-
Články
- Časopisy
- Kurzy
- Témy
- Kongresy
- Videa
- Podcasty
De Novo Origin of Human Protein-Coding Genes
The de novo origin of a new protein-coding gene from non-coding DNA is considered to be a very rare occurrence in genomes. Here we identify 60 new protein-coding genes that originated de novo on the human lineage since divergence from the chimpanzee. The functionality of these genes is supported by both transcriptional and proteomic evidence. RNA–seq data indicate that these genes have their highest expression levels in the cerebral cortex and testes, which might suggest that these genes contribute to phenotypic traits that are unique to humans, such as improved cognitive ability. Our results are inconsistent with the traditional view that the de novo origin of new genes is very rare, thus there should be greater appreciation of the importance of the de novo origination of genes.
Vyšlo v časopise: De Novo Origin of Human Protein-Coding Genes. PLoS Genet 7(11): e32767. doi:10.1371/journal.pgen.1002379
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1002379Souhrn
The de novo origin of a new protein-coding gene from non-coding DNA is considered to be a very rare occurrence in genomes. Here we identify 60 new protein-coding genes that originated de novo on the human lineage since divergence from the chimpanzee. The functionality of these genes is supported by both transcriptional and proteomic evidence. RNA–seq data indicate that these genes have their highest expression levels in the cerebral cortex and testes, which might suggest that these genes contribute to phenotypic traits that are unique to humans, such as improved cognitive ability. Our results are inconsistent with the traditional view that the de novo origin of new genes is very rare, thus there should be greater appreciation of the importance of the de novo origination of genes.
Zdroje
1. LongMBetránEThorntonKWangW 2003 The origin of new genes: glimpses from the young and old. Nat Rev Genet 4 865 875
2. KaessmannH 2010 Origins, evolution, and phenotypic impact of new genes. Genome Res 20 1313 1326
3. OhnoS 1970 Evolution by gene duplication Springer
4. JacobF 1977 Evolution and tinkering. Science 196 1161 1166
5. KnowlesDGMcLysaghtA 2009 Recent de novo origin of human protein-coding genes. Genome Res 19 1752 1759
6. LevineMTJonesCDKernADLindforsHABegunDJ 2006 Novel genes derived from noncoding DNA in Drosophila melanogaster are frequently X-linked and exhibit testis-biased expression. Proc Natl Acad Sci USA 103 9935 9939
7. BegunDJLindforsHAThompsonMEHollowayAK 2006 Recently evolved genes identified from Drosophila yakuba and D. erecta accessory gland expressed sequence tags. Genetics 172 1675 1681
8. BegunDJLindforsHAKernADJonesCD 2007 Evidence for de novo evolution of testis-expressed genes in the Drosophila yakuba/Drosophila erecta clade. Genetics 176 1131 1137
9. ChenSTChengHCBarbashDAYangHP 2007 Evolution of hydra, a recently evolved testis-expressed gene with nine alternative first exons in Drosophila melanogaster. PLoS Genet 3 e107 doi:10.1371/journal.pgen.0030107
10. ZhouQZhangGZhangYXuSZhaoR 2008 On the origin of new genes in Drosophila. Genome Res 18 1446 1455
11. LiC-YZhangYWangZZhangYCaoC 2010 A human-specific de novo protein-coding gene associated with human brain functions. PLoS Comput Biol 6 e1000734 doi:10.1371/journal.pcbi.1000734
12. CaiJZhaoRJiangHWangW 2008 De novo origination of a new protein-coding gene in Saccharomyces cerevisiae. Genetics 179 487 496
13. LiDDongYJiangYJiangHCaiJ 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
14. XiaoWLiuHLiYLiXXuC 2009 A rice gene of de novo origin negatively regulates pathogen-induced defense response. PLoS ONE 4 e4603 doi:10.1371/journal.pone.0004603
15. YangZHuangJ 2011 De novo origin of new genes with introns in Plasmodium vivax. FEBS letters 585 641 644
16. GontijoAMMiguelaVWhitingMFWoodruffRCDominguezM 2011 Intron retention in the Drosophila melanogaster Rieske iron sulphur protein gene generated a new protein. Nat Commun 2 323
17. WangJLiSTZhangYZhengHKXuZ 2003 Vertebrate gene predictions and the problem of large genes. Nat Rev Genet 4 741 749
18. YehRFLimLPBurgeCB 2001 Computational inference of homologous gene structures in the human genome. Genome Res 11 803 816
19. KarolchikDBaertschRDiekhansMFureyTSHinrichsA 2003 The UCSC genome browser database. Nucleic Acid Res 31 51 54
20. JonesPC téRGChoSYKlieSMartensL 2008 PRIDE: new developments and new datasets. Nucleic Acid Res 36 D878 D883
21. DeutschEWLamHAebersoldR 2008 PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. EMBO reports 9 429 434
22. Bornberg-BauerEHuylmansAKSikosekT 2010 How do new proteins arise? Curr Opin Struc Biol 20 390 396
23. WangZGersteinMSnyderM 2009 RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10 57 63
24. CaiJJPetrovDA 2010 Relaxed purifying selection and possibly high rate of adaptation in primate lineage-specific genes. Genome Biol Evol 2 393 409
25. PanDZhangL 2007 Quantifying the major mechanisms of recent gene duplications in the human and mouse genomes: a novel strategy to estimate gene duplication rates. Genome Biol 8 R158
26. LynchMConeryJS 2000 The evolutionary fate and consequences of duplicate genes. Science 290 1151 1154
27. KandelERSchwartzJHJessellTM 2000 Principles of neural science Fourth Edition McGraw-Hill
28. HillRSWalshCA 2005 Molecular insights into human brain evolution. Nature 437 64 67
29. SabetiPCSchaffnerSFFryBLohmuellerJVarillyP 2006 Positive natural selection in the human lineage. Science 312 1614 1620
30. GigerTKhaitovichPSomelMLorencALizanoE 2010 Evolution of neuronal and endothelial transcriptomes in primates. Genome Biol Evol 2 284 292
31. KhaitovichPTangKFranzHKelsoJHellmannI 2006 Positive selection on gene expression in the human brain. Curr Biol 16 R356 R358
32. CáceresMLachuerJZapalaMARedmondJCKudoL 2003 Elevated gene expression levels distinguish human from non-human primate brains. Proc Natl Acad Sci USA 100 13030 13035
33. LinLShenSJiangPSatoSDavidsonBL 2010 Evolution of alternative splicing in primate brain transcriptomes. Hum Mol Genet 19 2958 2973
34. HeinenTJAJStaubachFHamingDTautzD 2009 Emergence of a new gene from an intergenic region. Curr Biol 19 1527 1531
35. McCarreyJRThomasK 1987 Human testis-specific PGK gene lacks introns and possesses characteristics of a processed gene. Nature 326 501 505
36. LongMLangleyCH 1993 Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila. Science 260 91 95
37. BetránEThorntonKLongM 2002 Retroposed new genes out of the X in Drosophila. Genome Res 12 1854 1859
38. MarquesACDupanloupIVinckenboschNReymondAKaessmannH 2005 Emergence of young human genes after a burst of retroposition in primates. PLoS Biol 3 e357 doi:10.1371/journal.pbio.0030357
39. KleeneKC 2001 A possible meiotic function of the peculiar patterns of gene expression in mammalian spermatogenic cells. Mech Dev 106 3 23
40. SiepelA 2009 Darwinian alchemy: Human genes from noncoding DNA. Genome Res 19 1693 1695
41. WangETSandbergRLuoSKhrebtukovaIZhangL 2008 Alternative isoform regulation in human tissue transcriptomes. Nature 456 470 476
42. PanQShaiOLeeLJFreyBJBlencoweBJ 2008 Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 40 1413 1415
43. XiongYChenXChenZWangXShiS 2010 RNA sequencing shows no dosage compensation of the active X-chromosome. Nat Genet 42 1043 1047
44. BakewellMAShiPZhangJ 2007 More genes underwent positive selection in chimpanzee evolution than in human evolution. Proc Natl Acad Sci USA 104 7489 7494
45. ThompsonJDHigginsDGGibsonTJ 1994 CLUSTALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acid Res 22 4673 4680
46. YangZ 1997 PAML: a program package for phylogenetic analysis by maximum likelihood. CABIOS 13 555 556
Štítky
Genetika Reprodukčná medicína
Článok vyšiel v časopisePLOS Genetics
Najčítanejšie tento týždeň
2011 Číslo 11- Gynekologové a odborníci na reprodukční medicínu se sejdou na prvním virtuálním summitu
- Je „freeze-all“ pro všechny? Odborníci na fertilitu diskutovali na virtuálním summitu
-
Všetky články tohto čísla
- De Novo Origins of Human Genes
- Duplication Hotspots Are Associated with Late-Replicating Regions of the Genome
- De Novo Origin of Human Protein-Coding Genes
- Cyclin D/CDK4 and Cyclin E/CDK2 Induce Distinct Cell Cycle Re-Entry Programs in Differentiated Muscle Cells
- Short Day–Mediated Cessation of Growth Requires the Downregulation of AINTEGUMENTALIKE1 Transcription Factor in Hybrid Aspen
- Physiological IRE-1-XBP-1 and PEK-1 Signaling in Larval Development and Immunity
- Role of Pirh2 in Mediating the Regulation of p53 and c-Myc
- Signatures of Environmental Genetic Adaptation Pinpoint Pathogens as the Main Selective Pressure through Human Evolution
- FOXO Regulates Organ-Specific Phenotypic Plasticity In
- Heritable Epigenetic Variation among Maize Inbreds
- Foxn1 Regulates Lineage Progression in Cortical and Medullary Thymic Epithelial Cells But Is Dispensable for Medullary Sublineage Divergence
- Attenuation of the Sensing Capabilities of PhoQ in Transition to Obligate Insect–Bacterial Association
- A Novel Protein LZTFL1 Regulates Ciliary Trafficking of the BBSome and Smoothened
- Activation of Bmp2-Smad1 Signal and Its Regulation by Coordinated Alteration of H3K27 Trimethylation in -Induced Senescence
- Histone H3K56 Acetylation, CAF1, and Rtt106 Coordinate Nucleosome Assembly and Stability of Advancing Replication Forks
- The SUN Protein Mps3 Is Required for Spindle Pole Body Insertion into the Nuclear Membrane and Nuclear Envelope Homeostasis
- Evidence-Based Annotation of Gene Function in MR-1 Using Genome-Wide Fitness Profiling across 121 Conditions
- Effect of Host Species on the Distribution of Mutational Fitness Effects for an RNA Virus
- Pch2 Acts through Xrs2 and Tel1/ATM to Modulate Interhomolog Bias and Checkpoint Function during Meiosis
- SOX9 Governs Differentiation Stage-Specific Gene Expression in Growth Plate Chondrocytes via Direct Concomitant Transactivation and Repression
- from the Aphid : A Missing Link from Facultative to Obligate Insect Endosymbiont
- Recessive Antimorphic Alleles Overcome Functionally Redundant Loci to Reveal Function in Flowers and Meristems
- Over-Expression of DSCAM and COL6A2 Cooperatively Generates Congenital Heart Defects
- Consequences of Eukaryotic Enhancer Architecture for Gene Expression Dynamics, Development, and Fitness
- Distinct Genetic Architectures for Male and Female Inflorescence Traits of Maize
- Capture of MicroRNA–Bound mRNAs Identifies the Tumor Suppressor miR-34a as a Regulator of Growth Factor Signaling
- For Male , Sperm Activation Is a “Just-in-Time” Event
- PcG Complexes Set the Stage for Epigenetic Inheritance of Gene Silencing in Early S Phase before Replication
- The Gene Contains Hotspots for L1 Endonuclease-Dependent Insertion
- Relative Burden of Large CNVs on a Range of Neurodevelopmental Phenotypes
- Multiple Means to the Same End: The Genetic Basis of Acquired Stress Resistance in Yeast
- Genome-Wide Crossover Distribution in Meiosis Reveals Sex-Specific Patterns along Chromosomes
- TRY-5 Is a Sperm-Activating Protease in Seminal Fluid
- Homologs of Retinoblastoma-Associated Protein 46/48 Associate with a Histone Deacetylase to Act Redundantly in Chromatin Silencing
- Genetic Interaction Maps in Reveal Functional Crosstalk among Cell Envelope Biogenesis Pathways
- The ERI-6/7 Helicase Acts at the First Stage of an siRNA Amplification Pathway That Targets Recent Gene Duplications
- PBX1 Genomic Pioneer Function Drives ERα Signaling Underlying Progression in Breast Cancer
- PLOS Genetics
- Archív čísel
- Aktuálne číslo
- Informácie o časopise
Najčítanejšie v tomto čísle- Evidence-Based Annotation of Gene Function in MR-1 Using Genome-Wide Fitness Profiling across 121 Conditions
- De Novo Origins of Human Genes
- Capture of MicroRNA–Bound mRNAs Identifies the Tumor Suppressor miR-34a as a Regulator of Growth Factor Signaling
- TRY-5 Is a Sperm-Activating Protease in Seminal Fluid
Prihlásenie#ADS_BOTTOM_SCRIPTS#Zabudnuté hesloZadajte e-mailovú adresu, s ktorou ste vytvárali účet. Budú Vám na ňu zasielané informácie k nastaveniu nového hesla.
- Časopisy