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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
...changes during this developmental transition. The active histone modification H3K4me3 shows particularly dynamic remodeling as germ cells differentiate into oocytes, which suggests a mechanism for establishing early transcription of essential genes during zygotic activation. This analysis highlights...
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Resource: Genome-wide discovery of active regulatory elements and transcription factor footprints in Caenorhabditis elegans using DNase-seq
- Margaret C.W. Ho,
- Porfirio Quintero-Cadena,
- and Paul W. Sternberg
Genome Res. December 2017 27: 2108-2119; Published in Advance October 26, 2017, doi:10.1101/gr.223735.117
...data set for genes likely to be involved in L1 arrest (P < 1.6 × 10−8) (Supplemental Fig. S7D; expression data from Baugh et al. 2009; Maxwell et al. 2014). While this difference in expression is not large, it is worth noting that the majority of C. elegans genes are transcriptionally quiescent during...
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Resource: The transcription start site landscape of C. elegans
- Taro Leo Saito,
- Shin-ichi Hashimoto,
- Sam Guoping Gu,
- J. Jason Morton,
- Michael Stadler,
- Thomas Blumenthal,
- Andrew Fire,
- and Shinichi Morishita
Genome Res. August 2013 23: 1348-1361; Published in Advance May 1, 2013, doi:10.1101/gr.151571.112
....’’ Caenorhabditis elegans has been a valuable model system for studying a variety of aspects of gene expression (including transsplicing) (Krause and Hirsh 1987; Lasda and Blumenthal 2011). Approximately 70% of C. elegans genes are subject to trans-splicing (Allen et al. 2011; Lasda and Blumenthal 2011). C. elegans...
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Research: Complex expression dynamics and robustness in C. elegans insulin networks
- Ashlyn D. Ritter,
- Yuan Shen,
- Juan Fuxman Bass,
- Sankarganesh Jeyaraj,
- Bart Deplancke,
- Arnab Mukhopadhyay,
- Jian Xu,
- Monica Driscoll,
- Heidi A. Tissenbaum,
- and Albertha J.M. Walhout
Genome Res. June 2013 23: 954-965; Published in Advance March 28, 2013, doi:10.1101/gr.150466.112
...: 10.1895/wormbook.1.144.1. http://www.wormbook.org. Kelly WG, Xu S, Montgomery MK, Fire A. 1997. Distinct requirements for somatic and germline expression of a generally expressedCaenorhabditis elegans gene. Genetics 146: 227–238. Kenyon C. 2011. The first long-lived mutants: Discovery of the insulin...
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ARTICLE: Comparative Genomics of Gene Expression in the Parasitic and Free-Living Nematodes Strongyloides stercoralis and Caenorhabditis elegans
- Makedonka Mitreva,
- James P. McCarter,
- John Martin,
- Mike Dante,
- Todd Wylie,
- Brandi Chiapelli,
- Deana Pape,
- Sandra W. Clifton,
- Thomas B. Nutman,
- and Robert H. Waterston
Genome Res. February 2004 14: 209-220; doi:10.1101/gr.1524804
...of dauer entry and exit ( Riddle and Albert 1997 ). In S. stercoralis , host factors are likely critical to the exit of L3i from arrest, but little is known about the genes involved. Nematode Comparative Genomics The C. elegans is complete ( The C. elegans Sequencing Consortium 1998 ), and substantial...
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LETTER: Quantitative evidence for conserved longevity pathways between divergent eukaryotic species
- Erica D. Smith,
- Mitsuhiro Tsuchiya,
- Lindsay A. Fox,
- Nick Dang,
- Di Hu,
- Emily O. Kerr,
- Elijah D. Johnston,
- Bie N. Tchao,
- Diana N. Pak,
- K. Linnea Welton,
- Daniel E.L. Promislow,
- James H. Thomas,
- Matt Kaeberlein,
- and Brian K. Kennedy
Genome Res. April 2008 18: 564-570; Published in Advance March 13, 2008, doi:10.1101/gr.074724.107
...by developmental arrest genes in Caenorhabditis elegans . Aging Cell 6 : 525 – 533 . ↵ Curran, S.P. , Ruvkun, G. ( 2007 ) Lifespan regulation by evolutionarily conserved genes essential for viability . PLoS Genet. 3 : e56 , doi: 10.1370/journal.pgen.0030056 . ↵ Dillin, A. , Hsu, A.L. , Arantes-Oliveira, N...
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ARTICLE: Analysis of long-lived C. elegans daf-2 mutants using serial analysis of gene expression
- Julius Halaschek-Wiener,
- Jaswinder S. Khattra,
- Sheldon McKay,
- Anatoli Pouzyrev,
- Jeff M. Stott,
- George S. Yang,
- Robert A. Holt,
- Steven J.M. Jones,
- Marco A. Marra,
- Angela R. Brooks-Wilson,
- and Donald L. Riddle
Genome Res. May 2005 15: 603-615; Published in Advance April 18, 2005, doi:10.1101/gr.3274805
...Molecular Biology Program and Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211, USA Abstract We have identified longevity-associated genes in a long-lived Caenorhabditis elegans daf-2 (insulin/IGF receptor) mutant using serial analysis of gene expression (SAGE...
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Research: Vertebrates show coordinated elevated expression of mitochondrial and nuclear genes after birth
- Hadar Medini and
- Dan Mishmar
Genome Res. March 2025 35: 459-474; Published in Advance March 4, 2025, doi:10.1101/gr.279700.124
...al. 2020). Specifically, knockout of mitochondrial regulatory proteins such as mtDNA polymerase gamma (Polg) (Hance et al. 2005) and mtDNA transcription factor A (Tfam) (Larsson et al. 1998) resulted in developmental arrest between embryonic days 7.5 and 8.5 (upon Polg knockout) and lethality on day...
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Method: Multimodal RNA-seq using single-strand, double-strand, and CircLigase-based capture yields a refined and extended description of the C. elegans transcriptome
- Ayelet T. Lamm,
- Michael R. Stadler,
- Huibin Zhang,
- Jonathan I. Gent,
- and Andrew Z. Fire
Genome Res. February 2011 21: 265-275; Published in Advance December 22, 2010, doi:10.1101/gr.108845.110
.... 2009). Despite the localized variations between methods within genes, we note that the nucleotide preferences do not seem to affect gene coverage (Fig. 2). Refining and expanding models of the C. elegans transcriptome The diversity of starting material (genetic backgrounds and developmental stages...
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PERSPECTIVE: Genomics in C. elegans: So many genes, such a little worm
- LaDeana W. Hillier,
- Alan Coulson,
- John I. Murray,
- Zhirong Bao,
- John E. Sulston,
- and Robert H. Waterston
Genome Res. December 2005 15: 1651-1660; doi:10.1101/gr.3729105
.... In 1965 Sydney Brenner selected Caenorhabditis elegans for his studies of development and the nervous system because of its simple anatomy, its stereotyped behavior, and the ease of genetic manipulation. Even at inception, the goal of studying the worm was an understanding of how genes dictated form...

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