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Resource: The full-length transcriptome of C. elegans using direct RNA sequencing
- Nathan P. Roach,
- Norah Sadowski,
- Amelia F. Alessi,
- Winston Timp,
- James Taylor,
- and John K. Kim
Genome Res. February 2020 30: 299-312; Published in Advance February 5, 2020, doi:10.1101/gr.251314.119
...nanopore-based direct RNA sequencing to characterize the developmental polyadenylated transcriptome of C. elegans. Taking advantage of long reads spanning the full length of mRNA transcripts, we provide support for 23,865 splice isoforms across 14,611 genes, without the need for computational...
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Research: tRNA-derived small RNAs are embedded in the gene regulatory network instructing Drosophila metamorphosis
- Junling Shi,
- Jiaqi Xu,
- Jun Ma,
- and Feng He
Genome Res. December 2023 33: 2119-2132; Published in Advance November 16, 2023, doi:10.1101/gr.278128.123
...RNA-mRNA interaction that can best explain our mRNA-seq data in response to sponge perturbations. These software had been used to predict the post-transcriptional regulation of specific tsRNAs on putative target genes in human and Drosophila cells (Luo et al. 2018; Chen et al. 2022; Tu et al. 2023). We note...
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Research: Transposon accumulation at xenobiotic gene family loci in aphids
- Tobias Baril,
- Adam Pym,
- Chris Bass,
- and Alex Hayward
Genome Res. October 2023 33: 1718-1733; Published in Advance October 18, 2023, doi:10.1101/gr.277820.123
...examining the contribution of TEs to resistance evolution suggest that there can be an additive effect of successive TE insertions at focal host loci over time. For example, in the well-known case of the CYP gene CYP6G1 and DDT resistance in Drosophila, successive TE insertions are linked with an increasing...
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Research: Transposable element accumulation drives size differences among polymorphic Y Chromosomes in Drosophila
- Alison H. Nguyen,
- Weixiang Wang,
- Emily Chong,
- Kamalakar Chatla,
- and Doris Bachtrog
Genome Res. June 2022 32: 1074-1088; Published in Advance May 2, 2022, doi:10.1101/gr.275996.121
...genes are involved in the regulation of chromatin and transcription such as aub, Ulp1, and mxc (Supplemental Table S16). Taken together, our results underline the impact Y Chromosomes can have on -wide expression regulation.Repeated TE mobilization causes Y expansion in other Drosophila speciesOur data...
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LETTER: Gene Expression Profiling in Human Fetal Liver and Identification of Tissue- and Developmental-Stage-Specific Genes through Compiled Expression Profiles and Efficient Cloning of Full-Length cDNAs
- Yongtao Yu,
- Chenggang Zhang,
- Gangqiao Zhou,
- Songfeng Wu,
- Xianghu Qu,
- Handong Wei,
- Guichun Xing,
- Chunna Dong,
- Yun Zhai,
- Jinghong Wan,
- Shuguang Ouyang,
- Li Li,
- Shaowen Zhang,
- Kaixin Zhou,
- Yinan Zhang,
- Chutse Wu,
- and Fuchu He
Genome Res. August 1, 2001 11: 1392-1403; doi:10.1101/gr.175501
...primary structure with those derived from such organisms as Arabidopsis thaliana, Schizosaccharomyces pombe, Kluyveromyces lactis, Plasmodium chabaudi, Tetrahymena thermophila, Caenorhabditis elegans, Drosophila melanogaster (Table 6 ), and other mammals ( Qu et al. 2001 ). These novel genes might...
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Method: Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegans
- Wei-Jen Chung,
- Phaedra Agius,
- Jakub O. Westholm,
- Michael Chen,
- Katsutomo Okamura,
- Nicolas Robine,
- Christina S. Leslie,
- and Eric C. Lai
Genome Res. February 2011 21: 286-300; Published in Advance December 22, 2010, doi:10.1101/gr.113050.110
...of longer introns, even when these exhibit continuous duplex. Unusual structural features of known Drosophila mirtrons Extensive cloning of canonical miRNA genes suggests that preferred substrates of RNase III enzymes have extensive duplex structure and a tendency for smaller, symmetric internal loops...
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RESOURCE: Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis reveals post-tetraploidization transcriptome remodeling
- Ryan D. Morin,
- Elbert Chang,
- Anca Petrescu,
- Nancy Liao,
- Malachi Griffith,
- Robert Kirkpatrick,
- Yaron S. Butterfield,
- Alice C. Young,
- Jeffrey Stott,
- Sarah Barber,
- Ryan Babakaiff,
- Mark C. Dickson,
- Corey Matsuo,
- David Wong,
- George S. Yang,
- Duane E. Smailus,
- Keith D. Wetherby,
- Peggy N. Kwong,
- Jane Grimwood,
- Charles P. Brinkley III,
- Mabel Brown-John,
- Natalie D. Reddix-Dugue,
- Michael Mayo,
- Jeremy Schmutz,
- Jaclyn Beland,
- Morgan Park,
- Susan Gibson,
- Teika Olson,
- Gerard G. Bouffard,
- Miranda Tsai,
- Ruth Featherstone,
- Steve Chand,
- Asim S. Siddiqui,
- Wonhee Jang,
- Ed Lee,
- Steven L. Klein,
- Robert W. Blakesley,
- Barry R. Zeeberg,
- Sudarshan Narasimhan,
- John N. Weinstein,
- Christa Prange Pennacchio,
- Richard M. Myers,
- Eric D. Green,
- Lukas Wagner,
- Daniela S. Gerhard,
- Marco A. Marra,
- Steven J.M. Jones,
- and Robert A. Holt
Genome Res. June 2006 16: 796-803; Published in Advance May 3, 2006, doi:10.1101/gr.4871006
...) Rapid divergence of gene duplicates on the Drosophila melanogaster X chromosome. Mol. Biol. Evol. 19 : 918 – 925 . ↵ Wernersson R. , Pedersen A.G. ( 2003 ) RevTrans: Multiple alignment of coding DNA from aligned amino acid sequences. Nucleic Acids Res. 31 : 3537 – 3539 . ↵ Wilson R.K. , Mardis E...
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Resource: The Drosophila melanogaster transcriptome by paired-end RNA sequencing
- Bryce Daines,
- Hui Wang,
- Liguo Wang,
- Yumei Li,
- Yi Han,
- David Emmert,
- William Gelbart,
- Xia Wang,
- Wei Li,
- Richard Gibbs,
- and Rui Chen
Genome Res. February 2011 21: 315-324; Published in Advance December 22, 2010, doi:10.1101/gr.107854.110
...of Drosophila melanogaster encode dynein heavy chain polypeptides. Proc Natl Acad Sci 97: 13239–13244. Carvalho AB, Dobo BA, Vibranovski MD, Clark AG. 2001. Identification of five new genes on the Y chromosome of Drosophila melanogaster. Proc Natl Acad Sci 98: 13225–13230. Carvalho AB, Vibranovski MD, Carlson...
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Research: Genome-wide analysis of promoter architecture in Drosophila melanogaster
- Roger A. Hoskins,
- Jane M. Landolin,
- James B. Brown,
- Jeremy E. Sandler,
- Hazuki Takahashi,
- Timo Lassmann,
- Charles Yu,
- Benjamin W. Booth,
- Dayu Zhang,
- Kenneth H. Wan,
- Li Yang,
- Nathan Boley,
- Justen Andrews,
- Thomas C. Kaufman,
- Brenton R. Graveley,
- Peter J. Bickel,
- Piero Carninci,
- Joseph W. Carlson,
- and Susan E. Celniker
Genome Res. February 2011 21: 182-192; Published in Advance December 22, 2010, doi:10.1101/gr.112466.110
...://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi) under accession nos. SRX015329, SRA008141, and SRX015869.] TheDrosophila melanogaster embryo is an important model system used to study transcriptional regulation of gene expression during development (for review, see Biggin and Tjian 2001). Much recent work has focused on the -wide identification...
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Method: CRISPR-based modular assembly of a UAS-cDNA/ORF plasmid library for more than 5500 Drosophila genes conserved in humans
- Ping Wei,
- Wen Xue,
- Yun Zhao,
- Guang Ning,
- and Jiwu Wang
Genome Res. January 2020 30: 95-106; Published in Advance November 13, 2019, doi:10.1101/gr.250811.119
...-Broad Lentiviral Expression Library (Yang et al. 2011), and one Drosophila DUB ortholog clone is available from the mouse Mammalian Gene Collection (MGC). These human and mouse DUB clones allow us to examine whether CRISPRmass can apply to cDNA/ORF libraries of other species. The remaining three Drosophila DUBs do...

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