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Literature DB >> 24457212

Origin and spread of de novo genes in Drosophila melanogaster populations.

Li Zhao¹, Perot Saelao, Corbin D Jones, David J Begun.

Abstract

Comparative genomic analyses have revealed that genes may arise from ancestrally nongenic sequence. However, the origin and spread of these de novo genes within populations remain obscure. We identified 142 segregating and 106 fixed testis-expressed de novo genes in a population sample of Drosophila melanogaster. These genes appear to derive primarily from ancestral intergenic, unexpressed open reading frames, with natural selection playing a significant role in their spread. These results reveal a heretofore unappreciated dynamism of gene content.

Entities: Chemical Disease Gene Species

Mesh：

Year: 2014 PMID： 24457212 PMCID： PMC4391638 DOI： 10.1126/science.1248286

Source DB: PubMed Journal: Science ISSN： 0036-8075 Impact factor: 47.728

54 in total

1. Why are "natively unfolded" proteins unstructured under physiologic conditions?

Authors: V N Uversky; J R Gillespie; A L Fink
Journal: Proteins Date: 2000-11-15

Review 2. Natively unfolded proteins: a point where biology waits for physics.

Authors: Vladimir N Uversky
Journal: Protein Sci Date: 2002-04 Impact factor: 6.725

3. The HMMTOP transmembrane topology prediction server.

Authors: G E Tusnády; I Simon
Journal: Bioinformatics Date: 2001-09 Impact factor: 6.937

4. TM or not TM: transmembrane protein prediction with low false positive rate using DAS-TMfilter.

Authors: Miklos Cserzo; Frank Eisenhaber; Birgit Eisenhaber; Istvan Simon
Journal: Bioinformatics Date: 2004-01-01 Impact factor: 6.937

5. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias.

Authors: B M Bolstad; R A Irizarry; M Astrand; T P Speed
Journal: Bioinformatics Date: 2003-01-22 Impact factor: 6.937

6. WebLogo: a sequence logo generator.

Authors: Gavin E Crooks; Gary Hon; John-Marc Chandonia; Steven E Brenner
Journal: Genome Res Date: 2004-06 Impact factor: 9.043

7. MUSCLE: multiple sequence alignment with high accuracy and high throughput.

Authors: Robert C Edgar
Journal: Nucleic Acids Res Date: 2004-03-19 Impact factor: 16.971

8. Genetic control of alcohol dehydrogenase--a competition model for regulation of gene action.

Authors: D Schwartz
Journal: Genetics Date: 1971-03 Impact factor: 4.562

9. Gene discovery using computational and microarray analysis of transcription in the Drosophila melanogaster testis.

Authors: J Andrews; G G Bouffard; C Cheadle; J Lü; K G Becker; B Oliver
Journal: Genome Res Date: 2000-12 Impact factor: 9.043

10. An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments.

Authors: X Shirley Liu; Douglas L Brutlag; Jun S Liu
Journal: Nat Biotechnol Date: 2002-07-08 Impact factor: 54.908

92 in total

1. The "life histories" of genes.

Authors: Esther Betrán
Journal: J Mol Evol Date: 2015-02-03 Impact factor: 2.395

2. The Role of Microsatellites in Streptophyta Gene Evolution.

Authors: Abdulqader Jighly; Ayed M Al-Abdallat; Loai M Alnemer
Journal: J Mol Evol Date: 2017-01-23 Impact factor: 2.395

3. Reproductive Long Intergenic Noncoding RNAs Exhibit Male Gamete Specificity and Polycomb Repressive Complex 2-Mediated Repression.

Authors: Cameron Johnson; Liza J Conrad; Ravi Patel; Sarah Anderson; Chenxin Li; Andy Pereira; Venkatesan Sundaresan
Journal: Plant Physiol Date: 2018-05-29 Impact factor: 8.340

Origin and spread of de novo genes in Drosophila melanogaster populations.

1. Why are "natively unfolded" proteins unstructured under physiologic conditions?

Review 2. Natively unfolded proteins: a point where biology waits for physics.

3. The HMMTOP transmembrane topology prediction server.

4. TM or not TM: transmembrane protein prediction with low false positive rate using DAS-TMfilter.

5. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias.

6. WebLogo: a sequence logo generator.

7. MUSCLE: multiple sequence alignment with high accuracy and high throughput.

8. Genetic control of alcohol dehydrogenase--a competition model for regulation of gene action.

9. Gene discovery using computational and microarray analysis of transcription in the Drosophila melanogaster testis.

10. An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments.

1. The "life histories" of genes.

2. The Role of Microsatellites in Streptophyta Gene Evolution.

3. Reproductive Long Intergenic Noncoding RNAs Exhibit Male Gamete Specificity and Polycomb Repressive Complex 2-Mediated Repression.

4. Adaptation and Phenotypic Diversification in Arabidopsis through Loss-of-Function Mutations in Protein-Coding Genes.

5. In silico study of peptide inhibitors against BACE 1.

6. Did Neanderthals and Denisovans have our de novo genes?

7. The relative ages of eukaryotes and akaryotes.

8. Heterochromatin and genetic conflict.

Review 9. Open questions in the study of de novo genes: what, how and why.

10. Functional Segregation of Overlapping Genes in HIV.