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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
...are the colocalization of the opposing marks H3K27me3 and H3K4me3 (Macrae et al. 2023), a configuration not found in any germline chromatin state in C. elegans. Thus, this observation suggests the existence of an alternate mechanism that uses only H3K27me3 to temporally delay gene expression across the maternal-to-embryo...
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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
...a framework for the investigation of expression in individual cells.As the Caenorhabditis elegans embryo develops from one cell to 558 cells, the transcriptional profile of each cell undergoes unique changes to drive differentiation into distinct cell types and tissues. Although the invariant lineage...
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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
...improved predictions of tissue-specific expression compared with motifs alone. In a pilot functional test, 10 of 15 DHSs from pha-4, icl-1, and ceh-13 drove reporter gene expression in transgenic C. elegans. Overall, we provide experimental annotation of 26,644 putative CRMs in the embryo containing 55...
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LETTER: A Gene Recommender Algorithm to Identify Coexpressed Genes in C. elegans
- Art B. Owen,
- Josh Stuart,
- Kathy Mach,
- Anne M. Villeneuve,
- and Stuart Kim
Genome Res. August 2003 13: 1828-1837; doi:10.1101/gr.1125403
...and Botstein 1999 ). A previous report compiled data from a large number of C. elegans DNA microarray experiments, and then used a variant of multidimensional scaling to generate a gene expression terrain map (a topomap; Kim et al. 2001 ). In this topomap, gene clusters are represented as different mountains...
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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
...Analysis of long-lived C. elegans daf-2 mutants using serial analysis of gene expression Julius Halaschek-Wiener 1 , Jaswinder S. Khattra 1 , Sheldon McKay 1 , Anatoli Pouzyrev 2 , Jeff M. Stott 1 , George S. Yang 1 , Robert...
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Research: Single-cell transcriptome and metagenome profiling reveals the genetic basis of rumen functions and convergent developmental patterns in ruminants
- Juan Deng,
- Ya-Jing Liu,
- Wen-Tian Wei,
- Qi-Xuan Huang,
- Li-Ping Zhao,
- Ling-Yun Luo,
- Qi Zhu,
- Lin Zhang,
- Yuan Chen,
- Yan-Ling Ren,
- Shan-Gang Jia,
- Yu-Luan Lin,
- Ji Yang,
- Feng-Hua Lv,
- Hong-Ping Zhang,
- Feng-E Li,
- Li Li,
- and Meng-Hua Li
Genome Res. October 2023 33: 1690-1707; Published in Advance October 26, 2023, doi:10.1101/gr.278239.123
...associated with the development of ruminal cells, microbiota, and core transcriptional regulatory networks. In addition, we identified and validated potential cross-talk between host cells and microbiomes and revealed their roles in modulating the spatiotemporal expression of key genes in ruminal cells...
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Resource: Dynamic transcriptional and chromatin accessibility landscape of medaka embryogenesis
- Yingshu Li,
- Yongjie Liu,
- Hang Yang,
- Ting Zhang,
- Kiyoshi Naruse,
- and Qiang Tu
Genome Res. June 2020 30: 924-937; Published in Advance June 26, 2020, doi:10.1101/gr.258871.119
.... In the end, the PacBio gene models contribute 61% of the final gene set. Some genes or isoforms expressed at a low level or in the restricted domains are likely missed. For example, vasa is a germ cell specifically expressed gene (Shinomiya et al. 2000). In medaka embryos, vasa transcript presents in each...
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Review: Navigating the landscape of epitranscriptomics and host immunity
- Elaine Huang,
- Clara Frydman,
- and Xinshu Xiao
Genome Res. April 2024 34: 515-529; Published in Advance May 3, 2024, doi:10.1101/gr.278412.123
...of immunogenic RNAs, control of genes involved in innate immune response, and facilitation of adaptive immunity. Here, we provide an overview of recent research findings that elucidate the contributions of RNA modifications to each of these processes. We also discuss relevant methods for -wide identification...
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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
...including embryo, larva, pupa, and adult, undergoing a complete phenotypic metamorphosis (Lawrence 1992). These transitions are based on tightly regulated gene expression at the transcriptional, epigenetic, and translational level. Currently, most developmental gene expression studies in Drosophila rely...
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Perspective: Half dozen of one, six billion of the other: What can small- and large-scale molecular systems biology learn from one another?
- Ian A. Mellis and
- Arjun Raj
Genome Res. October 2015 25: 1466-1472; doi:10.1101/gr.190579.115
..., Tikhonov M, Gregor T. 2013. Precise developmental gene expression arises from globally stochastic transcriptional activity. Cell 154: 789–800. Maduro MF. 2006. Endomesoderm specification in Caenorhabditis elegans and other nematodes. Bioessays 28: 1010–1022. Maduro MF, Rothman JH. 2002. Making worm guts...
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