Biology subjects

Cochella, L.

Publications and source records attributed to Cochella, L..

8 recordsLinked to original sources

bioRxiv2025

Core microRNAs regulate neural crest delamination and condensation in the developing trigeminal ganglion

Cranial neural crest cells (NCCs) undergo dynamic processes during embryonic development, including delamination from the neural tube by epithelial-to-mesenchymal transition (EMT), migration to the periphery, condensation via mesenchymal-to-epithelial transition (MET) and differentiation into structures like the trigeminal ganglion. Here, we identify and characterize the function of a core set of miRNAs involved in these transitions during the formation of the trigeminal ganglion in the chick embryo. We further identify putative targets of miRNAs involved in neural crest EMT and MET. Notably, introducing MET-involved miRNAs into trunk NCCs endows these cells with the ability to condense and differentiate into neurons in vivo in a manner reminiscent of cranial rather than trunk NCCs. Our findings shed light on the intricate regulatory networks governing NCC behavior, positioning miRNAs as key regulatory elements required for migratory transitions and axial level specific differentiation capabilities.

developmental biology↗

bioRxiv2024

An inducible and reversible system to regulate unsaturated fatty acid biosynthesis in C. elegans

Unsaturated fatty acids (UFAs) play crucial roles in various physiological and pathological processes. In animals, these lipids are synthesized from saturated fatty acids through the action of delta 9 ({Delta}9) desaturases. In C. elegans, three {Delta}9 desaturases are encoded by the genes fat-5, fat-6, and fat-7. The presence of multiple {Delta}9 desaturases has posed a significant challenge in developing a rapid and efficient approach to control UFA production in C. elegans and other model organisms. Utilizing the auxin-inducible degradation system, we specifically targeted the C. elegans fat-7 gene, responsible for the major stearoyl-CoA desaturase (SCD), while deleting fat-5 and fat-6. This design resulted in a strain that can be reversibly depleted of UFAs in the cells of interest. Conditional depletion in all somatic cells exhibited a pronounced auxin-dependent defect in UFA production. Using this system, we uncovered an essential requirement for de novo UFA production during L1 and L2 stage. Moreover, our results support a direct connection between UFA levels, fat storage and increased lipid turnover. This system will enable further studies exploring the cellular and physiological consequences of impairing UFA biosynthesis at different developmental stages or in specific tissues. SummaryUnsaturated fatty acids (UFAs) are essential for life. In animals, UFAs are synthesized by {Delta}9 desaturase enzymes. Caenorhabditis elegans possesses three {Delta}9 desaturase genes: fat-5, fat-6, and fat-7. We engineered a strain where fat-7 can be reversibly switched off while fat-5 and fat-6 are deleted, allowing precise control of UFA levels throughout the life cycle. Our findings demonstrate the critical role of UFA biosynthesis in early development and its direct link to fat storage and lipid turnover. This strain enables the study of UFA-related physiological and pathological processes in animals.

genetics↗

bioRxiv2024

TRIM52 is a primate-specific player in the DNA repair process under tight proteolytic control by a triad of giant E3 ligases

Tripartite motif 52 (TRIM52) exhibits strong positive selection in humans, yet is lost in many other mammals. In contrast to what one would expect for such a non-conserved factor, TRIM52 loss compromises cell fitness. We set out to determine the cellular function of TRIM52. Genetic and proteomic analyses revealed TRIM52s involvement in resolving topoisomerase 2 (TOP2)-DNA cross-links, mitigating DNA damage and preventing cell-cycle arrest. Consistent with a fitness-promoting function, TRIM52 is upregulated in various cancers, prompting us to investigate its regulatory pathways. We found TRIM52 to be targeted for ultra-rapid proteasomal degradation by the giant E3 ubiquitin ligases BIRC6, HUWE1, and UBR4/KCMF1. BIRC6 mono-ubiquitinates TRIM52, with subsequent extension by UBR4/KCMF1. These findings underscore TRIM52s pivotal role in DNA damage repair and regulation of its own abundance through multi-ligase degradation.

molecular biology↗

bioRxiv2023

Mime-seq 2.0: a method to sequence microRNAs from specific mouse cell types

Many microRNAs (miRNAs) are expressed with high spatiotemporal specificity during organismal development, with some being limited to rare cell types, often embedded in complex tissues. Yet most miRNA profiling efforts remain at the tissue and organ levels. To overcome challenges in accessing the microRNomes from tissue-embedded cells, we had previously developed mime-seq (miRNome by methylation dependent sequencing), a technique in which cell-specific miRNA methylation in C. elegans and Drosophila enabled chemo-selective sequencing without the need for cell sorting or biochemical purification. Here, we present mime-seq 2.0 for profiling miRNAs from specific mouse cell types. We engineered a chimeric RNA methyltransferase that is tethered to Argonaute and efficiently methylates miRNAs at their 3-terminal 2OH in mouse and human cell lines. We also generated a transgenic mouse for conditional expression of this methyltransferase, which can be used to direct methylation of miRNAs in a cell-type of choice. We validated the use of this mouse by profiling miRNAs from B cells and bone marrow plasma cells.

molecular biology↗

bioRxiv2020

A deeply conserved miR-1 dependent regulon supports muscle cell physiology

Muscles are not only essential for force generation but are also key regulators of systemic energy homeostasis1. Both these roles rely heavily on mitochondria and lysosome function as providers of energy and building blocks, but also as metabolic sensors2-4. Perturbations in these organelles or their crosstalk lead to a wide range of pathologies5. Here, we uncover a deeply conserved regulon of mitochondria and lysosome homeostasis under control of the muscle-specific microRNA miR-1. Animals lacking miR-1 display a diverse range of muscle cell defects that have been attributed to numerous different targets6. Guided by the striking conservation of miR-1 and some of its predicted targets, we identified a set of direct targets that can explain the pleiotropic function of miR-1. miR-1-mediated repression of multiple subunits of the vacuolar ATPase (V-ATPase) complex, a key player in the acidification of internal compartments and a hub for metabolic signaling7,8, and of DCT-1/BNIP3, a mitochondrial protein involved in mitophagy and apoptosis9,10, accounts for the function of this miRNA in C. elegans. Surprisingly, although multiple V-ATPase subunits are upregulated in the absence of miR-1, this causes a loss-of-function of V-ATPase due to altered levels or stoichiometry, which negatively impact complex assembly. Finally, we demonstrate the conservation of the functional relationship between miR-1 and the V-ATPase complex in Drosophila.

cell biology↗

bioRxiv2020

Two microRNAs are sufficient for embryogenesis in C. elegans

The Microprocessor, composed of Drosha and Pasha/DGCR8, is necessary for the biogenesis of canonical microRNAs (miRNAs) and essential for animal embryogenesis. However, the cause for this requirement is largely unknown: the Microprocessor may be required to produce one or few essential miRNAs, or many individually non-essential miRNAs. Additionally, Drosha and Pasha/ DGCR8 may be required for processing non-miRNA substrates. To distinguish between these possibilities, we developed a system in C. elegans to stringently deplete embryos of Microprocessor activity. Microprocessor-depleted embryos fail to undergo morphogenesis or form organs. We show that this early embryonic arrest is rescued by the addition of two miRNAs from the miR-35 and miR-51 families, resulting in morphologically normal larvae. Thus, just two canonical miRNAs are sufficient for morphogenesis and organogenesis, and the processing of these miRNAs accounts for the essential requirement for Drosha and Pasha/DGCR8 during C. elegans embryonic development.Competing Interest StatementThe authors have declared no competing interest.View Full Text

developmental biology↗

bioRxiv2019

Evolution of neuronal anatomy and circuitry in two highly divergent nematode species

The nematodes C. elegans and P. pacificus populate diverse habitats and display distinct patterns of behavior. To understand how their nervous systems have diverged, we undertook a detailed examination of the neuroanatomy of the chemosensory system of P. pacificus. Using independent features such as cell body position, axon projections and lipophilic dye uptake, we have assigned homologies between the amphid neurons, their first-layer interneurons, and several internal receptor neurons of P. pacificus and C. elegans. We found that neuronal number and soma position are highly conserved. However, the morphological elaborations of several amphid cilia are different between them, most notably in the absence of winged cilia morphology in P. pacificus. We established a synaptic wiring diagram of amphid sensory neurons and amphid interneurons in P. pacificus and found striking patterns of conservation and divergence in connectivity relative to C. elegans, but very little changes in relative neighborhood of neuronal processes.\n\nImpact StatementThe substrate for evolutionary divergence does not lie in changes in neuronal cell number or targeting, but rather in sensory perception and synaptic partner choice within invariant, prepatterned neuronal processes.

neuroscience↗

bioRxiv2018

Olfaction regulates organismal proteostasis and longevity via microRNA-dependent signaling

Introductory Paragraph Introductory Paragraph Materials and Methods tir-1 3'UTR mutant tir-1::gfp CrispR/Cas9 repair templates References The maintenance of proteostasis is crucial for any organism to survive and reproduce in an ever-changing environment, but its efficiency declines with age1,2. Posttranscriptional regulators such as microRNAs control protein translation of target mRNAs with major consequences for development, physiology, and longevity3,4. However, the precise function of lifespan- determining microRNAs remains poorly understood. Here we show that the microRNA mir-71 controls organismal proteostasis and aging in Caenorhabditis elegans by regulating its conserved target tir-1 in AWC ol ...

cell biology↗