De Novo Gene Birth

Arroyo J.I., Nery M.F. 2018. Gene fusion of heterophyletic gamma-globin genes in platyrrhine primates. J. Genet. 97, 1473–1478.

Article  CAS  PubMed  Google Scholar 

Tautz D., Domazet-Lošo T. 2011. The evolutionary origin of orphan genes. Nat. Rev. Genet. 12, 692–702.

Article  CAS  PubMed  Google Scholar 

Van Oss S.B., Carvunis A.-R. 2019. De novo gene birth. PLoS Genet. 15, e1008160.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cherezov R.O., Vorontsova Yu.E., Simonova O.B. 2021. The phenomenon of evolutionary “de novo generation” of genes. Russ. J. Dev. Biol. 52, 390–400.

Article  CAS  Google Scholar 

Ruiz-Orera J., Hernandez-Rodriguez J., Chiva C., Sabidó E., Kondova I., Bontrop R., Marqués-Bonet T., Albà M.M. 2015. Origins of de novo genes in human and chimpanzee. PLoS Genet. 11, e1005721.

Article  PubMed  PubMed Central  Google Scholar 

Zhuang X., Yang C., Murphy K.R., Cheng C.-C. 2019. Molecular mechanism and history of non-sense to sense evolution of antifreeze glycoprotein gene in northern gadids. Proc. Natl. Acad. Sci. U. S. A. 116, 4400–4405.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Clark M.B., Amaral P.P., Schlesinger F.J., Dinger M.E., Taft R.J., Rinn J.L., Ponting C.P., Stadler P.F., Morris K.V., Morillon A., Rozowsky J.S., Gerstein M.B., Wahlestedt C., Hayashizaki Y., Carninci P., Gingeras T.R., Mattick J.S. 2011. The reality of pervasive transcription. PLoS Biol. 9, e1000625.

Article  CAS  PubMed  PubMed Central  Google Scholar 

David L., Huber W., Granovskaia M., Toedling J., Palm C.J., Bofkin L., Jones T., Davis R.W., Steinmetz L.M. 2006. A high-resolution map of transcription in the yeast genome. Proc. Natl. Acad. Sci. U. S. A. 103, 5320–5325.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yona A.H., Alm E.J., Gore J. 2018. Random sequences rapidly evolve into de novo promoters. Nat. Commun. 9, 1530.

Article  PubMed  PubMed Central  Google Scholar 

Ingolia N.T., Brar G.A., Stern-Ginossar N., Harris M.S., Talhouarne G.J.S., Jackson S.E., Wills M.R., Weissman J.S. 2014. Ribosome profiling reveals pervasive translation outside of annotated protein-coding genes. Cell Rep. 8, 1365–1379.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Parikh S.B., Houghton C., Van Oss S.B., Wacholder A., Carvunis A. 2022. Origins, evolution, and physiological implications of de novo genes in yeast. Yeast. 39, 471–481.

Article  CAS  PubMed  Google Scholar 

Xiao W., Liu H., Li Y., Li X., Xu C., Long M., Wang S. 2009. A rice gene of de novo origin negatively regulates pathogen-induced defense response. PLoS One. 4, e4603.

Article  PubMed  PubMed Central  Google Scholar 

Baalsrud H.T., Tørresen O.K., Solbakken M.H., Salzburger W., Hanel R., Jakobsen K.S., Jentoft S. 2018. De novo gene evolution of antifreeze glycoproteins in codfishes revealed by whole genome sequence data. Mol. Biol. Evol. 35, 593–606.

Article  CAS  PubMed  Google Scholar 

Vakirlis N., Vance Z., Duggan K.M., McLysaght A. 2022. De novo birth of functional microproteins in the human lineage. Cell Rep. 41, 111808.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Xie C., Zhang Y.E., Chen J.-Y., Liu C.-J., Zhou W.-Z., Li Y., Zhang M., Zhang R., Wei L., Li C.-Y. 2012. Hominoid-specific de novo protein-coding genes originating from long non-coding RNAs. PLoS Genet. 8, e1002942.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wu D.-D., Irwin D.M., Zhang Y.-P. 2011. De novo origin of human protein-coding genes. PLoS Genet. 7, e1002379.

Article  CAS  PubMed  PubMed Central  Google Scholar 

An N.A., Zhang J., Mo F., Luan X., Tian L., Shen Q.S., Li X., Li C., Zhou F., Zhang B., Ji M., Qi J., Zhou W.Z., Ding W., Chen J.Y., Yu J., Zhang L., Shu S., Hu B., Li C.Y. 2023. De novo genes with an lncRNA origin encode unique human brain developmental functionality. Nat. Ecol. Evol. 7 (2), 264–278.

Article  PubMed  PubMed Central  Google Scholar 

Rubtsova M., Naraykina Y., Vasilkova D., Meerson M., Zvereva M., Prassolov V., Lazarev V., Manuvera V., Kovalchuk S., Anikanov N., Butenko I., Pobeguts O., Govorun V., Dontsova O. 2018. Protein encoded in human telomerase RNA is involved in cell protective pathways. Nucleic Acids Res. 46, 8966–8977.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wu X., Sharp P.A. 2013. Divergent transcription: a driving force for new gene origination? Cell. 155, 990–996.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Vaishnav E.D., De Boer C.G., Molinet J., Yassour M., Fan L., Adiconis X., Thompson D.A., Levin J.Z., Cubillos F.A., Regev A. 2022. The evolution, evolvability and engineering of gene regulatory DNA. Nature. 603, 455–463.

Article  CAS  PubMed  Google Scholar 

Chung W.-Y., Wadhawan S., Szklarczyk R., Pond S.K., Nekrutenko A. 2007. A first look at ARFome: Dual-coding genes in mammalian genomes. PLoS Comput. Biol. 3, e91.

Article  PubMed  PubMed Central  Google Scholar 

Schmitz J.F., Ullrich K.K., Bornberg-Bauer E. 2018. Incipient de novo genes can evolve from frozen accidents that escaped rapid transcript turnover. Nat. Ecol. Evol. 2, 1626–1632.

Article  PubMed  Google Scholar 

Suenaga Y., Islam S.M., Alagu J., Kaneko Y., Kato M., Tanaka Y., Kawana H., Hossain S., Matsumoto D., Yamamoto M., Shoji W., Itami M., Shibata T., Nakamura Y., Ohira M., Haraguchi S., Takatori A., Nakagawara A. 2014. NCYM, a cis-antisense gene of MYCN, encodes a de novo evolved protein that inhibits GSK3β resulting in the stabilization of MYCN in human neuroblastomas. PLoS Genet. 10, e1003996.

Article  PubMed  PubMed Central  Google Scholar 

Li D., Yan Z., Lu L., Jiang H., Wang W. 2014. Pleiotropy of the de novo-originated gene MDF1. Sci. Rep. 4, 7280.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Li D., Dong Y., Jiang Y., Jiang H., Cai J., Wang W. 2010. A de novo originated gene depresses budding yeast mating pathway and is repressed by the protein encoded by its antisense strand. Cell Res. 20, 408–420.

Article  CAS  PubMed  Google Scholar 

Blevins W.R., Ruiz-Orera J., Messeguer X., Blasco-Moreno B., Villanueva-Cañas J.L., Espinar L., Díez J., Carey L.B., Albà M.M. 2021. Uncovering de novo gene birth in yeast using deep transcriptomics. Nat. Commun. 12, 604.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Pelechano V., Steinmetz L.M. 2013. Gene regulation by antisense transcription. Nat. Rev. Genet. 14, 880–893.

Article  CAS  PubMed  Google Scholar 

Begun D.J., Lindfors H.A., Kern A.D., Jones C.D. 2007. Evidence for de novo evolution of testis-expressed genes in the Drosophila yakuba/Drosophila erecta clade. Genetics. 176, 1131–1137.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Comments (0)

No login
gif