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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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Resource: Direct full-length RNA sequencing reveals unexpected transcriptome complexity during Caenorhabditis elegans development
- Runsheng Li,
- Xiaoliang Ren,
- Qiutao Ding,
- Yu Bi,
- Dongying Xie,
- and Zhongying Zhao
Genome Res. February 2020 30: 287-298; Published in Advance February 5, 2020, doi:10.1101/gr.251512.119
...Technologies to study the transcriptome complexity in Caenorhabditis elegans. We generated approximately six million reads using native poly(A)-tailed mRNAs from three developmental stages, with average read lengths ranging from 900 to 1100 nt. Around half of the reads represent full-length transcripts...
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Resource: The C. elegans embryonic transcriptome with tissue, time, and alternative splicing resolution
- Adam D. Warner,
- Louis Gevirtzman,
- LaDeana W. Hillier,
- Brent Ewing,
- and Robert H. Waterston
Genome Res. June 2019 29: 1036-1045; Published in Advance May 23, 2019, doi:10.1101/gr.243394.118
...Biol 358: 345–355. doi:10.1016/j.ydbio.2011.08.002 ↵Boeck ME, Huynh C, Gevirtzman L, Thompson OA, Wang G, Kasper DM, Reinke V, Hillier LW, Waterston RH. 2016. The time-resolved transcriptome of C. elegans. Genome Res 26: 1441–1450. doi:10.1101/gr.202663.115 ↵Burdick J, Walton T, Preston E, Zacharias A...
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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
..., Cummings Life Science Center, Chicago, IL 60637, USA Corresponding author: watersto@uw.eduAbstractRecently developed single-cell technologies allow researchers to characterize cell states at ever greater resolution and scale. Caenorhabditis elegans is a particularly tractable system for studying...
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Method: Nematode gene annotation by machine-learning-assisted proteotranscriptomics enables proteome-wide evolutionary analysis
- Alejandro Ceron-Noriega,
- Miguel V. Almeida,
- Michal Levin,
- and Falk Butter
Genome Res. January 2023 33: 112-128; Published in Advance January 18, 2023, doi:10.1101/gr.277070.122
...and completeness of our chosen transcriptome assembly approach. We thus generated 74 million paired-end RNA-seq reads of 79-base length from a nonsynchronized C. elegans culture containing all developmental stages ranging from embryos to adult worms. The RNA-seq reads were quality controlled and either used...
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Resource: The developmental proteome of Drosophila melanogaster
- Nuria Casas-Vila,
- Alina Bluhm,
- Sergi Sayols,
- Nadja Dinges,
- Mario Dejung,
- Tina Altenhein,
- Dennis Kappei,
- Benjamin Altenhein,
- Jean-Yves Roignant,
- and Falk Butter
Genome Res. July 2017 27: 1273-1285; Published in Advance April 5, 2017, doi:10.1101/gr.213694.116
...studied, we were particularly interested in proteome changes during embryogenesis. To investigate the process in a high time-resolved and systematicmanner, we collected whole embryos at narrow intervals: every hour after egg laying for up to 6 h and then every 2 h until 20 h (Fig. 6A). These 14 time...
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Resource: The mRNA-bound proteome of the early fly embryo
- Hans-Hermann Wessels,
- Koshi Imami,
- Alexander G. Baltz,
- Marcin Kolinski,
- Anastasia Beldovskaya,
- Matthias Selbach,
- Stephen Small,
- Uwe Ohler,
- and Markus Landthaler
Genome Res. July 2016 26: 1000-1009; Published in Advance April 28, 2016, doi:10.1101/gr.200386.115
...expressed during embryogenesis (0–24-h post egg laying) (n = 11,232) (Graveley et al. 2011) into six condensed, timely resolved clusters. (Left) Cluster median z-score-transformed expression values over time. Clusters sizes are indicated in order 1 through 6. (Right) Cluster proportions of all known RBP...
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Research: Global analyses of the dynamics of mammalian microRNA metabolism
- Elena R. Kingston and
- David P. Bartel
Genome Res. November 2019 29: 1777-1790; Published in Advance September 13, 2019, doi:10.1101/gr.251421.119
...RNA targets through base-pairing of the miRNA seed region (miRNA nucleotides [nt] 2–8) and sites in mRNA 3′ untranslated regions (UTRs) (Bartel 2018). Each miRNA has many sites throughout the transcriptome, and more than 60% of human protein-coding genes have evolutionarily conserved sites to at least one...

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