Erratum: Corrigendum: The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons

Braasch, Ingo; Gehrke, Andrew R.; Smith, Jeramiah J.; Kawasaki, Kazuhiko; Manousaki, Tereza; Pasquier, Jérémy; Amores, Angel; Desvignes, Thomas; Batzel, Peter; Catchen, Julian M.; Berlin, Aaron M.; Campbell, Michael S.; Barrell, Daniel; Martin, Kyle J.; Mulley, John F.; Ravi, Vydianathan; Lee, Alison; Nakamura, Tetsuya; Chalopin, Domitille; Fan, Shaohua; Wcisel, Dustin J.; Cañestro, Cristian; Sydes, Jason; Beaudry, Felix E.G.; Sun, Yi; Hertel, Jana; Beam, Michael J.; Fasold, Mario; Ishiyama, Mikio; Johnson, Jeremy; Kehr, Stephanie; Lara, Marcia; Letaw, John; Litman, Gary W.; Litman, Ronda T.; Mikami, Masato; Ota, Tomomi; Saha, Nil Ratan; Williams, Louise; Stadler, Peter F.; Wang, Han; Taylor, John S.; Fontenot, Quenton; Ferrara, Allyse; Searle, Stephen M. J.; Aken, Bronwen; Yandell, Mark; Schneider, Igor; Yoder, Jeffrey A.; Volff, Jean Nicolas; Meyer, Axel; Amemiya, Chris T.; Venkatesh, Byrappa; Holland, Peter W.H.; Guiguen, Yann; Bobe, Julien; Shubin, Neil H.; Palma, Federica Di; Alföldi, Jessica; Lindblad‐Toh, Kerstin; Postlethwait, John H.

doi:10.1038/ng0616-700c

Cited by 18 publications

(7 citation statements)

References 2 publications

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“…The highly conserved 3’UTR suggested that linc-mipep and linc-wrb derived from the same ancestral gene, either before or after the teleost-specific genome duplication. To address this question, we analyzed the regions syntenic to human HMGN1 in spotted gar, a slowly evolving species whose lineage diverged from teleosts before the teleost genome duplication, and in coelacanth, a lobe-finned fish with the slowest evolving bony vertebrate genome that split from ray-finned fish such as gar and zebrafish ( Braasch et al, 2016 ). In coelacanth, we only identified one protein sequence that aligns to HMGN1, syntenic to human HMGN1, with no ESTs or other sequences identified elsewhere ( Supplementary file 2 ).…”

Section: Resultsmentioning

confidence: 99%

linc-mipep and linc-wrb encode micropeptides that regulate chromatin accessibility in vertebrate-specific neural cells

Tornini

Miao

Lee

et al. 2023

eLife

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Thousands of long intergenic non-coding RNAs (lincRNAs) are transcribed throughout the vertebrate genome. A subset of lincRNAs enriched in developing brains have recently been found to contain cryptic open-reading frames and are speculated to encode micropeptides. However, systematic identification and functional assessment of these transcripts have been hindered by technical challenges caused by their small size. Here, we show that two putative lincRNAs (linc-mipep, also called lnc-rps25, and linc-wrb) encode micropeptides with homology to the vertebrate-specific chromatin architectural protein, Hmgn1, and demonstrate that they are required for development of vertebrate-specific brain cell types. Specifically, we show that NMDA receptor-mediated pathways are dysregulated in zebrafish lacking these micropeptides and that their loss preferentially alters the gene regulatory networks that establish cerebellar cells and oligodendrocytes – evolutionarily newer cell types that develop postnatally in humans. These findings reveal a key missing link in the evolution of vertebrate brain cell development and illustrate a genetic basis for how some neural cell types are more susceptible to chromatin disruptions, with implications for neurodevelopmental disorders and disease.

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Section: Resultsmentioning

confidence: 99%

linc-mipep and linc-wrb encode micropeptides that regulate chromatin accessibility in vertebrate-specific neural cells

Tornini

Miao

Lee

et al. 2023

eLife

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“…EMPs are part of family of proteins known as secretory calcium-binding phosphoproteins (SCPPs) that are critical for calcification of bone, dentin, and enamel ( Kawasaki, 2009 ). The zebrafish genome harbors two previously identified EMP-gene orthologs, including orthologs of human Enamelin (encoded by enam) and Ameloblastin (encoded by ambn), in addition to fish-specific orthologs that likely originated by tandem duplication ( Qu et al, 2015 ; Braasch et al, 2016 ; Kawasaki et al, 2017 ). We therefore analyzed the distribution of SCPP-encoding transcripts, predicting that EMP-transcript-expressing cells would be found among basal epidermal cells.…”

Section: Resultsmentioning

confidence: 99%

Transcriptomic profiling of tissue environments critical for post-embryonic patterning and morphogenesis of zebrafish skin

Aman

Saunders

Carr

et al. 2023

eLife

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Pigment patterns and skin appendages are prominent features of vertebrate skin. In zebrafish, regularly patterned pigment stripes and an array of calcified scales form simultaneously in the skin during post-embryonic development. Understanding mechanisms that regulate stripe patterning and scale morphogenesis may lead to discovery of fundamental mechanisms that govern development of animal form. To learn about cell types and signaling interactions that govern skin patterning and morphogenesis we generated and analyzed single cell transcriptomes of skin from wild-type fish as well as fish having genetic or transgenically induced defects in squamation or pigmentation. These data reveal a previously undescribed population of epidermal cells that express transcripts encoding enamel matrix proteins, suggest hormonal control of epithelial-mesenchymal signaling, clarify the signaling network that governs scale papillae development, and identify a critical role for the hypodermis in supporting pigment cell development. Additionally, these comprehensive single-cell transcriptomic data representing skin phenotypes of biomedical relevance should provide a useful resource for accelerating discovery of mechanisms that govern skin development and homeostasis.

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“…Medaka rec8a is one of two mammalian Rec8 orthologs originating from a teleost-specific whole-genome duplication event ( Braasch et al, 2016 ). rec8a encodes an α-kleisin subunit of the meiotic cohesin.…”

Section: Foxl3 Initiates Distinct Genetic Pathways Regulating Meiosis...mentioning

confidence: 99%

Functional Modules in Gametogenesis

Kikuchi

Tanaka

2022

Front. Cell Dev. Biol.

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Gametogenesis, the production of eggs and sperm, is a fundamental process in sexually reproducing animals. Following gametogenesis commitment and sexual fate decision, germ cells undergo several developmental processes to halve their genomic size and acquire sex-specific characteristics of gametes, including cellular size, motility, and cell polarity. However, it remains unclear how different gametogenesis processes are initially integrated. With the advantages of the teleost fish medaka (Oryzias latipes), in which germline stem cells continuously produce eggs and sperm in mature gonads and a sexual switch gene in germ cells is identified, we found that distinct pathways initiate gametogenesis cooperatively after commitment to gametogenesis. This evokes the concept of functional modules, in which functionally interlocked genes are grouped to yield distinct gamete characteristics. The various combinations of modules may allow us to explain the evolution of diverse reproductive systems, such as parthenogenesis and hermaphroditism.

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Erratum: Corrigendum: The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons

Cited by 18 publications

References 2 publications

linc-mipep and linc-wrb encode micropeptides that regulate chromatin accessibility in vertebrate-specific neural cells

linc-mipep and linc-wrb encode micropeptides that regulate chromatin accessibility in vertebrate-specific neural cells

Transcriptomic profiling of tissue environments critical for post-embryonic patterning and morphogenesis of zebrafish skin

Functional Modules in Gametogenesis

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