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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
.... simulans than in D. melanogaster (Drosophila 12 Genomes Consortium 2007), although it could have been owing to a difference in assembly quality (Drosophila 12 Genomes Consortium 2007; Rogers et al. 2010; Velandia-Huerto et al. 2016). We found -wide tRNA counts to be similar between the species, ranging...
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Method: Classification and clustering of RNA crosslink-ligation data reveal complex structures and homodimers
- Minjie Zhang,
- Irena T. Hwang,
- Kongpan Li,
- Jianhui Bai,
- Jian-Fu Chen,
- Tsachy Weissman,
- James Y. Zou,
- and Zhipeng Lu
Genome Res. May 2022 32: 968-985; Published in Advance March 24, 2022, doi:10.1101/gr.275979.121
...developed to determine its structures. Predicting the base-pairing of nucleotides, or RNA secondary structure, has long been the goal of algorithms that calculate minimal free energy conformations or exhaustively search for conserved structural motifs in multiple alignments of nucleotide sequences (Gutell...
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Research: Genome-wide mapping of nuclear mitochondrial DNA sequences links DNA replication origins to chromosomal double-strand break formation in Schizosaccharomyces pombe
- Sandrine Lenglez,
- Damien Hermand,
- and Anabelle Decottignies
Genome Res. September 2010 20: 1250-1261; Published in Advance August 5, 2010, doi:10.1101/gr.104513.109
....4% of the total S. pombe .NUMT16 is not associated with an ORI. (Gray rectangles) Centromeres. Lenglez et al. 1254 Genome Research www..org tRNA-rich regions of the mitochondrial (between cob1 and atp9 genes) (Fig. 7A). This enrichment of mtDNA fragments originating from cox1 introns or tRNA-rich regions...
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LETTER: Alu-mediated 100-kb deletion in the primate genome: The loss of the agouti signaling protein gene in the lesser apes
- Kazuhiro Nakayama and
- Takafumi Ishida
Genome Res. April 2006 16: 485-490; doi:10.1101/gr.4763906
.... 1992 ). Because of a 120- to 170-kb deletion, expression of ASIP in Ay mice is under the control of promoters of the hnRNP-associated with lethal yellow gene ( RALY, Fig. 1 ) that encodes ubiquitously expressed RNA-binding protein ( Michaud et al. 1993 ; Miller et al. 1993; Duhl et al. 1994 ). The over...
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Resource: Genome-based analysis of the nonhuman primate Macaca fascicularis as a model for drug safety assessment
- Martin Ebeling,
- Erich Küng,
- Angela See,
- Clemens Broger,
- Guido Steiner,
- Marco Berrera,
- Tobias Heckel,
- Leonardo Iniguez,
- Thomas Albert,
- Roland Schmucki,
- Hermann Biller,
- Thomas Singer,
- and Ulrich Certa
Genome Res. October 2011 21: 1746-1756; Published in Advance August 23, 2011, doi:10.1101/gr.123117.111
...-coding transcripts by three-way alignments of M. fascicularis, M. mulatta, and H. sapiensmRNAs.We developed an automated pipeline to identify human mRNA sequences that have a corresponding predicted mRNA in both M. fascicularis andM. mulatta. We applied rigorous filters to remove incomplete sequences to select only...
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Letter: Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production
- Juan Lucas Argueso,
- Marcelo F. Carazzolle,
- Piotr A. Mieczkowski,
- Fabiana M. Duarte,
- Osmar V.C. Netto,
- Silvia K. Missawa,
- Felipe Galzerani,
- Gustavo G.L. Costa,
- Ramon O. Vidal,
- Melline F. Noronha,
- Margaret Dominska,
- Maria G.S. Andrietta,
- Sílvio R. Andrietta,
- Anderson F. Cunha,
- Luiz H. Gomes,
- Flavio C.A. Tavares,
- André R. Alcarde,
- Fred S. Dietrich,
- John H. McCusker,
- Thomas D. Petes,
- and Gonçalo A.G. Pereira
Genome Res. December 2009 19: 2258-2270; Published in Advance October 7, 2009, doi:10.1101/gr.091777.109
...of the deletion/ underrepresentation peaks spanned regions containing genes known to be essential in S288c. The S288c-isogenic control strain used in A and B was the JAY309 diploid. Argueso et al. 2262 Genome Research www..org S288c reference , it became clear that most interruptions occurred at regions...
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ARTICLES: Regional assignment of 68 new human gene transcripts on chromosome 11.
- M F Rosier,
- I Reguigne-Arnould,
- P Couillin,
- M D Devignes,
- and C Auffray
Genome Res. August 1995 5: 60-70; doi:10.1101/gr.5.1.60
...been derived from selected partial cDNA se- quences established upon the sequencing of two cDNA libraries constructed from skeletal muscle and infant brain mRNA. The GDB D numbers of the 80 eSTS markers tudied here are listed in Ta- ble 1. In the case of multiassignments (8/80 eSTS markers...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...regarding GOI regulators, but it is critical to keep in mind the limitations of this technique.RT-qPCR can be employed to validate in silico predictions and determine whether the suspected TF plays a role in the transcription of the GOI. Total mRNA is first reverse-transcribed into complementary DNA (c...
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ARTICLE: Retrotransposons and Their Recognition of pol II Promoters: A Comprehensive Survey of the Transposable Elements From the Complete Genome Sequence of Schizosaccharomyces pombe
- Nathan J. Bowen,
- I. King Jordan,
- Jonathan A. Epstein,
- Valerie Wood,
- and Henry L. Levin
Genome Res. September 2003 13: 1984-1997; doi:10.1101/gr.1191603
...also served as footprints for previous insertion events by the Tf retrotransposons. Analysis of 186 genomic insertion events revealed a close association with RNA polymerase II promoters. These insertions clustered in the promoter-proximal regions of genes, upstream of protein coding regions by 100...
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LETTER: Millions of Years of Evolution Preserved: A Comprehensive Catalog of the Processed Pseudogenes in the Human Genome
- Zhaolei Zhang,
- Paul M. Harrison,
- Yin Liu,
- and Mark Gerstein
Genome Res. December 2003 13: 2541-2558; doi:10.1101/gr.1429003
...University, New Haven, Connecticut 06520-8114, USA Abstract Processed pseudogenes were created by reverse-transcription of mRNAs; they provide snapshots of ancient genes existing millions of years ago in the genome. To find them in the present-day human, we developed a pipeline using features...

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