Biology subjects

Aguilera, A.

Publications and source records attributed to Aguilera, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Infraslow modulation of theta synchrony in the hippocampus circuit during REM sleep

Sleep dynamically reorganizes hippocampal activity, but how this reconfiguration supports large-scale coordination across the hippocampal circuit remains unclear. We performed simultaneous recordings from dorsal (CA1d) and ventral (CA1v) hippocampus, retrosplenial cortex (RSC), prefrontal cortex (PFC), and dorsal thalamus in rats across brain states. Theta oscillations dominated hippocampal activity during active behaviour and REM sleep, while delta oscillations prevailed during nREM and quiet waking. Phase synchrony between CA1d and CA1v varied across states, peaking during REM sleep and exhibiting infraslow fluctuations (0.02 Hz) unique to this stage. These slow modulations persisted after controlling for theta power, suggesting a genuine modulation of interregional synchrony. Transitions into REM were marked by rising CA1d-CA1v synchrony and widespread neuronal activation, with thalamic activity most strongly predicting coupling dynamics. During REM sleep, neuronal firing across hippocampal-cortical-thalamic circuits was phase-locked to the infraslow theta coupling cycle, indicating gain modulation at the network level. Such entrainment was strongest and most consistent in REM and aligned near a common phase, revealing temporally structured communication at multiple scales. Our findings identify an infraslow modulation of hippocampal theta coherence that temporally organizes neuronal excitability across brain regions during REM sleep, offering a systems-level mechanism for regulating inter-regional communication during sleep.

neuroscience↗

bioRxiv2026

Spatial memory performance is associated with region-specific coordination of hippocampo-cortical sleep oscillations

Sleep plays a critical role in memory consolidation, yet how coordination among sleep oscillations across hippocampo-cortical circuits relates to behavioral performance remains incompletely understood. Here, we examined how cross-regional coordination of cardinal sleep oscillations during non-rapid eye movement (nREM) sleep relates to spatial memory performance. Adult rats were trained in an object-place recognition task and allowed to sleep while local field potentials were recorded simultaneously from dorsal and ventral hippocampus (CA1d and CA1v) and retrosplenial, prefrontal, and lateral entorhinal cortices. We first confirm that nREM sleep duration, but not REM sleep, is positively associated with spatial memory performance. We then characterized the temporal relationships between hippocampal sharp-wave ripples and cortical spindles and slow oscillations, revealing region- and oscillation-specific coordination patterns that depend on the dorso-ventral origin of hippocampal ripple events. Finally, by comparing task-related changes in ripple-triggered cortical activity between low- and high-performing sessions, we identify selective, performance-dependent modulation of hippocampo-cortical coupling during task-related sleep. Spatial memory performance was consistently associated with enhanced ripple-spindle and ripple-slow oscillation coupling driven by dorsal hippocampal ripples, particularly in interactions with entorhinal and prefrontal cortices, whereas ventral hippocampal interactions failed to show behavioural association. Together, these results reveal that spatial memory performance is linked to region- and timing-specific coordination of sleep oscillations across hippocampo-cortical networks during nREM sleep, highlighting a functional differentiation of dorsal and ventral hippocampal contributions to sleep-dependent memory consolidation.

neuroscience↗

bioRxiv2025

Crossfrequency routing in a hippocampocortical circuit during probabilistic reversal learning

Learning under uncertainty requires detecting latent changes in environmental contingencies and flexibly adjusting choice strategy. To model this process and identify associated circuit dynamics, we trained rats on a two-armed bandit task with uncued reward reversals while simultaneously recording local field potentials from the circuit comprised by dorsal hippocampus (CA1d), lateral entorhinal cortex (LEC), and prefrontal cortex (PFC). Behavioral performance improved with training and progressively shifted from outcome-reactive exploration to an exploitation-biased strategy, quantified using a model-free index. Mixed-effects modeling combining behavioral and neural metrics identified tonic cortical synchrony in theta and fast-gamma bands as a negative session-scale performance marker. Theta and gamma oscillations were coordinated, as cross-regional phase-amplitude coupling showed that CA1d theta phase gated fast-gamma activity in PFC, while biasing both slow- and fast-gamma bursts in LEC, which selectively increased at goal-reaching. Neuronal spiking showed cross-regional phase-locking to both theta and gamma rhythms, indicating synchronized timing across the hippocampo-cortical circuit. Finally, distributed neuronal spiking across the circuit represented goal-approach, yet only prefrontal neurons ramped during goal-reaching, suggesting a role in outcome assessment, while hippocampal and entorhinal units transiently suppressed, consistent with locomotor tracking and resetting. These results reveal a tonic cortical connectivity marker of ongoing performance during reversal learning and dissociate it from hippocampal theta mechanisms that selectively organize cortical gamma bursts and spike timing. Together, these results provide mechanistic insight into how frequency-specific hippocampo-cortical interactions dynamically reconfigure to support strategy transitions, offering a circuit-level framework for understanding adaptive decision-making under uncertainty. Significance StatementAnimals often learn in uncertain environments, where they must decide whether to keep exploiting a known option or explore alternatives. We trained rats on a probabilistic choice task while recording brain activity from hippocampus, entorhinal cortex, and prefrontal cortex. We found that performance improvements were linked to an ongoing interaction between entorhinal and prefrontal areas, whereas hippocampal signals changed mainly with training and controlled the timing of brief, fast activity bursts in cortex. Near reward, prefrontal neurons ramped up while hippocampal and entorhinal neurons were suppressed. Together, these results separate brain signals that track current performance from those that shape cortical dynamics during learning.

neuroscience↗

bioRxiv2025

HDAC1 has a role in double strand break repair by regulating γH2AX signalling

Genome integrity is challenged by DNA damage. DNA double-strand breaks are the most harmful DNA lesions as they block DNA replication and transcription leading to chromosome reorganisations or cell death if not properly repaired. In addition, increasing evidence points to chromatin as a relevant modulator of the efficiency of repair in eukaryotes. Here, we show that inhibition or depletion of human histone deacetylase 1 (HDAC1) regulates DSB repair by controlling the phosphorylation of H2AX, an early step of the DNA damage response. Thus, DSB repair is regulated by a crosstalk between histone acetylation and phosphorylation. Our study provides evidence that histone acetylation regulates DSB signalling supporting that histone deacetylase inhibitors could enhance genotoxic treatment of cancer.

molecular biology↗

bioRxiv2025

Hippocampo-supramammillary coupling across sleep and wake

Hippocampal communication with subcortical circuits reorganizes across sleep-wake states, yet the dynamics of such interactions remain incompletely defined. We simultaneously recorded neuronal spiking and local field potentials from the dorsal hippocampus (CA1 and dentate gyrus) and limbic subcortical nuclei (supramammillary nucleus (SuM) and lateral septum (LS)) in freely behaving rats across the sleep-wake cycle. During quiescent states (non-rapid eye movement (nREM) sleep and quiet wakefulness), sharp-wave ripples dominated hippocampal activity and produced fast, top-down excitation, with large population surges locally in CA1 and DG, and more modest but significant activation in LS and SuM, whereas dentate spikes elicited smaller state-invariant responses. Conversely, in the bottom-up direction, epochs of high-discharge SuM activity were associated with slower, state-dependent activation of hippocampal populations that was larger in wake than in sleep, revealing distinct temporal scales and state dependence for reciprocal pathways. During activated, theta-enriched states (rapid eye movement (REM) sleep and active wakefulness), spike-field coupling revealed circuit-wide theta coordination. In active wakefulness, SuM bursts produced brief inhibition of CA1 spiking while theta oscillations organized a multiregional firing sequence around the theta cycle trough; yet SuM neurons were not significantly phase-locked. In REM sleep, this pattern inverted, with only SuM neurons significantly phase-locking to theta waves, and preferred firing near the theta cycle peak. Together, these findings identify state-dependent, bidirectional coordination between hippocampus and subcortical nuclei, characterized by ripple-locked top-down hippocampal output during quiescent states and SuM-mediated bottom-up modulation that reconfigures under theta during activated states.

neuroscience↗

bioRxiv2025

Hippocampal Synchrony Dynamically Gates Cortical Connectivity Across Brain States

Memory consolidation is thought to rely on hippocampo-cortical dialogue orchestrated by three cardinal sleep oscillations: cortical slow oscillations, thalamic spindles, and hippocampal sharp-wave ripples. However, how hippocampal outputs are routed to specific cortical targets and dynamically regulated across brain states remains incompletely understood. Here, we performed simultaneous multisite recordings from the dorsal and ventral hippocampus, and frontal and parietal cortex in rats alternating between wakefulness and sleep. Frontal slow oscillations operated as a global clock, resetting thalamic circuits and initiating spindle volleys that propagated from anterior to posterior cortex, while parietal slow oscillations more effectively recruited hippocampal ripples. Hippocampal ripples reflected anatomical connectivity, as dorsal ripples preferentially enhanced parietal spindles, whereas ventral ripples engaged mainly frontal spindling. Notably, when ripples synchronized in dorsal and ventral hippocampus, local excitatory drive sharply decreased and neuronal spiking redistributed, associated cortical slow oscillations and spindle responses diminished, and cortical neuronal reactivation was suppressed, indicating that dorso-ventral ripple synchrony gates, rather than amplifies, hippocampo-cortical communication. This gating effect was most evident through interactions with brain state, as dorsal-driven reactivation persisted across vigilance states, while ventral pathways were more pronounced during sleep. Collectively, our results outline a multilayer architecture in which slow oscillations provide a global temporal scaffold, spindles implement anatomically specific reactivation channels, and ripple coordination gates hippocampo-cortical communication, likely shaping the precision and specificity of memory consolidation within a highly variable neural substrate. SignificanceSharp-wave ripples in the hippocampus are critical for memory consolidation, in part due to their precise temporal coordination with cortico-thalamic sleep rhythms. However, whether ripple synchronization along the hippocampal septo-temporal axis modulates cortical memory processing has remained unresolved. Here, we show that coordinated ripples, occurring simultaneously in dorsal and ventral CA1, are observed more frequently than predicted by independent occurrence and are associated with significant suppression of cortical reactivation compared to isolated episodes. This suppression does not reflect simple changes in ripple structure or increased inhibition, but instead is linked to a redistribution of excitatory drive across the hippocampal septo-temporal axis. Importantly, this gating effect is present across both sleep and wakefulness. These findings suggest that hippocampal synchrony dynamically gates, rather than amplifies, cortical engagement, thus refining systems consolidation models by highlighting the significance of network organization and precise temporal dynamics in shaping memory replay.

neuroscience↗

bioRxiv2024

Different alterations in mRNP composition trigger an increase in harmful R-loops

Understanding how the assembly of nascent mRNA into a ribonucleoprotein (mRNP) influences R-loop homeostasis is crucial for gaining insight into the cellular mechanisms that prevent genome instability. Here, we identify three RNA-binding proteins, Rie1, Rim4 and She2, whose stoichiometry is important to limit R-loop accumulation and, thus, to prevent DNA damage. Interestingly, Rim4 and She2 are overrepresented in mRNPs assembled in the absence of THO. In addition, we found that an excess of Dis3 impairs exosome function, promoting R-loops, particularly from non-coding RNAs, which cause genomic instability. Our results indicate that mRNP assembly is a precise process that, when perturbed by changes in the availability of different RBPs or RNAs, causes R-loop-mediated DNA damage in the cell. These results may help to understand the mechanism that promotes cancer, as several RBPs are overexpressed in different types of tumors. Author summaryR-loops are three-stranded structures formed by a DNA-RNA hybrid and the displaced ssDNA. The accumulation of R-loops damages the genome, highlighting the need for their tight regulation. One of the mechanisms that prevents R-loop formation is the co-transcriptional assembly of the nascent RNA into a messenger ribonucleoprotein (mRNP). Our study reveals that mRNP biogenesis is highly sensitive to perturbations. Not only the absence of mRNP components, but also the overexpression of specific RNA-binding proteins (RBPs) or the persistence of unstable transcripts, significantly stresses mRNP assembly, resulting in R-loop accumulation and consequent DNA damage. R-loops are involved in a number of neurodegenerative diseases and cancer, highlighting the importance of understanding the cellular processes that mitigate their accumulation.

genetics↗

bioRxiv2024

SMARCAD1 Regulates R-Loops at Active Replication Forks Linked to Cancer Mutation Hotspots

DNA replication often encounters obstacles like the stalled transcription machinery and R-loops. While ribonucleases and DNA-RNA helicases can resolve these structures, the role of chromatin remodelers remains understudied. Through a series of in vitro and in vivo experiments, we show that the chromatin remodeler SMARCAD1, which associates with active replication forks, is crucial for resolving nearby R-loops to maintain fork stability. SMARCAD1 directly binds R-loops via its ATPase domain and associates with the replisome through its N-terminus region. Both interactions are critical for resolving R-loops within cells. Genome-wide assays reveal that cells expressing mutant SMARCAD1 accumulate significantly more R-loops than wild-type cells, particularly in regions distinct from known fork blockage-prone sites. These R-loop-enriched regions in SMARCAD1 mutants also exhibit increased mutagenesis in germline tumors, suggesting they are mutation hotspots in cancer. Therefore, SMARCAD1 acts as an R-loop sensor and resolvase at actively progressing forks, maintaining genome stability and preventing tumorigenesis.

genetics↗

bioRxiv2024

Dbf4-Dependent Kinase Finetunes INO80 Function at Chromosome Replication Origins

The highly conserved Dbf4-Dependent Kinase (DDK) plays a pivotal role in the nucleus during S phase, where it directly phosphorylates the replicative helicase, the minichromosome maintenance (MCM) complex. This leads to the initiation of chromosome replication. However, aside from the MCM complex, few other targets have been identified to date, leaving DDK an understudied kinase. Here, we describe a two-pronged mass spectrometry-based approach and define the nuclear DDK-dependent phosphoproteome, which consists of approximately 400 phosphorylation events. Within this network, we found that DDK directly phosphorylates the Arp8 subunit of the multi-subunit chromatin remodeler complex INO80. Arp8 phosphorylation stabilises INO80s intramolecular complex integrity, which finetunes its nucleosome spacing activity at replication origins. This adjustment of origin chromatin architecture stimulates replication and is important for the response to replication stress. Our results represent a significant advance in our understanding of the molecular mechanisms underlying the regulation of replication origins.

biochemistry↗

bioRxiv2024

The histone variant H2A.Z is required for efficient transcription-coupled NER and to maintain genome integrity in UV challenged yeast cells.

The genome of living cells is constantly challenged by DNA lesions that interfere with cellular processes such as transcription and replication. A manifold of mechanisms act in concert to ensure adequate DNA repair, gene expression, and genome stability. Bulky DNA lesions, such as those induced by UV light or the DNA-damaging agent 4-nitroquinoline oxide, act as transcriptional and replicational roadblock and thus represent a major threat to cell metabolism. When located on the transcribed strand of active genes, these lesions are handled by transcription-coupled nucleotide excision repair (TC-NER), a yet incompletely understood NER sub-pathway. Here, using a genetic screen in the yeast Saccharomyces cerevisiae, we identified histone variant H2A.Z as an important component to safeguard transcription and DNA integrity following UV irradiation. In the absence of H2A.Z, repair by TC-NER is severely impaired and RNA polymerase II clearance reduced, leading to an increase in double-strand breaks. Thus, H2A.Z enables proficient TC-NER and plays a major role in the maintenance of genome stability upon UV irradiation. Author summaryThe genome of living organisms is constantly challenged by intrinsic and extrinsic DNA damaging agents. The resulting DNA lesions must be readily repaired to maintain genome integrity. This is particularly important for bulky DNA lesions, such as those produced by UV light, as they will block the progress of elongating RNA polymerases on transcribed genes. These DNA lesions are repaired by a specific pathway called transcription-coupled nucleotide excision repair (TC-NER), the dysfunction of which is associated with severe human diseases. In this work, we used budding yeast as a eukaryotic model organism to perform a genetic screen for new TC-NER factors. We discovered that the HTZ1 gene, encoding the histone variant H2A.Z, is required for efficient DNA repair by TC-NER. Our molecular and genetic analyses showed that in the absence of H2A.Z, RNA polymerases persist on damaged DNA, causing interference with DNA replication and genome instability. Our findings further highlight the importance of chromatin plasticity for the maintenance of genome integrity.

genetics↗

bioRxiv2024

IFI207, a young and fast-evolving protein, controls retroviral replication via the STING pathway

Mammalian AIM-2-like receptor (ALR) proteins bind nucleic acids and initiate production of type I interferons or inflammasome assembly, thereby contributing to host innate immunity. In mice, the Alr locus is highly polymorphic at the sequence and copy number level and we show here, is one of the most dynamic regions of the genome. One rapidly evolving gene within this region, Ifi207, was introduced to the Mus genome by gene conversion or an unequal recombination event a few million years ago. Ifi207 has a large, distinctive repeat region that differs in sequence and length among Mus species and even closely related inbred Mus musculus strains. We show that IFI207 controls MLV infection in vivo and that it plays a role in the STING-mediated response to cGAMP, dsDNA, DMXXA and MLV. IFI207 binds to STING and inclusion of its repeat region appears to stabilize STING protein. The Alr locus and Ifi207 provide a clear example of the evolutionary innovation of gene function, possibly as a result of host-pathogen co-evolution. IMPORTANCEThe Red Queen hypothesis predicts that the arms race between pathogens and the host may accelerate evolution of both sides, and therefore cause higher diversity in virulence factors and immune-related proteins, respectively (1). The Alr gene family in mice has undergone rapid evolution in the last few million years and includes the creation of two novel members, MndaL and Ifi207. Ifi207 in particular became highly divergent, with significant genetic changes between highly related inbred mice. IFI207 protein acts in the STING pathway and contributes to anti-retroviral resistance via a novel mechanism. The data show that under the pressure of host-pathogen coevolution in a dynamic locus, gene conversion and recombination between gene family members creates new genes with novel and essential functions that play diverse roles in biological processes.

immunology↗

bioRxiv2024

Topological regulation of the estrogen transcriptional response by ZATT-mediated inhibition of TOP2B activity

Human type-II topoisomerases, TOP2A and TOP2B, remove transcription associated DNA supercoiling, thereby affecting gene-expression programs, and have recently been associated with 3D genome architecture. Here, we study the regulatory roles of TOP2 paralogs in response to estrogen, which triggers an acute transcriptional induction that involves rewiring of genome organization. We find that, whereas TOP2A facilitates transcription, as expected for a topoisomerase, TOP2B limits the estrogen response. Consistent with this, TOP2B activity is locally downregulated upon estrogen treatment to favor the establishment and stabilization of regulatory chromatin contacts, likely through an accumulation of DNA supercoiling. We show that estrogen-mediated inhibition of TOP2B requires estrogen receptor (ER), a non-catalytic function of TOP2A, and the action of the atypical SUMO-ligase ZATT. This mechanism of topological transcriptional-control, which may be shared by additional gene-expression circuits, highlights the relevance of DNA topoisomerases as central actors of genome dynamics.

molecular biology↗

bioRxiv2023

IFI207, a young and fast-evolving antiviral factor, stabilizes STING

Mammalian ALR proteins bind nucleic acids and initiate production of type I interferons or inflammasome assembly, thereby contributing to host innate immunity. ALRs are encoded at a single genetic locus. In mice, the Alr locus is highly polymorphic at the sequence and copy number level. We suggest that one rapidly evolving member of the Alr family, Ifi207, was introduced to the Mus genome by a recent recombination event. Ifi207 has a large, distinctive repeat region that differs in sequence and length in different Mus strains. We show that IFI207 plays a key role in the STING-mediated response to cGAMP, DNA, and MLV, and that IFI207 controls MLV infection in vivo. Uniquely, IFI207 acts by stabilizing STING protein via its repeat region. Our studies suggest that under the pressure of host-pathogen coevolution, in a dynamic locus such as the Alr, recombination between gene family members creates new genes with novel and essential functions that play diverse roles in biological processes.

microbiology↗

bioRxiv2023

Actin nucleators safeguard replication forks by limiting nascent strand degradation

Accurate genome replication is essential for all life and a key mechanism of disease prevention, underpinned by the ability of cells to respond to replicative stress (RS) and protect replication forks. These responses rely on the formation of Replication Protein A (RPA)-single stranded (ss) DNA complexes, yet this process remains largely uncharacterized. Here we establish that actin nucleation-promoting factors (NPFs) associate with replication forks, promote efficient DNA replication and facilitate association of RPA with ssDNA at sites of RS. Accordingly, their loss leads to deprotection of ssDNA at perturbed forks, impaired ATR activation, global replication defects and fork collapse. Supplying an excess of RPA restores RPA foci formation and fork protection, suggesting a chaperoning role for actin nucleators (ANs) (i.e., Arp2/3, DIAPH1) and NPFs (i.e, WASp, N-WASp) in regulating RPA availability upon RS. We also discover that {beta}-actin interacts with RPA directly in vitro, and in vivo a hyper-depolymerizing {beta}-actin mutant displays a heightened association with RPA and the same dysfunctional replication phenotypes as loss of ANs/NPFs, which contrasts with the phenotype of a hyper-polymerizing {beta}-actin mutant. Thus, we identify components of actin polymerization pathways that are essential for preventing ectopic nucleolytic degradation of perturbed forks by modulating RPA activity.

molecular biology↗

bioRxiv2021

ADAR2-mediated RNA editing of DNA:RNA hybrids is required for DNA double strand break repair

The maintenance of genomic stability requires the coordination of multiple cellular tasks upon the appearance of DNA lesions. RNA editing, the post-transcriptional sequence alteration of RNA, has a profound effect on cell homeostasis, but its implication in the response to DNA damage was not previously explored. Here we show that, in response to DNA breaks, an overall change of the Adenosine-to-Inosine RNA editing is observed, a phenomenon we call the RNA Editing DAmage Response (REDAR). REDAR relies on the checkpoint kinase ATR and the recombination factor CtIP. Moreover, depletion of the RNA editing enzyme ADAR2 renders cells hypersensitive to genotoxic agents, increases genomic instability and hampers homologous recombination by impairing DNA resection. Such a role of ADAR2 in DNA repair goes beyond the recoding of specific transcripts, but depends on ADAR2 editing DNA:RNA hybrids to ease their dissolution. One sentence summaryDNA recombination requires RNA editing of DNA:RNA hybrids to ease their melting and facilitate DNA end resection

genetics↗

bioRxiv2020

A CDK-regulated chromatin segregase promoting chromosome replication

The replication of chromosomes during S phase is critical for cellular and organismal function. Replicative stress can result in genome instability, which is a major driver of cancer. Yet how chromatin is made accessible during eukaryotic DNA synthesis is poorly understood. Here, we report the identification of a novel class of chromatin remodeling enzyme, entirely distinct from classical SNF2-ATPase family remodelers. Yta7 is a AAA+-ATPase that assembles into ~ 1 MDa hexameric complexes capable of segregating histones from DNA. Yta7 chromatin segregase promotes chromosome replication both in vivo and in vitro. Biochemical reconstitution experiments using purified proteins revealed that Yta7s enzymatic activity is regulated by S phase-forms of Cyclin-Dependent Kinase (S-CDK). S-CDK phosphorylation stimulates ATP hydrolysis by Yta7, promoting nucleosome disassembly and chromatin replication. Our results present a novel mechanism of how cells orchestrate chromatin dynamics in co-ordination with the cell cycle machinery to promote genome duplication during S phase.

biochemistry↗

bioRxiv2020

Context-dependent functional compensation between Ythdf m6A readers

The N6-methyladenosine (m6A) modification is the most prevalent post-transcriptional mRNA modification, regulating mRNA decay, translation and splicing. It plays a major role during normal development, differentiation, and disease progression. The modification is dynamically regulated by a set of writer, eraser and reader proteins. The YTH-domain family of proteins: Ythdf1, Ythdf2, and Ythdf3, are three homologous m6A binding proteins, which have different cellular functions. However, their sequence similarity and their tendency to bind the same targets suggest that they may have overlapping roles. We systematically knocked out (KO) the Mettl3 writer for each of the Ythdf readers and for the three readers together (triple-KO). We then estimated the effect in-vivo, in mouse gametogenesis and viability, and in-vitro, in mouse embryonic stem cells (mESCs). We show that in gametogenesis, Mettl3-KO severity is increased as the deletion occurs earlier in the process, and Ythdf2 has a dominant role that cannot be compensated by Ythdf1 or Ythdf3, possibly due to differences in readers expression, both in quantity and in spatial location. By knocking out the three readers together and systematically testing offspring genotypes, we have revealed a redundancy in the readers role during early development, a redundancy which is dosage-dependent. Additionally, we show that in mESCs there is compensation between the three readers, since the inability to differentiate and the significant effect on mRNA decay occur only in the triple-KO cells and not in the single KOs. Thus, we suggest a novel model for the Ythdf readers function. There is a dosage-dependent redundancy when all three readers are co-expressed in the same location in the cells.

developmental biology↗

bioRxiv2020

TDP-43 deficiency links Amyotrophic Lateral Sclerosis with R-loop homeostasis and R loop-mediated DNA damage

TDP-43 is a DNA and RNA binding protein involved in RNA processing and with structural resemblance to heterogeneous ribonucleoproteins (hnRNPs), whose depletion sensitizes neurons to double strand DNA breaks (DSBs). Amyotrophic Lateral Sclerosis (ALS) is a neurodegenerative disorder, in which 97% of patients are familial and sporadic cases associated with TDP-43 proteinopathies and conditions clearing TDP-43 from the nucleus, but we know little about the molecular basis of the disease. Here, we prove that mislocalization of mutated TDP-43 (A382T) in transfected neuronal SH-SY5Y and lymphoblastoid cell lines (LCLs) from an ALS patient cause R-loop accumulation, and R loop-dependent increased DSBs and Fanconi Anemia repair centers. Similar results were observed in a non-neuronal model of HeLa cells depleted of TDP-43. These results uncover a new role of TDP-43 in the control of co-transcriptional R-loops and the maintenance of genome integrity by preventing harmful R-loop accumulation. Our findings thus link TDP-43 pathology to increased R-loops and R loop-mediated DNA damage opening the possibility that R-loop modulation in TDP-43-defective cells might help develop ALS therapies.

molecular biology↗