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Research: Motif conservation, stability, and host gene expression are the main drivers of snoRNA expression across vertebrates
- Étienne Fafard-Couture,
- Pierre-Étienne Jacques,
- and Michelle S. Scott
Genome Res. April 2023 33: 525-540; Published in Advance April 18, 2023, doi:10.1101/gr.277483.122
...of the Genotype-Tissue Expression (GTEx) project (Lonsdale et al. 2013) matching the tissue composition of our TGIRT-seq data set or the same number of unmatched tissues (both highly concordant regarding the host gene expression status), we find that our models display a highly comparable performance to what...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
..., hinging on the precise binding of transcription factors (TFs) and cofactors to gene regulatory elements such as promoters and enhancers. Although it is relatively routine to profile -wide DNA binding landscapes of proteins, identifying the specific proteins that bind to, and regulate the transcription of...
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Research: Comparative transcriptomics of primary cells in vertebrates
- Tanvir Alam,
- Saumya Agrawal,
- Jessica Severin,
- Robert S. Young,
- Robin Andersson,
- Erik Arner,
- Akira Hasegawa,
- Marina Lizio,
- Jordan A. Ramilowski,
- Imad Abugessaisa,
- Yuri Ishizu,
- Shohei Noma,
- Hiroshi Tarui,
- Martin S. Taylor,
- Timo Lassmann,
- Masayoshi Itoh,
- Takeya Kasukawa,
- Hideya Kawaji,
- Luigi Marchionni,
- Guojun Sheng,
- Alistair R.R. Forrest,
- Levon M. Khachigian,
- Yoshihide Hayashizaki,
- Piero Carninci,
- and Michiel J.L. de Hoon
Genome Res. July 2020 30: 951-961; Published in Advance July 27, 2020, doi:10.1101/gr.255679.119
...reflect differences in cell type composition of each tissue in different species. Here, we compare expression profiles in matching primary cells in human, mouse, rat, dog, and chicken using Cap Analysis Gene Expression (CAGE) and short RNA (sRNA) sequencing data from FANTOM5. While we find that expression...
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Research: Fixation of allelic gene expression landscapes and expression bias pattern shape the transcriptome of the clonal Amazon molly
- Yuan Lu,
- David Bierbach,
- Jenny Ormanns,
- Wesley C. Warren,
- Ronald B. Walter,
- and Manfred Schartl
Genome Res. March 2021 31: 372-379; Published in Advance February 5, 2021, doi:10.1101/gr.268870.120
...the parental alleles inherited by P. formosa form tightly regulated genetic networks that lead to a stable transcriptomic landscape within clonal individuals.The Amazon molly, Poecilia formosa, is a small freshwater fish species representing a paradigm for vertebrate asexual reproduction. As with other asexual...
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Research: GC-biased gene conversion drives accelerated evolution of ultraconserved elements in mammalian and avian genomes
- Anguo Liu,
- Nini Wang,
- Guoxiang Xie,
- Yang Li,
- Xixi Yan,
- Xinmei Li,
- Zhenliang Zhu,
- Zhuohui Li,
- Jing Yang,
- Fanxin Meng,
- Mingle Dou,
- Weihuang Chen,
- Nange Ma,
- Yu Jiang,
- Yuanpeng Gao,
- and Yu Wang
Genome Res. October 2023 33: 1673-1689; Published in Advance October 26, 2023, doi:10.1101/gr.277784.123
...-adjacent genes.To further explore the changes of ultraconservation along vertebrate evolution, we examined the conservation of our UCEs in all vertebrate taxa, including representatives of Reptilia, Amphibia, Osteichthyes, Chondrichthyes, and Cyclostomata (list in Supplemental Table S5). Most (>80%) mUCEs and a...
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Research: tRNA-derived small RNAs are embedded in the gene regulatory network instructing Drosophila metamorphosis
- Junling Shi,
- Jiaqi Xu,
- Jun Ma,
- and Feng He
Genome Res. December 2023 33: 2119-2132; Published in Advance November 16, 2023, doi:10.1101/gr.278128.123
..., referred to as tsRNAs, is emerging with a potential to exert a new layer in gene regulation. These RNAs are breakdown products of tRNAs, either through active processing or passive cleavage or both. Since tRNAs are part of the general machinery for translation, their expression levels and activities...
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Research: The identification and functional annotation of RNA structures conserved in vertebrates
- Stefan E. Seemann,
- Aashiq H. Mirza,
- Claus Hansen,
- Claus H. Bang-Berthelsen,
- Christian Garde,
- Mikkel Christensen-Dalsgaard,
- Elfar Torarinsson,
- Zizhen Yao,
- Christopher T. Workman,
- Flemming Pociot,
- Henrik Nielsen,
- Niels Tommerup,
- Walter L. Ruzzo,
- and Jan Gorodkin
Genome Res. August 2017 27: 1371-1383; Published in Advance May 9, 2017, doi:10.1101/gr.208652.116
...for this article.] Computational analyses have suggested many conserved structured RNAs in vertebrate s (Washietl et al. 2005; Torarinsson et al. 2008; Parker et al. 2011; Smith et al. 2013). Recent transcriptome-wide experiments also support a diverse RNA structure landscape (Ding et al. 2014; Rouskin et al. 2014...
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Resource: Remodeling of epigenome and transcriptome landscapes with aging in mice reveals widespread induction of inflammatory responses
- Bérénice A. Benayoun,
- Elizabeth A. Pollina,
- Param Priya Singh,
- Salah Mahmoudi,
- Itamar Harel,
- Kerriann M. Casey,
- Ben W. Dulken,
- Anshul Kundaje,
- and Anne Brunet
Genome Res. April 2019 29: 697-709; Published in Advance March 11, 2019, doi:10.1101/gr.240093.118
...enhancers of genes that are cell- or tissue-specific and highly transcribed in that specific cell or tissue. Importantly, ChIP-seq data sets for the H3K4me3 and H3K27ac histone mark were normalized to paired total Histone H3 ChIP-seq data to account for potential changes in the local nucleosome landscape...
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Research: Long-range promoter–enhancer contacts are conserved during evolution and contribute to gene expression robustness
- Alexandre Laverré,
- Eric Tannier,
- and Anamaria Necsulea
Genome Res. February 2022 32: 280-296; Published in Advance December 20, 2021, doi:10.1101/gr.275901.121
...conservation of cis-regulatory landscapes, indicating that selective pressures act to preserve not only regulatory element sequences but also their chromatin contacts with target genes. The extent of evolutionary conservation is remarkable for long-range promoter–enhancer contacts, illustrating how...
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Research: Snake venom gene expression is coordinated by novel regulatory architecture and the integration of multiple co-opted vertebrate pathways
- Blair W. Perry,
- Siddharth S. Gopalan,
- Giulia I.M. Pasquesi,
- Drew R. Schield,
- Aundrea K. Westfall,
- Cara F. Smith,
- Ivan Koludarov,
- Paul T. Chippindale,
- Mark W. Pellegrino,
- Edward B. Chuong,
- Stephen P. Mackessy,
- and Todd A. Castoe
Genome Res. June 2022 32: 1058-1073; Published in Advance June 1, 2022, doi:10.1101/gr.276251.121
...find evidence that two conserved vertebrate pathways, the extracellular signal-regulated kinase and unfolded protein response pathways, were co-opted to regulate snake venom. In one large venom gene family (snake venom serine proteases), this co-option was likely facilitated by the activity...
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