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Research: Phylogenetic modeling of enhancer shifts in African mole-rats reveals regulatory changes associated with tissue-specific traits
- Elise Parey,
- Diego Fernandez-Aroca,
- Stephanie Frost,
- Ainhoa Uribarren,
- Thomas J. Park,
- Markus Zöttl,
- Ewan St. John Smith,
- Camille Berthelot,
- and Diego Villar
Genome Res. September 2023 33: 1513-1526; Published in Advance August 25, 2023, doi:10.1101/gr.277715.123
...component of mole-rat adaptations. Last, we investigated the contribution of repetitive elements to lineage-specific gene regulation in the mole-rat clade.ResultsComparative epigenomics of liver and heart regulatory activities in mole-ratsTo investigate the contribution of enhancer evolution to tissue-specific...
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Research: Arabidopsis retrotransposon virus-like particles and their regulation by epigenetically activated small RNA
- Seung Cho Lee,
- Evan Ernst,
- Benjamin Berube,
- Filipe Borges,
- Jean-Sebastien Parent,
- Paul Ledon,
- Andrea Schorn,
- and Robert A. Martienssen
Genome Res. April 2020 30: 576-588; Published in Advance April 17, 2020, doi:10.1101/gr.259044.119
...). Mean RPM mapped reads and 95% confidence intervals of three biological replicates are shown for ddm1 (blue) and ddm1rdr6 (orange). Conserved protein domains, PBS and PPT, small RNA profiles, and miRNA target sites are indicated as in Figure 1.easiRNA require miRNA triggers that target these transcripts...
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Method: Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegans
- Wei-Jen Chung,
- Phaedra Agius,
- Jakub O. Westholm,
- Michael Chen,
- Katsutomo Okamura,
- Nicolas Robine,
- Christina S. Leslie,
- and Eric C. Lai
Genome Res. February 2011 21: 286-300; Published in Advance December 22, 2010, doi:10.1101/gr.113050.110
.... Unexpectedly, we uncovered examples of clustered mirtrons in both fly and worm genomes, including a &lt;8-kb region in C. elegans harboring eight distinct mirtrons. Altogether, we demonstrate that discovery of functional mirtrons, unlike canonical miRNAs, is amenable to computational methods independent...
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Method: Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage
- Lukas Chavez,
- Justyna Jozefczuk,
- Christina Grimm,
- Jörn Dietrich,
- Bernd Timmermann,
- Hans Lehrach,
- Ralf Herwig,
- and James Adjaye
Genome Res. October 2010 20: 1441-1450; Published in Advance August 27, 2010, doi:10.1101/gr.110114.110
...K. 2007. High-resolution profiling of histonemethylations in the human . Cell 129: 823–837. Birney E, Andrews TD, Bevan P, Caccamo M, Chen Y, Clarke L, Coates G, Cuff J, Curwen V, Cutts T, et al. 2004. An overview of Ensembl. Genome Res 14: 925–928. Bock C, Halachev K, Buch J, Lengauer T. 2009. Epi...
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LETTER: Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses
- Besma Ben Amor,
- Sonia Wirth,
- Francisco Merchan,
- Philippe Laporte,
- Yves d’Aubenton-Carafa,
- Judith Hirsch,
- Alexis Maizel,
- Allison Mallory,
- Antoine Lucas,
- Jean Marc Deragon,
- Herve Vaucheret,
- Claude Thermes,
- and Martin Crespi
Genome Res. January 2009 19: 57-69; Published in Advance November 7, 2008, doi:10.1101/gr.080275.108
..., indicative of a young miRNA gene. Abiotic stress altered the accumulation of 22 npcRNAs among the 76, a fraction significantly higher than that observed for the RNA binding protein-coding fraction of the transcriptome. Overexpression analyses in Arabidopsis identified two npcRNAs as regulators of root...
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Method: Genome-wide dynamics of RNA synthesis, processing, and degradation without RNA metabolic labeling
- Mattia Furlan,
- Eugenia Galeota,
- Nunzio Del Gaudio,
- Erik Dassi,
- Michele Caselle,
- Stefano de Pretis,
- and Mattia Pelizzola
Genome Res. October 2020 30: 1492-1507; Published in Advance September 25, 2020, doi:10.1101/gr.260984.120
...% of genes were modulated at the level of their processing and/or degradation rates (Fig. 5D).Finally, we reanalyzed the total RNA-seq temporal response to the activation of miRNA-124 (Eichhorn et al. 2014). We expected to see a strong and specific post-transcriptional regulation of the miRNA target...
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Research: Preferential formation of Z-RNA over intercalated motifs in long noncoding RNA
- Uditi Bhatt,
- Anne Cucchiarini,
- Yu Luo,
- Cameron W. Evans,
- Jean-Louis Mergny,
- K. Swaminathan Iyer,
- and Nicole M. Smith
Genome Res. February 2024 34: 217-230; Published in Advance February 14, 2024, doi:10.1101/gr.278236.123
...of lncRNAs is their high tissue specificity relative to other forms of RNA (Cabili et al. 2011; Hon et al. 2017). We compared our G4-iM Grinder and QmRLFS-finder results with the lncSpA integration lncRNA tissue expression data set to examine if the presence of noncanonical structures correlated...
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Research: Genome-wide analysis of plant miRNA action clarifies levels of regulatory dynamics across developmental contexts
- Xiaoli Ma,
- Tom Denyer,
- Marie Javelle,
- Antje Feller,
- and Marja C.P. Timmermans
Genome Res. May 2021 31: 811-822; Published in Advance April 16, 2021, doi:10.1101/gr.270918.120
....ResultsSubfunctionalization within miRNA familiesTo understand parameters that shape the spatiotemporal patterns of miRNA activity during development, we took advantage of a recently described high-resolution maize shoot apex expression atlas (Knauer et al. 2019). The SAM is a specialized niche located at the tip of the growing...
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Method: Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data
- Song Li,
- Louisa M. Liberman,
- Neelanjan Mukherjee,
- Philip N. Benfey,
- and Uwe Ohler
Genome Res. October 2013 23: 1730-1739; Published in Advance July 1, 2013, doi:10.1101/gr.149310.112
...computational method based on a model comparison framework that incorporates the inherent variable efficiency of generating perfectly strand-specific libraries. Applying the method to new ssRNA-seq data from whole-root and cell-type–specific Arabidopsis libraries confirmed most of the known cis -NAT pairs...
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Method: Degradation dynamics of microRNAs revealed by a novel pulse-chase approach
- Matteo J. Marzi,
- Francesco Ghini,
- Benedetta Cerruti,
- Stefano de Pretis,
- Paola Bonetti,
- Chiara Giacomelli,
- Marcin M. Gorski,
- Theresia Kress,
- Mattia Pelizzola,
- Heiko Muller,
- Bruno Amati,
- and Francesco Nicassio
Genome Res. April 2016 26: 554-565; Published in Advance January 28, 2016, doi:10.1101/gr.198788.115
...( Eulalio et al. 2008 ; Bartel 2009 ; Jonas and Izaurralde 2015 ). Most miRNAs display a tightly regulated expression pattern that is often tissue specific or even cell type specific, emphasizing their importance in defining the space, time, and developmental stage of gene expression ( Bushati and Cohen...
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