{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T23:37:20Z","timestamp":1768520240851,"version":"3.49.0"},"posted":{"date-parts":[[2024,12,9]]},"group-title":"Neuroscience","reference-count":97,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2024,12,9]],"date-time":"2024-12-09T00:00:00Z","timestamp":1733702400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.biorxiv.org\/about\/FAQ#license"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,1,23]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  In the early stages of development, correlated activity known as retinal waves causes periodic depolarizations of retinal ganglion cells (RGCs). The \u03b22KO mouse, which lacks the \u03b22 subunit of the nicotinic acetylcholine receptor, serves as a model for understanding the role of these cholinergic waves. \u03b22KO mice have disruptions in several developmental processes of the visual system, including reduced retinotopic and eye-specific refinement of RGC axonal projections to their primary brain targets and an impact on the retinal circuits underlying direction selectivity. However, the effects of this mutation on gene expression in individual functional RGC types remain unclear. Here, we performed single-cell RNA sequencing on RGCs isolated at the end of the first postnatal week from wild-type and \u03b22KO mice. We found that in \u03b22KO mice, the molecular programs governing RGC differentiation were not impacted and the magnitude of transcriptional changes was modest compared to those observed during two days of normal postnatal maturation. This contrasts with the substantial transcriptomic changes seen in downstream visual system areas under wave disruption in recent studies. However, we identified \u223c238 genes whose expression was altered in a type-specific manner. We confirmed this result via\n                  <jats:italic>in situ<\/jats:italic>\n                  hybridization and whole-cell recording by focusing on one of the downregulated genes in aRGCs,\n                  <jats:italic>Kcnk9<\/jats:italic>\n                  , which encodes the two-pore domain leak potassium channel TASK3. Our study reveals a limited transcriptomic impact of cholinergic signaling in the retina and instead of affecting all RGCs uniformly, these waves show subtle modulation of molecular programs in a type-specific manner.\n                <\/jats:p>\n                <jats:sec>\n                  <jats:title>SIGNIFICANCE STATEMENT<\/jats:title>\n                  <jats:p>Spontaneous retinal waves are critical for the development of the mammalian visual system. However, their role in transcriptional regulation in the retina across the diverse retinal ganglion cell (RGC) types that underpin the detection and transmission of visual features is unclear. Using single-cell RNA sequencing, we analyzed RGC transcriptome from wild-type mice and mice with disrupted retinal waves. We identified several genes that show RGC-type-specific regulation in their expression, including multiple neuropeptides and ion channels. However, wave-dependent changes in the transcriptome were more subtle than developmental changes, indicating that spontaneous activity-dependent molecular changes in retinal ganglion cells are not primarily manifested at the transcriptomic level.<\/jats:p>\n                <\/jats:sec>","DOI":"10.1101\/2024.12.05.627027","type":"posted-content","created":{"date-parts":[[2024,12,9]],"date-time":"2024-12-09T16:20:44Z","timestamp":1733761244000},"source":"Crossref","is-referenced-by-count":0,"title":["Cholinergic waves have a modest influence on the transcriptome of retinal ganglion cells"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1190-1192","authenticated-orcid":false,"given":"Rachana Deven","family":"Somaiya","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthew A.","family":"Po","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9137-5849","authenticated-orcid":false,"given":"Marla B.","family":"Feller","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4349-6600","authenticated-orcid":false,"given":"Karthik","family":"Shekhar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"54368","reference":[{"key":"2025012417401321000_2024.12.05.627027v2.1","unstructured":"10X Genomics (n.d.) What fraction of mRNA transcripts are captured per cell? 10X Genomics Available at: https:\/\/kb.10xgenomics.com\/hc\/en-us\/articles\/360001539051-What-fraction-of-mRNA-transcripts-are-captured-per-cell [Accessed December 2, 2024]."},{"key":"2025012417401321000_2024.12.05.627027v2.2","doi-asserted-by":"publisher","DOI":"10.1038\/nature11529"},{"key":"2025012417401321000_2024.12.05.627027v2.3","doi-asserted-by":"publisher","DOI":"10.1016\/J.CUB.2022.07.064"},{"key":"2025012417401321000_2024.12.05.627027v2.4","doi-asserted-by":"crossref","unstructured":"Arroyo DA , Feller MB (2016) Spatiotemporal Features of Retinal Waves Instruct the Wiring of the Visual Circuitry. 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Available at: http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2024.04.05.588143 [Accessed November 11, 2024].","DOI":"10.1101\/2024.04.05.588143"},{"key":"2025012417401321000_2024.12.05.627027v2.14","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuron.2014.10.051"},{"key":"2025012417401321000_2024.12.05.627027v2.15","doi-asserted-by":"crossref","unstructured":"Chen T , Guestrin C (2016) XGBoost: A Scalable Tree Boosting System. 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