Biology subjects

Carbajal, A.

Publications and source records attributed to Carbajal, A..

6 recordsLinked to original sources

bioRxiv2025

A novel CHD4-CTCF regulatory axis drives key developmental programs and transitions in male germ cells.

Sustained gamete production and testis development relies in developmental programs and transitions such as spermatogonia differentiation, meiosis, and spermiogenesis. Chromatin remodeling complexes and CTCF are key regulators of these processes by controlling specific patterns of gene expression across gamete development. Although the CHD4 chromatin remodeler and CTCF have been implicated in spermatogonia development, a mechanism explaining their cooperation is missing. We also do not know CHD4 and CTCF role in later stages of spermatogenesis. Our studies reveal that germ cell-specific deletion of CHD4 results in spermatogonia development defects and affects meiotic-specific functions such as homologous chromosome synapsis. Combined analysis of genome-wide chromatin binding and single cell gene transcription showed that CHD4 controls specific gene expression programs important for spermatogonia differentiation, transition into meiosis, and meiotic specific processes. Mechanistically, this can be explained by a pervasive role for CHD4 in controlling CTCF chromatin binding and transcriptional function. The discovery of a functional interplay between CHD4 and CTCF reveals a novel axis of gene expression control, integrating chromatin structure and transcriptional outcomes. This interaction is essential in orchestrating early testis development and meiotic processes, ensuring that the correct number of chromosomes is faithfully transmitted to the next generation.

developmental biology↗

bioRxiv2025

Kinesin drive meiotic chromosome dynamics via interaction with the KASH5-LINC complex

Telomere-led rapid prophase chromosome movements (RPMs) during meiotic prophase are critical for homologous chromosome pairing and proper meiotic progression. These movements are generated by the cytoskeleton and are transmitted to the telomeres via the LINC complex, yet the cytoplasmic components that generate these forces remain poorly defined. Among candidates of microtubule-associated motor proteins in mouse primary spermatocytes, we confirmed KIF5B as a specific interactor of the KASH5-LINC complex. Total internal reflection fluorescence microscopy and microtubule sedimentation assays performed with purified recombinant proteins suggest a direct interaction between KASH5 and KIF5B on microtubules, enhanced by MAP7, a known KIF5B-recruiting and activating cofactor. Mapping the KIF5B-binding surface of KASH5 revealed that KASH5 N-terminal EF-hand domains mediate the interaction. Further, in vivo KIF5B-KASH5 interaction and KIF5B role in RPMs are evidenced as (1) KIF5B is recruited by KASH5-SUN1 to the nuclear envelope in two different cultured somatic cell models, (2) KIF5B is telomere-associated and colocalizes with KASH5, and microtubules associated with the nuclear envelope in mouse spermatocytes, and (3) chemical inhibition of KIF5B reduces telomere-led chromosome motions. Altogether, our findings identify the KIF5B kinesin as a previously unrecognized component of the force-generating machinery that drives chromosome movement during meiotic prophase I, acting through KASH5 as a specific nuclear membrane adaptor.

cell biology↗

bioRxiv2022

Relationships of scale cortisol content suggests stress resilience in freshwater fish vulnerable to catch-and-release angling in recreational fisheries

The capture by angling of an individual fish is recognised as a short-term physiologically stressor. In fish populations exploited by catch and release angling (C&R), there is potential for some individual fishes to be captured on multiple occasions, but the longer term physiological consequences of this remain uncertain. Using scale cortisol content as a biomarker of chronic stress and scale samples from two fish populations exploited by C&R angling, we developed proxies of angling capture vulnerability before testing these proxies against scale cortisol content. In a riverine population of European barbel Barbus barbus, fish with the highest scale cortisol content were predicted as those sampled by angling rather than electric fishing, as angled fish had significantly smaller home ranges and diets based primarily on angling baits. In a population of common carp Cyprinus carpio in a small pond fishery, we predicted that fish with the highest scale cortisol content would be those with higher proportions of angling bait in their diet. In both species, however, the fish predicted to be most vulnerable to angling capture had the lowest levels of scale cortisol content. We suggest that this is through fish that are captured regularly being highly stress resilient (with this independent of other traits) or fish with traits that suggest high capture vulnerability being able to minimise their recapture rates through developing hook avoidance behaviours after an initial capture. Overall, these results suggest that scale cortisol content is a useful biomarker for measuring chronic stress from C&R angling. HighlightsO_LIIn catch-and-release angling (C&R), a single capture event is a short-term stressor C_LIO_LIThe effect of multiple capture events on individual fishes in C&R is unknown C_LIO_LIScale cortisol content was used as a biomarker of chronic stress C_LIO_LIFish of high vulnerability to capture had relatively low scale cortisol content C_LIO_LIFish with high exposure to C&R appear to have high stress resilience. C_LI

ecology↗

bioRxiv2022

Efficient enrichment of synchronized mouse spermatocytes suitable for genome-wide analysis.

Chromatin-based mechanisms regulating developmental transitions during meiosis are fundamental but understudied aspects of male gametogenesis. Indeed, chromatin undergoes extensive remodeling during meiosis, leading to specific patterns of gene expression and chromosome organization, which ultimately controls fundamental meiotic processes such as recombination and homologous chromo-some associations. Recent game-changing advances have been made by analysis of chromatin binding sites of meiotic specific proteins genome-wide in mouse spermatocytes. However, further progress is still highly dependent on the reliable isolation of sufficient quantities of spermatocytes at specific stages of prophase I. Here, we describe a combination of methodologies adapted for rapid and reliable isolation of synchronized fixed mouse spermatocytes. We show that chromatin isolated from these cells can be used to study chromatin binding sites by ChIP-seq. High quality data we obtained from INO80 ChIP-seq in zygotene cells was used for functional analysis of chromatin binding sites.

systems biology↗

bioRxiv2020

The hunt for ancient prions: Archaeal prion-like domains form amyloids and substitute for yeast prion domains

Prions are proteins capable of acquiring an alternate conformation that can then induce additional copies to adopt this same alternate conformation. Although initially discovered in relation to mammalian disease, subsequent studies have revealed the presence of prions in Bacteria and Viruses, suggesting an ancient evolutionary origin. Here we explore whether prions exist in Archaea - the last domain of life left unexplored with regard to prions. After searching for potential prion-forming protein sequences computationally, we tested candidates in vitro and in organisms from the two other domains of life: Escherichia coli and Saccharomyces cerevisiae. Out of the 16 candidate prion-forming domains tested, 8 bound to amyloid-specific dye, and six acted as protein-based elements of information transfer, driving non-Mendelian patterns of inheritance. We additionally identified short peptides from archaeal prion candidates that can form amyloid fibrils independently. Candidates that tested positively in our assays had significantly higher tyrosine and phenylalanine content than candidates that tested negatively, suggesting that the presence of these amino acids may help distinguish functional prion domains from nonfunctional ones. Our data establish the presence of amyloid-forming prion-like domains in Archaea. Their discovery in all three domains of life further suggests the possibility that they were present at the time of the last universal common ancestor (LUCA). Significance StatementThis work establishes that amyloid-forming, prion-like domains exist in Archaea and are capable of vertically transmitting their prion phenotype - allowing them to function as protein-based elements of inheritance. These observations, coupled with prior discoveries in Eukarya and Bacteria, suggest that prion-based self-assembly was likely present in lifes last universal common ancestor (LUCA), and therefore may be one of the most ancient epigenetic mechanisms.

evolutionary biology↗

bioRxiv2019

CHD4-NURD controls spermatogonia survival and differentiation

Testis development and sustained germ cell production in adults rely on the establishment and maintenance of spermatogonia stem cells and their proper differentiation into spermatocytes. Chromatin remodeling complexes regulate critical processes during gamete development by restricting or promoting accessibility of DNA repair and gene expression machineries to the chromatin. Here, we investigated the role of CHD4 and CHD3 catalytic subunits of the NURD complex during spermatogenesis. Germ cell-specific deletion of Chd4 early in gametogenesis, but not Chd3, resulted in arrested early gamete development due to failed cell survival of neonate undifferentiated spermatogonia stem cell population. Candidate assessment revealed that CHD4 controls expression of Dmrt1 and its downstream target Plzf, both described as prominent regulators of spermatogonia stem cell maintenance. Our results show the requirement of CHD4 in mammalian gametogenesis pointing to functions in gene expression early in the process.

developmental biology↗