profiles. We applied ecCLIP to 67 endogenously tagged RBPs in HEK293T cells, generating a high-quality transcriptome-scale atlas that recovered known binding preferences and captured post-transcriptional regulons linked to RNA half-life. To test the utility of the atlas, we incorporated ecCLIP into Borzuki, a Borzoi-derived sequence-to-function model trained on complementary RNA degradation, expression, CLIP, and Perturb-seq data. Inclusion of ecCLIP data improved RNA half-life prediction and assessment of 3' UTR variant effects on RNA stability, demonstrating that our atlas helps capture RNA dynamics. To directly model the cis-regulatory grammar underlying these RBP-RNA interactions, we developed Pythia, a structure-aware neural network architecture that incorporates context-free grammar-inspired fixed convolutions to explicitly encode RNA base-pairing features. Pythia predicted RBP binding from sequence and structural context and decomposed predictions into sequence- and structure-dependent components. We tested this decomposition for five RBPs using massively parallel reporter CLIP (MPRC) binding assays in cells, using synthetic RNA libraries containing mutations designed to preserve or disrupt predicted RNA structures across nominated binding sites. We used the same MPRC strategy to confirm allele-specific binding effects for variants prioritized by Pythia. Together, ecCLIP and Pythia provide a resource for structure-aware decoding of RNA-protein interaction grammar and interpretation of post-transcriptional regulatory variation.

genomics↗

bioRxiv2026

TACC3-driven translation reprogramming dictates susceptibility or tolerance to mitotic stress

Translation reprogramming is central to cancer cell plasticity under stress. However, the molecular players coordinating translation and epitranscriptomic rewiring to determine adaptive responses to mitotic stress remain elusive. Here, we found that microtubule targeting agent (MTA)-induced CDK1 blocks global translation while it phosphorylates and degrades TACC3, a multifunctional adaptor, releasing eIF4A/eIF4E/eIF4G2 initiation factors. This promotes selective m7G cap-dependent translation of mRNAs with MTAup motif that are functionally required for apoptosis by disrupting proteostasis, promoting MTA-sensitivity. On the other hand, selectively translated TACC3 interacts with eIF3d/eIF4G1 and the m6A writer METTL3, mediating switch to m6A methylation and m7G cap-independent translation of mRNAs with hnRNPC-motif involved in chromosome segregation, driving MTA tolerance. TACC3 inhibition overcomes MTA resistance via restoring translation reprogramming. These findings demonstrate that TACC3 is a pivotal coordinator of translation/epitranscriptomic reprogramming and a therapeutic target in MTA-refractory cancers.

cancer biology↗

bioRxiv2026

Non-canonical ribosome organization enables translation stalling in neuronal RNA granules.

Neuronal outgrowth to support cognitive functions relies on a timely supply of proteins to distal sites in the neuron. To meet this demand, neurons transport mRNAs and ribosomes in large assemblies called "neuronal RNA granules". Ribosomes that integrate into these granules initiate protein synthesis in the soma, stall the process, and then become packaged into clusters that are transported to distal sites, where protein synthesis can be reactivated. The exact mechanisms and structure of these ribosome clusters remain unknown. We combined cryo-electron microscopy and cryo-electron tomography to examine these dense ribosome clusters purified from rat brains, which are included in neuronal RNA granules. We found that these clusters contain ribosomes stalled at various stages of elongation and that the mRNA sequences where the ribosomes stall facilitate stalling. The ribosome clusters contain multiple polysomal units, and ribosomes from nearby polysomes interact through rRNA expansion segments, only seen before in disomes of inactive or hibernating ribosomes in neurons. The ribosomes in the clusters form unique three-dimensional arrays that evade detection by the ribosome-associated quality-control and NO-GO decay responses, which normally lead to recycling of 40S and 60S subunits, and degradation of the mRNA and arrested nascent proteins. Overall, this study helps uncover specialized mechanisms in neurons that enable local protein translation at distal sites, supporting proper protein homeostasis, both crucial for neurodevelopment and optimal neuronal function. KEY POINTSO_LIRibosomes in neurons organize into unique clusters that are incorporated into "neuronal RNA granules". C_LIO_LIApproximately half of the ribosomes in these clusters are stalled in elongation. C_LIO_LIThe mRNA sequences read by these ribosomes facilitate stalling. C_LIO_LIRibosomes within the clusters interact through rRNA expansion segments. C_LIO_LIRibosomes in the clusters form unique 3D structures that are not detected by the ribosome-associated quality-control response. C_LI

neuroscience↗

bioRxiv2026

Recursive mutational robustness in cancer through intra- and inter-genic compensation

Mutational robustness is a fundamental property of biological systems allowing phenotypic stability against genotypic perturbation. At the gene level, this is primarily attributed to inter-genic functional redundancy driven by paralogs. Here, we show that intra-genic functional redundancy, driven by alternatively spliced isoforms, is another prevalent source of mutational robustness. Integrating isoform-resolved pan-cancer genomics and transcriptomics data across tumors and cancer cell lines, we show that alternative isoforms often bypass deleterious somatic mutations. Mutation-skipping isoforms exhibit compensatory upregulation indicative of robustness against deleterious effects, especially in highly expressed genes. We found that intra-genic robustness is strongly associated with perturbation tolerance, is highly context-specific and, notably, can be complemented and augmented recursively by inter-genic robustness. Non-tumour-suppressor genes generally show higher robustness than tumour suppressor genes, and intra-genic compensation of their mutations is associated with worse disease outcome in most cancer types. Furthermore, intra-genic compensation by mutation-skipping isoforms associates with differential isoform usage among proximal interactors, suggesting restorative protein interaction rewiring at isoform-level. Mechanistically, self-transcriptional adaptation (self-TA) following nonsense-mediated decay of perturbed isoforms provides an explanation for the observed up-regulation of mutation-skipping isoforms. Overall, the proposed recursive mutational robustness framework opens new avenues for deeper mechanistic investigation into cancer evolution and identification of selective vulnerabilities in cancer cells. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=155 SRC="FIGDIR/small/727768v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@1b0f79aorg.highwire.dtl.DTLVardef@14fa261org.highwire.dtl.DTLVardef@12da16aorg.highwire.dtl.DTLVardef@c03dee_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2026

A Multiomic Analysis of Cachectic Mice Reveals Cancer Driven Suppression of Muscle Stem Cell Differentiation

Cancer cachexia affects a large proportion of cancer patients, inducing a rapid decline in muscle mass. Patients with cachexia have a worse prognosis and are less responsive to cancer therapies. The exact cause of cachexia remains unknown, nor are there any effective treatments for the condition. In this study, we use the C26 adenocarcinoma cell line to determine how cancer cells affect myofiber and muscle stem cell function. We determined that C26 cancer cells adapt to the host environment, in both male and female mice, greatly altering their transcriptome to promote their survival and growth. C26 cells directly communicate with muscle stem cells via GDF15 and MMP9. These circulatory factors cause the muscle stem cells to upregulate the EMT pathway and become less capable of undergoing differentiation and contributing to muscle regeneration. Muscle stem cells from tumor bearing mice are less proliferative and less prone to differentiation, Chromatin accessibility data shows that there are fewer accessible myogenic regulatory binding sites. Cytokine array determined that circulating GDF15 and MMP9 were highly upregulated and were derived form C26 tumor cells. However, blocking tumor derived GDF15 is not sufficient to prevent the onset of cachexia and rescue the loss of muscle stem cell function. Together, these findings establish a new conceptual paradigm in which cancer orchestrates muscle wasting through coordinated transcriptional, metabolic, and epigenetic suppression of muscle stem cell differentiation.

cell biology↗

bioRxiv2024

GHT-SELEX demonstrates unexpectedly high intrinsic sequence specificity and complex DNA binding of many human transcription factors

Precise identification of transcription factor (TF) binding sites is a long standing challenge in human regulatory genomics: TF binding motifs are short and degenerate, while the genome is large. Motif scans, therefore, often produce excessive binding site predictions. By surveying 179 TFs across 25 families using >1,500 cyclic in vitro selection experiments with fragmented, naked, and unmodified genomic DNA - a method we term GHT-SELEX (Genomic HT-SELEX) - we find that many human TFs possess much higher sequence specificity than anticipated. Moreover, genomic binding regions from GHT-SELEX are often surprisingly similar to those obtained in vivo (i.e., ChIP-seq peaks). Contrary to conventional wisdom, we find that high specificity can also be obtained from motif scans, but performance is highly dependent on the derivation and use of the motifs, including accounting for multiple local matches. We also observe alternative engagement of multiple DNA-binding domains within the same protein: long C2H2 zinc finger proteins often utilize modular DNA recognition, engaging different subsets of their DNA-binding domain (DBD) arrays to recognize multiple types of distinct target sites, frequently evolving via internal duplication and divergence of one or more DBDs. Thus, it is common for TFs to possess sufficient intrinsic specificity to delineate a large fraction of in vivo genomic targets, independently of other cellular factors.

genomics↗

bioRxiv2024

Extensive binding of uncharacterized human transcription factors to genomic dark matter

The functional impact of a large portion of the human genome known as "dark matter DNA", which is composed mainly of repeat sequences, remains enigmatic. The genome also encodes hundreds of putative and poorly characterized transcription factors (TFs). Here, we determined genomic binding locations of 166 poorly characterized human TFs in living cells. Nearly half of them associate strongly with known regulatory regions such as promoters and enhancers, frequently co-localizing with each other at conserved motif matches. The other half often associate with genomic dark matter, however, at largely non-overlapping (i.e., unique) sites, via intrinsic sequence recognition. Fifty-four of the latter half, which we term "Dark TFs", mainly bind within regions of closed chromatin, with each recognizing a unique set of repeat sequences. The Dark TFs include many KZNFs, which are known to bind and silence TEs, and other TFs with apparent repressive functions. By contrast, some may be pioneers: we find that induction of TPRX1, a known regulator of zygotic preimplantation, leads to chromatin opening at many of its binding sites in the dark matter genome. Altogether, our results shed light on a large fraction of poorly characterized human TFs and simultaneously illuminate the diversity of function within the dark matter genome.

genomics↗

bioRxiv2021

A base-resolution panorama of the in vivo impact of cytosine methylation on transcription factor binding

While methylation of CpG dinucleotides is traditionally considered antagonistic to the DNA-binding activity of most transcription factors (TFs), recent in vitro studies have revealed a more complex picture, suggesting that over a third of TFs may preferentially bind to methylated sequences. Expanding these in vitro observations to in vivo TF binding preferences, however, is challenging, as the effect of methylation of individual CpG sites cannot be easily isolated from the confounding effects of DNA accessibility and regional DNA methylation. As a result, the in vivo methylation preferences of most TFs remain uncharacterized. Here, we introduce joint accessibility-methylation-sequence (JAMS) models, which connect the strength of the binding signal observed in ChIP-seq to the DNA accessibility of the binding site, regional methylation level, DNA sequence, and base-resolution cytosine methylation. We show that JAMS models quantitatively explain the TF binding strength, recapitulate cell type-specific TF binding, and have high precision for inferring intra-motif methylation effects. Analysis of 2209 ChIP-seq experiments resulted in high-confidence JAMS models for 260 TFs, revealing that 45% of TFs are inhibited by intra-motif methylation in vivo. In contrast, only 16 TFs (6%) preferentially bind to methylated sites, including 11 novel methyl-binding TFs that are mostly from the multi-zinc finger family of TFs. Our study substantially expands the repertoire of in vivo methyl-binding TFs, but also suggests that most TFs that prefer methylated CpGs in vitro present themselves as methylation agnostic in vivo, potentially due to the balancing effect of competition with other methyl-binding proteins.

bioinformatics↗

bioRxiv2021

Transcriptional Reprogramming of Skeletal Muscle Stem Cells by the Niche Environment

Adult stem cells are indispensable for tissue regeneration. Tissue-specific stem cells reside in a specialized location called their niche, where they are in constant cross talk with neighboring niche cells and circulatory signals from their environment. Aging has a detrimental effect on the number and the regenerative function of various stem cells. However, whether the loss of stem cell function is a cause or consequence of their aging niche is unclear. Using skeletal muscle stem cells (MuSCs) as a model, we decouple cell-intrinsic from niche-mediated extrinsic effects of aging on their transcriptome. By combining in vivo MuSC heterochronic transplantation models and computational methods, we show that on a genome-wide scale, age-related altered genes fall into two distinct categories regarding their response to the niche environment. Genes that are inelastic in their response to the niche exhibit altered chromatin accessibility and are associated with differentially methylated regions (DMRs) between young and aged cells. On the other hand, genes that are restorable by niche exposure exhibit altered transcriptome but show no change in chromatin accessibility or DMRs. Taken together, our data suggest that the niche environment plays a decisive role in controlling the transcriptional activity of MuSCs, and exposure to a young niche can reverse approximately half of all age-associated changes that are not epigenetically encoded. The muscle niche therefore serves as an important therapeutic venue to mitigate the negative consequence of aging on tissue regeneration.

genetics↗

bioRxiv2021

Transcriptional Control of Brain Tumour Stem Cell Fate by a Carbohydrate Binding Protein

Brain tumour stem cells (BTSCs) and intratumoural heterogeneity represent major challenges in glioblastoma therapy. Here, we report that the LGALS1 gene, encoding the carbohydrate binding protein, galectin1, is a key regulator of BTSCs and glioblastoma resistance to therapy. Genetic deletion of LGALS1 alters BTSC gene expression profiles and results in downregulation of gene sets associated with mesenchymal subtype of glioblastoma. Using a combination of pharmacological and genetic approaches, we establish that inhibition of LGALS1 signalling in BTSCs impairs self-renewal, suppresses tumourigenesis, prolongs lifespan, and improves glioblastoma response to ionizing radiation in preclinical animal models. Mechanistically, we show that LGALS1 is a direct transcriptional target of STAT3 with its expression robustly regulated by the ligand OSM. Importantly, we establish that galectin1 forms a complex with the transcription factor HOXA5 to reprogram BTSC transcriptional landscape. Our data unravel an oncogenic signalling pathway by which galectin1/HOXA5 complex maintains BTSCs and promotes glioblastoma.

cancer biology↗