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Resource: Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships
- Michelle Kudron,
- Louis Gevirtzman,
- Alec Victorsen,
- Bridget C. Lear,
- Jiahao Gao,
- Jinrui Xu,
- Swapna Samanta,
- Emily Frink,
- Adri Tran-Pearson,
- Chau Huynh,
- Dionne Vafeados,
- Ann Hammonds,
- William Fisher,
- Martha Wall,
- Greg Wesseling,
- Vanessa Hernandez,
- Zhichun Lin,
- Mary Kasparian,
- Kevin White,
- Ravi Allada,
- Mark Gerstein,
- LaDeana Hillier,
- Susan E. Celniker,
- Valerie Reinke,
- and Robert H. Waterston
Genome Res. December 2024 34: 2319-2334; Published in Advance October 22, 2024, doi:10.1101/gr.279037.124
...; Gerstein et al. 2010; The modENCODE Consortium et al. 2010; Boyle et al. 2014; Kudron et al. 2018). These efforts have resulted in the systematic collection of millions of -scale measurements of TF binding, RNA transcripts, and chromatin accessibility and organization in a variety of organisms.The nematode...
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Research: Characterization of the distribution and dynamics of chromatin states in the C. elegans germline reveals substantial H3K4me3 remodeling during oogenesis
- Mariateresa Mazzetto,
- Lauren E. Gonzalez,
- Nancy Sanchez,
- and Valerie Reinke
Genome Res. January 2024 34: 57-69; Published in Advance December 26, 2023, doi:10.1101/gr.278247.123
...assays in IGN, such as transcriptome profiling (RNA-seq), histone modification profiling via chromatin immunoprecipitation (ChIP-seq), and chromatin accessibility profiling via assay for transposon-accessible chromatin (ATAC-seq) (Sanchez et al. 2023).In this study, we characterized C. elegans chromatin...
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Research: Systematic transcriptome analysis associated with physiological and chronological aging in Caenorhabditis elegans
- Seokjin Ham,
- Sieun S. Kim,
- Sangsoon Park,
- Eun Ji E. Kim,
- Sujeong Kwon,
- Hae-Eun H. Park,
- Yoonji Jung,
- and Seung-Jae V. Lee
Genome Res. November/December 2022 32: 2003-2014; Published in Advance November 9, 2022, doi:10.1101/gr.276515.121
...S, Troyanskaya OG, Murphy CT. 2018. Transcriptome analysis of adult Caenorhabditis elegans cells reveals tissue-specific gene and isoform expression. PLoS Genet 14: e1007559. doi:10.1371/journal.pgen.1007559 ↵Kenyon CJ. 2010. The genetics of ageing. Nature 464: 504–512. doi:10.1038/nature08980...
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Resource: Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging
- Jacob C. Kimmel,
- Lolita Penland,
- Nimrod D. Rubinstein,
- David G. Hendrickson,
- David R. Kelley,
- and Adam Z. Rosenthal
Genome Res. December 2019 29: 2088-2103; Published in Advance November 21, 2019, doi:10.1101/gr.253880.119
...in death. Aging appears to be a conserved feature of eukaryotic biology, affecting organisms as phylogenetically diverse as the single-celled Saccharomyces cerevisiae, the eutelic nematode Caenorhabditis elegans, mice, and humans (Kenyon 2010; Longo et al. 2012; Tissenbaum 2014). Despite the near universal...
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Resource: A spatiotemporally resolved atlas of mRNA decay in the C. elegans embryo reveals differential regulation of mRNA stability across stages and cell types
- Felicia Peng,
- C. Erik Nordgren,
- and John Isaac Murray
Genome Res. August 2024 34: 1235-1252; Published in Advance August 14, 2024, doi:10.1101/gr.278980.124
...or in the context of cell culture systems, global studies in complex organisms will be necessary to establish the extent of developmentally regulated zygotic decay.The nematode Caenorhabditis elegans provides an ideal system for the global study of zygotic mRNA decay owing to its invariant cell lineage...
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Research: Comparative genome analysis of programmed DNA elimination in nematodes
- Jianbin Wang,
- Shenghan Gao,
- Yulia Mostovoy,
- Yuanyuan Kang,
- Maxim Zagoskin,
- Yongqiao Sun,
- Bing Zhang,
- Laura K. White,
- Alice Easton,
- Thomas B. Nutman,
- Pui-Yan Kwok,
- Songnian Hu,
- Martin K. Nielsen,
- and Richard E. Davis
Genome Res. December 2017 27: 2001-2014; Published in Advance November 8, 2017, doi:10.1101/gr.225730.117
...a sequence-independent mechanism for DNA breakage followed by telomere healing, with the formation of more accessible chromatin in the break regions prior to DNA elimination. Our assemblies and annotations also provide comprehensive resources for analysis of DNA elimination, parasitology research...
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Research: Distinctive regulatory architectures of germline-active and somatic genes in C. elegans
- Jacques Serizay,
- Yan Dong,
- Jürgen Jänes,
- Michael Chesney,
- Chiara Cerrato,
- and Julie Ahringer
Genome Res. December 2020 30: 1752-1765; Published in Advance October 22, 2020, doi:10.1101/gr.265934.120
...and elements, we specifically focus on the ubiquitous-uniform class and for simplicity refer to them as “ubiquitous.”The data provide a comprehensive view of chromatin accessibility and transcriptional landscapes in the five major C. elegans tissues. To facilitate access and analyses of these new tissue-specific...
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Resource: The time-resolved transcriptome of C. elegans
- Max E. Boeck,
- Chau Huynh,
- Lou Gevirtzman,
- Owen A. Thompson,
- Guilin Wang,
- Dionna M. Kasper,
- Valerie Reinke,
- LaDeana W. Hillier,
- and Robert H. Waterston
Genome Res. October 2016 26: 1441-1450; Published in Advance August 16, 2016, doi:10.1101/gr.202663.115
...University, New Haven, Connecticut 06520, USA Corresponding author: waterston@gs.washington.edu Abstract We generated detailed RNA-seq data for the nematode Caenorhabditis elegans with high temporal resolution in the embryo as well as representative samples from post...
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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
...(A) tail length and 3′-UTR length. Finally, we have formatted this data as a publicly accessible track hub, enabling researchers to explore this data set easily in a browser.The nematode Caenorhabditis elegans is an ideal experimental model organism due to its compact, well-annotated (The C. elegans...
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Methods: Identification of muscle-specific regulatory modules in Caenorhabditis elegans
- Guoyan Zhao,
- Lawrence A. Schriefer,
- and Gary D. Stormo
Genome Res. March 2007 17: 348-357; Published in Advance February 6, 2007, doi:10.1101/gr.5989907
...information lags far behind. For example, Caenorhabditis elegans is the first metazoan organism whose was sequenced. However, our understanding of the sequences that control tissue-specific gene expression is still limited. This limited understanding comes mainly from experimental investigation...

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