Biology subjects

Leyva-Diaz, E.

Publications and source records attributed to Leyva-Diaz, E..

8 recordsLinked to original sources

bioRxiv2026

CUT homeobox factors modulate chromatin accessibility in neurons

Neuronal identity relies on coordinated transcriptional programs that include both neuron type-specific features and broadly shared pan-neuronal properties. While transcription factors that control neuronal gene expression have been defined, how these regulators interface with chromatin accessibility at neuronal loci remains poorly understood. CUT homeobox factors are broadly expressed in the C. elegans nervous system and provide a genetically defined system to examine transcription factor associated chromatin accessibility in neurons. Here, we establish a fluorescence-activated sorting workflow to enrich neuronal nuclei using a pan-neuronal nuclear marker and apply bulk ATAC-seq to profile chromatin accessibility in wild-type and CUT mutant animals. We identify CUT-dependent accessibility differences in neuronal nuclei, with changes concentrated at promoter-proximal regions and linked to neuronal genes, including neuronally enriched and pan-neuronal categories. Together, this work provides in vivo neuronal chromatin accessibility profiles and defines CUT-dependent changes at a subset of neuronal regulatory regions.

neuroscience↗

bioRxiv2025

PHA-4/FoxA controls the function of pharyngeal and extrapharyngeal enteric neurons of C. elegans

FoxA transcription factors pattern gut tissue across animal phylogeny. Beyond their early patterning function, little is known about whether they control the terminal differentiation and/or function of the fully mature enteric nervous system, the intrinsic nervous system of the gut. We show here that the expression and function of the sole C. elegans FoxA homolog, PHA-4, reaches beyond its previously described pioneer factor roles in patterning the foregut. Through the engineering of neuron-specific cis-regulatory alleles, Cre-mediated cell-specific knockouts and degron-mediated, temporally controlled PHA-4/FoxA removal in postmitotic neurons, we found that PHA-4/FoxA is required not only to initiate the terminal differentiation program of foregut-associated enteric neurons, but also to maintain their functional properties throughout the life of the animal. Moreover, we discovered novel sites of expression of PHA-4/FoxA in extrapharyngeal enteric neurons that innervate the hindgut (AVL and DVB), a GABAergic interneuron that controls foregut function during sleep (RIS), and a peptidergic neuron, PVT, which we implicate here in controlling defecation behavior. We show that while PHA-4/FoxA is not required for the developmental specification of AVL, DVB, RIS, and PVT, it is required to enable these neurons to control enteric functions. Taken together, pha-4 is the only transcription factor known to date that is expressed in and required for the proper function of all distinct types of enteric neurons in a nervous system.

neuroscience↗

bioRxiv2024

Alternative splicing controls pan-neuronal homeobox gene expression

The pan-neuronally expressed and phylogenetically conserved CUT homeobox gene ceh-44/CUX orchestrates pan-neuronal gene expression throughout the nervous system of C. elegans. As in many other species, including humans, ceh-44/CUX is encoded by a complex locus that also codes for a Golgi-localized protein. How gene expression from this complex locus is controlled and, in C. elegans, directed to all cells of the nervous system has not been investigated. We show here that pan-neuronal expression of CEH-44/CUX is controlled by a pan-neuronal RNA splicing factor, UNC-75/CELF, the C. elegans homolog of vertebrate CELF proteins. UNC-75/CELF temporally and spatially specifies the production of an alternative, CEH-44/CUX homeobox gene-encoding transcript from a ubiquitously expressed gene locus, which also produces a Golgi apparatus-localized golgin protein, CONE-1 ("CASP of nematodes"). During embryogenesis the cone-1/ceh-44 locus exclusively produces the Golgi-localized CONE-1/CASP protein in all tissues, but upon the onset of postmitotic terminal differentiation of neurons, UNC-75/CELF induces the production of the alternative CEH-44/CUX CUT homeobox gene-encoding transcript, exclusively in the nervous system. Hence, UNC-75/CELF-mediated alternative splicing not only directs pan-neuronal gene expression, but also excludes a phylogenetically deeply conserved golgin from the nervous system, paralleling surprising spatial specificities of another golgin that we describe here as well. In summary, our findings provide novel insights into how all cells in a nervous system acquire pan-neuronal identity features.

developmental biology↗

bioRxiv2022

Restricted effects of the sole C. elegans Daughterless/E homolog, HLH-2, on nervous system development

Are there common mechanisms of neurogenesis used throughout an entire nervous system? Making use of the well-defined and relatively small size of the nervous system of the nematode C. elegans, we explored to what extent canonical proneural class I/II bHLH complexes are responsible for neurogenesis throughout the entire C. elegans nervous system. Distinct, lineage-specific proneural "class II" bHLH factors are generally thought to operate via interaction with a common, "class I" bHLH subunit, encoded by Daugtherless in flies, the E (E2A, E2-2, HEB) proteins in vertebrates, and hlh-2 in C. elegans. To eliminate function of all proneuronal class I/II bHLH complexes, we therefore genetically removed maternal and zygotic hlh-2 gene activity. We observed broad effects on neurogenesis, but still detected normal neurogenesis in many distinct neuron-producing lineages of the central and peripheral nervous system. Moreover, we find that hlh-2 selectively affects some aspects of neuron differentiation while leaving others unaffected. While our studies confirm the function of proneuronal class I/II bHLH complexes in many different lineages throughout a nervous system, we conclude that their function is not universal, but rather restricted by lineage, cell type and components of differentiation programs affected.

neuroscience↗

bioRxiv2022

Widespread employment of conserved C. elegans homeobox genes in neuronal identity specification

Homeobox genes are prominent regulators of neuronal identity, but the extent to which their function has been probed in animal nervous systems remains limited. In the nematode Caenorhabditis elegans, each individual neuron class is defined by the expression of unique combinations of homeobox genes, prompting the question of whether each neuron class indeed requires a homeobox gene for its proper identity specification. We present here progress in addressing this question by extending previous mutant analysis of homeobox gene family members and describing multiple examples of homeobox gene function in different parts of the C. elegans nervous system. To probe homeobox function, we make use of a number of reporter gene tools, including a novel multicolor reporter transgene, NeuroPAL, which permits simultaneous monitoring of the execution of multiple differentiation programs throughout the entire nervous system. Using these tools, we add to the previous characterization of homeobox gene function by identifying neuronal differentiation defects for 12 homeobox genes in 20 distinct neuron classes that are mostly unrelated by location, function and lineage history. 10 of these 20 neuron classes had no homeobox gene function ascribed to them before, while in the other 10 neuron classes, we extend the combinatorial code of transcription factors required for specifying terminal differentiation programs. Furthermore, we demonstrate that in a particular lineage, homeotic identity transformations occur upon loss of a homeobox gene and we show that these transformations are the result of changes in homeobox codes. Combining the present with past analysis, 111 of the 118 neuron classes of C. elegans are now known to require a homeobox gene for proper execution of terminal differentiation programs. Such broad deployment indicates that homeobox function in neuronal identity specification may be an ancestral feature of animal nervous systems.

neuroscience↗

bioRxiv2021

Robust regulatory architecture of pan-neuronal gene expression

Pan-neuronally expressed genes, such as genes involved in the synaptic vesicle release cycle or in neuropeptide maturation, are critical for proper function of all neurons, but the transcriptional control mechanisms that direct such genes to all neurons of a nervous system remain poorly understood. We show here that six members of the CUT family of homeobox genes control pan-neuronal identity specification in C. elegans. Single CUT mutants show barely any effects on pan-neuronal gene expression or global nervous system function, but such effects become apparent and progressively worsen upon removal of additional CUT family members, indicating a critical role of gene dosage. Overexpression of each individual CUT gene rescued the phenotype of compound mutants, corroborating that gene dosage, rather than the activity of specific members of the gene family, is critical for CUT gene function. Genome-wide binding profiles as well as mutation of CUT binding sites by CRISPR/Cas9 genome engineering show that CUT genes directly control the expression of pan-neuronal features. Moreover, CUT genes act in conjunction with neuron-type specific transcription factors to control pan-neuronal gene expression. Our study, therefore, provides a previously missing key insight into how neuronal gene expression programs are specified and reveals a highly buffered and robust mechanism that controls the most critical functional features of all neuronal cell types.

neuroscience↗

bioRxiv2020

Astrocytes and neurons share brain region-specific transcriptional signatures

Neuronal cell diversity is essential to endow distinct brain regions with specific functions. During development, progenitors within these regions are characterised by specific gene expression programs, contributing to the generation of diversity in postmitotic neurons and glia. While the region-specific molecular diversity of neurons and astrocytes is increasingly understood, whether these cells share region-specific programs remains unknown. Here, we show that in the neocortex and thalamus, neurons and astrocytes express shared region-specific transcriptional and epigenetic signatures. These signatures not only distinguish cells across brain regions but are also detected across substructures within regions, such as distinct thalamic nuclei, where clonal analysis revealed the existence of common nucleus-specific progenitors for neurons and glia. Consistent with their shared molecular signature, regional specificity was maintained following astrocyte-to-neuron reprogramming. A detailed understanding of these regional-specific signatures may thus inform strategies for future cell-based brain repair.

neuroscience↗

bioRxiv2017

pals-22, A Member Of An Expanded C. elegans Gene Family, Controls Silencing Of Repetitive DNA

Repetitive DNA sequences are subject to gene silencing in various animal species. Under specific circumstances repetitive DNA sequences can escape such silencing. For example, when exogenously added, extrachromosomal DNA sequences that are stably inherited in multicopy repetitive arrays in the nematode C. elegans are frequently silenced in the germline, whereas such silencing often does not occur in the soma. This indicates that somatic cells might utilize factors that prevent repetitive DNA silencing. Indeed, such \"anti-silencing\" factors have been revealed through genetic screens that identified mutant loci in which repetitive transgenic arrays are aberrantly silenced in the soma. We describe here a novel locus, pals-22 (for protein containing ALS2CR12 domain), required to prevent silencing of repetitive transgenes in neurons and other somatic tissue types. pals-22 deficiency also severely impacts animal vigor and confers phenotypes reminiscent of accelerated aging. We find that pals-22 is a member of a large family of divergent genes (39 members), defined by the presence of an ALS2CR12 domain. While gene family members are highly divergent, they show striking patterns of genomic clustering. The family expansion appears C. elegans-specific and has not occurred to the same extent in other nematode species. Previous transcriptome analysis has revealed that most of the pals genes are induced under stress conditions or upon infection by intracellular parasites. The transgene silencing phenotype observed upon loss of cytoplasmically localized PALS-22 protein depends on the biogenesis of small RNAs, since silencing is abolished in the RNAi defective mutant rde-4, suggesting that pals-22 might regulate RNAi dependent silencing in the cytoplasm of neurons and other tissues. We speculate that the pals gene family may be part of a species-specific cellular defense mechanism.

genetics↗