The Origins and Functions of De Novo Genes: Against All Odds?

Weisman, Caroline M.

doi:10.1007/s00239-022-10055-3

Cited by 36 publications

(46 citation statements)

References 116 publications

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“…Our results point towards a lack of novel, synapomorphic genes for Echinodermata. Indeed, this is consistent with a growing body of research suggesting that novel genes may not be the primary drivers of novel features [ 61 ].…”

Section: Discussionsupporting

confidence: 87%

Evolutionary analyses of genes in Echinodermata offer insights towards the origin of metazoan phyla

et al. 2022

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Section: Discussionsupporting

confidence: 87%

Evolutionary analyses of genes in Echinodermata offer insights towards the origin of metazoan phyla

et al. 2022

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“…The identification of multiple novel mucin genes within the SCPP locus provides a unique opportunity to address the question whether these genes have evolved through neofunctionalization after gene duplication (17), as de novo genes from noncoding sequences (23)(24)(25), or through some other mechanism (Fig. 3A).…”

Section: Muc10 As a Case Example For De Novo Mucin Evolutionmentioning

confidence: 99%

A mechanism of gene evolution generating mucin function

Pajic

Shen

et al. 2022

Sci. Adv.

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How novel gene functions evolve is a fundamental question in biology. Mucin proteins, a functionally but not evolutionarily defined group of proteins, allow the study of convergent evolution of gene function. By analyzing the genomic variation of mucins across a wide range of mammalian genomes, we propose that exonic repeats and their copy number variation contribute substantially to the de novo evolution of new gene functions. By integrating bioinformatic, phylogenetic, proteomic, and immunohistochemical approaches, we identified 15 undescribed instances of evolutionary convergence, where novel mucins originated by gaining densely O-glycosylated exonic repeat domains. Our results suggest that secreted proteins rich in proline are natural precursors for acquiring mucin function. Our findings have broad implications for understanding the role of exonic repeats in the parallel evolution of new gene functions, especially those involving protein glycosylation.

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“…Overall, this study highlights the power of using a high-throughput, genetically tractable vertebrate model to systematically screen for micropeptide function within putative lincRNAs, behavioral phenotypes, signaling pathways, and cell type susceptibilities in early vertebrate development. How novel protein-coding genes may be born from non-coding genomic elements remains an elusive question 47 . Several short open reading frames encoding for functional, evolutionarily conserved peptides now have been discovered within putative non-coding RNAs 13 , and some of these genes may have emerged along vertebrate lineages (for example, libra/ NREP 48 ).…”

Section: Discussionmentioning

confidence: 99%

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

Tornini

Lee

Miao

et al. 2022

Preprint

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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 has 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 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 highlight the power of screening for unexplored micropeptide functions by revealing a key missing link in the evolution of vertebrate brain cell development and illustrating 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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The Origins and Functions of De Novo Genes: Against All Odds?

Cited by 36 publications

References 116 publications

Evolutionary analyses of genes in Echinodermata offer insights towards the origin of metazoan phyla

Evolutionary analyses of genes in Echinodermata offer insights towards the origin of metazoan phyla

A mechanism of gene evolution generating mucin function

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

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