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Research: Intergenic ORFs as elementary structural modules of de novo gene birth and protein evolution
- Chris Papadopoulos,
- Isabelle Callebaut,
- Jean-Christophe Gelly,
- Isabelle Hatin,
- Olivier Namy,
- Maxime Renard,
- Olivier Lespinet,
- and Anne Lopes
Genome Res. December 2021 31: 2303-2315; Published in Advance November 22, 2021, doi:10.1101/gr.275638.121
...the DNA, thereby resulting in different amino acid compositions from CDSs. If and how these amino acid compositions can account for the structural states observed in proteomes are crucial questions to understand the relationship, if any, between the noncoding and the protein structure universe. So far...
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Research: Transposons contribute to the functional diversification of the head, gut, and ovary transcriptomes across Drosophila natural strains
- Marta Coronado-Zamora and
- Josefa González
Genome Res. September 2023 33: 1541-1553; Published in Advance October 4, 2023, doi:10.1101/gr.277565.122
...and by insertion group, body part, and strain (Supplemental Table S4D), where it can be observed that, overall, the previous patterns hold at the body part level.Retrotransposons and DNA transposons contribute to chimeric gene–TE transcriptsWe assessed the contribution of TE families to chimeric gene...
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Research: Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster
- Anna Grandchamp,
- Lucas Kühl,
- Marie Lebherz,
- Kathrin Brüggemann,
- John Parsch,
- and Erich Bornberg-Bauer
Genome Res. June 2023 33: 872-890; Published in Advance July 13, 2023, doi:10.1101/gr.277482.122
...nucleotide diversity on the X Chromosome compared to the autosomes. These results were also observed in Drosophila simulans (Begun et al. 2007). Our results show exactly the same pattern, with reduced nucleotide diversity π between lines in telomeres and centromeres. Moreover, the average and median...
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Research: Evolution of genome structure in the Drosophila simulans species complex
- Mahul Chakraborty,
- Ching-Ho Chang,
- Danielle E. Khost,
- Jeffrey Vedanayagam,
- Jeffrey R. Adrion,
- Yi Liao,
- Kristi L. Montooth,
- Colin D. Meiklejohn,
- Amanda M. Larracuente,
- and J.J. Emerson
Genome Res. March 2021 31: 380-396; Published in Advance February 9, 2021, doi:10.1101/gr.263442.120
...introns containing repetitive DNA are ∼10% longer in D. melanogaster than sim-complex species, (Supplemental Information, methods and analyses). However, although the sim-complex does harbor less TE content than D. melanogaster (Fig. 4A; Drosophila 12 Genomes Consortium 2007), we observe only ∼17% less...
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Research: De novo DNA demethylation and noncoding transcription define active intergenic regulatory elements
- Felix Schlesinger,
- Andrew D. Smith,
- Thomas R. Gingeras,
- Gregory J. Hannon,
- and Emily Hodges
Genome Res. October 2013 23: 1601-1614; Published in Advance June 28, 2013, doi:10.1101/gr.157271.113
...constraint on the methylation state. Together, these data show that intergenic loci, specifically putative enhancers, with methylation states that dynamically change during differentiation are also the most likely to vary both between individuals and between species. Discussion Patterns of DNA methylation...
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Research: DNA-guided establishment of nucleosome patterns within coding regions of a eukaryotic genome
- Leslie Y. Beh,
- Manuel M. Müller,
- Tom W. Muir,
- Noam Kaplan,
- and Laura F. Landweber
Genome Res. November 2015 25: 1727-1738; Published in Advance September 1, 2015, doi:10.1101/gr.188516.114
...DNA-guided establishment of nucleosome patterns within coding regions of a eukaryotic Leslie Y. Beh,1 Manuel M. Müller,2 Tom W. Muir,2 Noam Kaplan,3 and Laura F. Landweber1 1Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey 08544, USA; 2Department...
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ARTICLE: Analysis of Conserved Noncoding DNA in Drosophila Reveals Similar Constraints in Intergenic and Intronic Sequences
- Casey M. Bergman and
- Martin Kreitman
Genome Res. August 1, 2001 11: 1335-1345; doi:10.1101/gr.178701
...Analysis of Conserved Noncoding DNA in Drosophila Reveals Similar Constraints in Intergenic and Intronic Sequences Casey M. Bergman 1 and Martin Kreitman Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA...
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Research: Critical roles of long noncoding RNAs in Drosophila spermatogenesis
- Kejia Wen,
- Lijuan Yang,
- Tuanlin Xiong,
- Chao Di,
- Danhui Ma,
- Menghua Wu,
- Zhaoyu Xue,
- Xuedi Zhang,
- Li Long,
- Weimin Zhang,
- Jiaying Zhang,
- Xiaolin Bi,
- Junbiao Dai,
- Qiangfeng Zhang,
- Zhi John Lu,
- and Guanjun Gao
Genome Res. September 2016 26: 1233-1244; Published in Advance August 11, 2016, doi:10.1101/gr.199547.115
...contamination of RNA by genomic DNA. (C ) Expression of selected lncRNAs in Drosophila testis, analyzed by whole-mount in situ hybridization. Cyclin B RNAwas used as a positive control, and RFP RNA in nontransgenic testis (w1118) was used as a negative control. Critical roles of lncRNAs in fly spermatogenesis...
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Research: A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence
- Tina T. Hu,
- Michael B. Eisen,
- Kevin R. Thornton,
- and Peter Andolfatto
Genome Res. January 2013 23: 89-98; Published in Advance August 30, 2012, doi:10.1101/gr.141689.112
...(Drosophila 12 Genomes Consortium et al. 2007). It is generally expected that repetitive DNA should limit the efficiency of de novo assembly (Treangen and Salzberg 2012). We find that our 500-bp insert libraries, combined with the published 3-kb insert paired-end Sanger data, is sufficient to assemble contigs...
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Research: Deep sequencing of natural and experimental populations of Drosophila melanogaster reveals biases in the spectrum of new mutations
- Zoe June Assaf,
- Susanne Tilk,
- Jane Park,
- Mark L. Siegal,
- and Dmitri A. Petrov
Genome Res. December 2017 27: 1988-2000; Published in Advance October 27, 2017, doi:10.1101/gr.219956.116
...precision estimate of context-dependency yet available in Drosophila, a demonstration that our detected mutational patterns are relevant to the course of evolution within coding regions. The context-dependent rates of mutations, as measured from rare polymorphisms, predict the spectra of substitutions which...

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