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Resource: CGC1, a new reference genome for Caenorhabditis elegans
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Dae-Eun Jeong,
- Chie Owa,
- Haruka Kobayashi,
- Yoshihiko Suzuki,
- Manami Kanamori,
- Yu Toyoshima,
- Yuichi Iino,
- Ann E. Rougvie,
- Lamia Wahba,
- Andrew Z. Fire,
- Erich M. Schwarz,
- and Shinichi Morishita
Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
...CGC1, a new reference for Caenorhabditis elegans Kazuki Ichikawa1, Massa J. Shoura2,8, Karen L. Artiles2, Dae-Eun Jeong2, Chie Owa1, Haruka Kobayashi1, Yoshihiko Suzuki1, Manami Kanamori3, Yu Toyoshima3, Yuichi Iino3, Ann E. Rougvie4, Lamia Wahba5, Andrew Z. Fire2,6, Erich M. Schwarz7 and Shinichi...
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GENOME METHODS: Analysis of the Quality and Utility of Random Shotgun Sequencing at Low Redundancies
- John Bouck,
- Webb Miller,
- James H. Gorrell,
- Donna Muzny,
- and Richard A. Gibbs
Genome Res. October 1, 1998 8: 1074-1084; doi:10.1101/gr.8.10.1074
.... ( 1998 ) A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res. 8 : 967 – 974 . ↵ Goodman L. ( 1998 ) Random shotgun fire. Genome Res. 8 : 567 – 568 . ↵ Green P. ( 1997 ) Against a whole- shotgun. Genome Res. 7 : 410 – 417 . ↵ Hardison R.C. , Oeltjen J. , Miller W...
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Resource: Comprehensive characterization of tissue-specific chromatin accessibility in L2 Caenorhabditis elegans nematodes
- Timothy J. Durham,
- Riza M. Daza,
- Louis Gevirtzman,
- Darren A. Cusanovich,
- Olubusayo Bolonduro,
- William Stafford Noble,
- Jay Shendure,
- and Robert H. Waterston
Genome Res. October 2021 31: 1952-1969; Published in Advance April 22, 2021, doi:10.1101/gr.271791.120
...topic to the number we would expect if the overlaps were random (i.e., if topics were not cell type–specific), and we expressed this comparison as a log2 ratio between observed and random overlap counts (Fig. 4). We find topics with specific enrichment for overlaps with peaks from each TF (95...
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Method: High resolution mapping of modified DNA nucleobases using excision repair enzymes
- D. Suzi Bryan,
- Monica Ransom,
- Biniam Adane,
- Kerri York,
- and Jay R. Hesselberth
Genome Res. September 2014 24: 1534-1542; Published in Advance July 11, 2014, doi:10.1101/gr.174052.114
...to positions downstream from T residues (Fig. 2A), indicating robust recovery of uracil sites. In post-digestion Excision-seq libraries for uracil, we expected a more random distribution of base identity at the sites of linker ligation (Fig. 1B) and found relatively uniform levels of base identity near...
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Research: Cooperative target mRNA destabilization and translation inhibition by miR-58 microRNA family in C. elegans
- Deni Subasic,
- Anneke Brümmer,
- Yibo Wu,
- Sérgio Morgado Pinto,
- Jochen Imig,
- Martin Keller,
- Marko Jovanovic,
- Helen Louise Lightfoot,
- Sara Nasso,
- Sandra Goetze,
- Erich Brunner,
- Jonathan Hall,
- Ruedi Aebersold,
- Mihaela Zavolan,
- and Michael O. Hengartner
Genome Res. November 2015 25: 1680-1691; Published in Advance July 31, 2015, doi:10.1101/gr.183160.114
...and multiple miR-58 mutant backgrounds available in C. elegans. We utilized selected reaction monitoring (SRM) assays to quantify 22 proteins whose corresponding transcripts are predicted by TargetScan (Friedman et al. 2009; Jan et al. 2011) to be miR58 family targets, as well as 22 random control proteins...
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Research: Profiling the RNA editomes of wild-type C. elegans and ADAR mutants
- Han-Qing Zhao,
- Pan Zhang,
- Hua Gao,
- Xiandong He,
- Yanmei Dou,
- August Y. Huang,
- Xi-Ming Liu,
- Adam Y. Ye,
- Meng-Qiu Dong,
- and Liping Wei
Genome Res. January 2015 25: 66-75; Published in Advance November 4, 2014, doi:10.1101/gr.176107.114
...analysis, we analyzed a random selection of clustered RNA editing regions, all RNA editing sites at the coding regions, and seven non-A-to-G editing sites by Sanger sequencing of PCR-amplified DNA and cDNA samples. The cDNA was synthesized from the total RNA using the PrimeScript II First Strand c...
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Method: Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions
- Alicia N. Schep,
- Jason D. Buenrostro,
- Sarah K. Denny,
- Katja Schwartz,
- Gavin Sherlock,
- and William J. Greenleaf
Genome Res. November 2015 25: 1757-1770; Published in Advance August 27, 2015, doi:10.1101/gr.192294.115
...Random tiling 19,185 0.512 0.273 0.242 0.061 Schep et al. 1760 Genome Research www..org intensity of this 10.5-bp periodicity.We also computed a pair-wise correlationof dinucleotide frequencies between every dinucleotide for each species (Fig. 4B). For the twoyeast species, all dinucleotides show 10.5-bp...
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Research: Deep small RNA sequencing from the nematode Ascaris reveals conservation, functional diversification, and novel developmental profiles
- Jianbin Wang,
- Benjamin Czech,
- Amanda Crunk,
- Adam Wallace,
- Makedonka Mitreva,
- Gregory J. Hannon,
- and Richard E. Davis
Genome Res. September 2011 21: 1462-1477; Published in Advance June 17, 2011, doi:10.1101/gr.121426.111
...to amplify the silencing trigger (Ambros et al. 2003b; Chicas et al. 2004; Ruby et al. 2006; Pak and Fire 2007; Sijen et al. 2007). piRNAs are 21- to 30-nt RNAs that specifically associate with Piwi-clade Argonaute proteins and are derived from discrete genomic loci (called piRNA clusters) by a dicer...
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Research: CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize
- Jonathan I. Gent,
- Nathanael A. Ellis,
- Lin Guo,
- Alex E. Harkess,
- Yingyin Yao,
- Xiaoyu Zhang,
- and R. Kelly Dawe
Genome Res. April 2013 23: 628-637; Published in Advance December 26, 2012, doi:10.1101/gr.146985.112
...to direct these heterochromatic structural states, often overlapping with defense mechanisms against foreign nucleic acids. A prominent example is RNA interference (RNAi) (Fire et al. 1998), which can not only degrade RNA, but can also induce transcriptional gene silencing. In fact, short interfering RNA...
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Method: Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome
- Jakob Skou Pedersen,
- Eivind Valen,
- Amhed M. Vargas Velazquez,
- Brian J. Parker,
- Morten Rasmussen,
- Stinus Lindgreen,
- Berit Lilje,
- Desmond J. Tobin,
- Theresa K. Kelly,
- Søren Vang,
- Robin Andersson,
- Peter A. Jones,
- Cindi A. Hoover,
- Alexei Tikhonov,
- Egor Prokhortchouk,
- Edward M. Rubin,
- Albin Sandelin,
- M. Thomas P. Gilbert,
- Anders Krogh,
- Eske Willerslev,
- and Ludovic Orlando
Genome Res. March 2014 24: 454-466; Published in Advance December 3, 2013, doi:10.1101/gr.163592.113
.... Substitution rates at CpG reveal methylation of DNA. (A) C!Tmismatch rates (gray) versus rate of other mismatches (black) between a random subset of 1,000,000 Phusion (left) or HiFi (right) reads mapping uniquely. Reads are split by those starting with CpG (top; 26,864 Phusion and 25,568 HiFi reads) and other...
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