Functional unknomics: Systematic screening of conserved genes of unknown function

Rocha, João J.; Jayaram, Satish Arcot; Stevens, Tim J.; Muschalik, Nadine; Shah, Rajen D.; Emran, Sahar; Robles, Cristina; Freeman, Matthew; Munro, Sean

doi:10.1371/journal.pbio.3002222

Cited by 27 publications

(18 citation statements)

References 117 publications

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“…Despite their lack of highly penetrant developmental phenotypes, they may play roles in stress responses such as wound repair. Our work also underscores the insights that can be gained from analysis of relatively unstudied proteins (Perdigao et al, 2015; Rocha et al, 2023).…”

Section: Discussionmentioning

confidence: 57%

C. elegansepicuticlins define specific compartments in the apical extracellular matrix and function in wound repair

Pooranachithra,

Jyo,

Ernst

et al. 2024

Preprint

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The apical extracellular matrix (aECM) of external epithelia often contains lipid-rich outer layers that contribute to permeability barrier function. The external aECM of nematode is known as the cuticle and contains an external lipid-rich layer, the epicuticle. Epicuticlins are a family of tandem repeat proteins originally identified as components of the insoluble fraction of the cuticular aECM and thought to localize in or near epicuticle. However, there has been little in vivo analysis of epicuticlins. Here, we report the localization analysis of the three C. elegans epicuticlins (EPIC proteins) using fluorescent protein knock-ins to visualize endogenously expressed proteins, and further examine their in vivo function using genetic null mutants. By TIRF microscopy, we find that EPIC-1 and EPIC-2 localize to the surface of the cuticle in larval and adult stages in close proximity to the outer lipid layer. EPIC-1 and EPIC-2 also localize to interfacial cuticles and adult-specific cuticle struts. EPIC-3 expression is restricted to the stress-induced dauer stage, where it localizes to interfacial aECM in the buccal cavity. Strikingly, skin wounding in the adult induces epic-3 expression, and EPIC-3::mNG localizes to wound scars. Null mutants lacking one, two, or all three EPIC proteins display reduced survival after skin wounding yet are viable with low penetrance defects in epidermal morphogenesis. Our results suggest EPIC proteins define specific aECM compartments and have roles in wound repair.

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Section: Discussionmentioning

confidence: 57%

C. elegansepicuticlins define specific compartments in the apical extracellular matrix and function in wound repair

Pooranachithra,

Jyo,

Ernst

et al. 2024

Preprint

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“…Efforts to address the gaps in detailed knowledge about most genes have crystallized as initiatives promoting the investigation of understudied sets of genes 16,43-47 , an approach to gene scholarship recently termed ‘unknomics’ 48 . We believe that enabling scientists to consciously engage with bias in research target selection will enable more biomedical researchers to participate in unknomics, to the potential benefit of their own research impact and towards the advancement of our collective understanding of the entire human genome.…”

Section: Discussionmentioning

confidence: 99%

Meta-Research: understudied genes are lost in a leaky pipeline between genome-wide assays and reporting of results

Richardson¹,

Navarro²,

Amaral³

et al. 2023

Preprint

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“…"Conserved hypothetical proteins" (Galperin and Koonin, 2004;Rocha et al, 2023) have emerged as important foci for functional research. The importance of looking at these types of unannotated genes was highlighted by this project; unannotated genes made up approximately 40% of DEGs between clusters, both neuronal and non-neuronal.…”

Section: The Prevalence Of Unannotated Genesmentioning

confidence: 99%

Cellular-resolution gene expression mapping reveals organization in the head ganglia of the gastropod,Berghia stephanieae

Ramirez

Bui

Katz

2023

Preprint

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Gastropod molluscs, such as Aplysia, Lymnaea, and Tritonia have been important for determining fundamental rules of motor control and learning and memory because they have individually identifiable neurons. This has allowed neural circuits to be worked out using pair-wise microelectrode recordings. However, neuronal identification that relies on electrophysiology, dye tracing, and immunohistochemistry, limits research to the small number of large neurons, ignoring the much larger number of small neurons. Here we combined high throughput, single-cell RNA sequencing (scRNAseq) with in situ hybridization chain reaction (HCR) to examine gene expression in the head ganglia of the gastropod, Berghia stephanieae. Cluster analysis of the transcriptomic data uncovered multiple neuronal cell clusters, as well as glial, fibroblast, and endothelial cell clusters in the central ring ganglia (CRG: cerebral, pleural, pedal, and buccal ganglia) and the rhinophore ganglia (rhg). Combinatorial molecular signatures were layered on top of size and position using HCR with multiplexed marker genes to help establish specific neuronal class and type phenotypes. Unannotated genes made up significant proportions of the top differentially expressed genes for each cluster, including the most ubiquitously expressed pan-neuronal marker. Neuronal classes expressing major neurotransmitter phenotypes of glutamatergic, cholinergic, and serotonergic neurons were identified. Some neurons co-expressed genes for two neurotransmitters. Serotonergic neurons, not cholinergic neurons, were found to express Unc-4. Among the neurons found to be glutamatergic were a single photoreceptor in the eye and Soluble guanylate cyclase (Sgc)-expressing neurons in the rhg. A sampling of expression patterns from 8 out of the 40 molluscan neuropeptides identified in the single-cell dataset showed the tremendous diversity of neuron types, with few neuropeptides co-expressed in the same neurons. A visually identifiable giant ventral neuron was found to express three peptides and Chat. A subset of neurons in rhg, which contain only small somata (<15 microns), separated into three clusters: 1) glutamatergic + Sgc neurons, 2) nitric oxide synthase (Nos) + pigment dispersing factor (Pdf), and 3) Nos/Pdf-. The three groups were spatially restricted in the rhg. Transcription factors marked a cluster of newly differentiated neurons and were expressed in mature neurons. Six3/6 was expressed only in neurons from the rhinophore and cerebral ganglia, which are anterior-most of the major head ganglia, consistent with Six3/6 anterior segregation in other animals. This study provides the foundation for understanding the fundamental neuronal organization of the gastropod nervous system.

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Functional unknomics: Systematic screening of conserved genes of unknown function

Cited by 27 publications

References 117 publications

C. elegansepicuticlins define specific compartments in the apical extracellular matrix and function in wound repair

C. elegansepicuticlins define specific compartments in the apical extracellular matrix and function in wound repair

Meta-Research: understudied genes are lost in a leaky pipeline between genome-wide assays and reporting of results

Cellular-resolution gene expression mapping reveals organization in the head ganglia of the gastropod,Berghia stephanieae

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