Searching journal content for articles similar to Tollervey et al. 21 (10): 1572.

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Research: Oxygen-induced stress reveals context-specific gene regulatory effects in human brain organoids
- Benjamin D. Umans and
- Yoav Gilad
Genome Res. August 2025 35: 1689-1700; Published in Advance June 2, 2025, doi:10.1101/gr.280219.124
...between genetic variants and environmental stressors is key to understanding the mechanisms underlying neurological diseases. In this study, we use human brain organoids to explore how varying oxygen levels expose context-dependent gene regulatory effects. By subjecting a genetically diverse panel of 21...
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Research: RNA components of the spliceosome regulate tissue- and cancer-specific alternative splicing
- Heidi Dvinge,
- Jamie Guenthoer,
- Peggy L. Porter,
- and Robert K. Bradley
Genome Res. October 2019 29: 1591-1604; Published in Advance August 21, 2019, doi:10.1101/gr.246678.118
...@wisc.edu, rbradley@fredhutch.orgAbstractAlternative splicing of pre-mRNAs plays a pivotal role during the establishment and maintenance of human cell types. Characterizing the trans-acting regulatory proteins that control alternative splicing has therefore been the focus of much research. Recent work has established...
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Resource: Genome-wide identification of tandem repeats associated with splicing variation across 49 tissues in humans
- Kohei Hamanaka,
- Daisuke Yamauchi,
- Eriko Koshimizu,
- Kei Watase,
- Kaoru Mogushi,
- Kinya Ishikawa,
- Hidehiro Mizusawa,
- Naomi Tsuchida,
- Yuri Uchiyama,
- Atsushi Fujita,
- Kazuharu Misawa,
- Takeshi Mizuguchi,
- Satoko Miyatake,
- and Naomichi Matsumoto
Genome Res. March 2023 33: 435-447; Published in Advance March 27, 2023, doi:10.1101/gr.277335.122
...an intron relative to all split reads sharing the same junction as the intron (Mertes et al. 2021), and defined the effect size of a TR–splicing association as the difference in ψ per repeat unit. When clustering pairwise correlation of effect sizes across tissues, tissue similarities were captured: brain...
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Research: Transposon expression in the Drosophila brain is driven by neighboring genes and diversifies the neural transcriptome
- Christoph D. Treiber and
- Scott Waddell
Genome Res. November 2020 30: 1559-1569; Published in Advance September 24, 2020, doi:10.1101/gr.259200.119
...-containing transcripts are chimeric, which suggests that somatic expression of these transposons is largely driven by cellular genes. We propose that chimeric mRNAs produced by alternative splicing into polymorphic transposons, rather than transposon mobilization, may contribute to functional differences between...
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Resource: Genetic compendium of 1511 human brains available through the UK Medical Research Council Brain Banks Network Resource
- Michael J. Keogh,
- Wei Wei,
- Ian Wilson,
- Jon Coxhead,
- Sarah Ryan,
- Sara Rollinson,
- Helen Griffin,
- Marzena Kurzawa-Akanbi,
- Mauro Santibanez-Koref,
- Kevin Talbot,
- Martin R. Turner,
- Chris-Anne McKenzie,
- Claire Troakes,
- Johannes Attems,
- Colin Smith,
- Safa Al Sarraj,
- Chris M. Morris,
- Olaf Ansorge,
- Stuart Pickering-Brown,
- James W. Ironside,
- and Patrick F. Chinnery
Genome Res. January 2017 27: 165-173; Published in Advance December 21, 2016, doi:10.1101/gr.210609.116
...between tissue and cell type (Dimas et al. 2009) and also because several neurodegenerative diseases are modulated by age-related comorbidity. Both factors are extremely challenging to model in vitro and in animals. The analysis of postmortem human brain tissue circumvents some of these difficulties...
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Research: Deep sequencing the circadian and diurnal transcriptome of Drosophila brain
- Michael E. Hughes,
- Gregory R. Grant,
- Christina Paquin,
- Jack Qian,
- and Michael N. Nitabach
Genome Res. July 2012 22: 1266-1281; Published in Advance April 3, 2012, doi:10.1101/gr.128876.111
...that affect key circadian genes. These studies demonstrate extensive circadian control of ncRNA expression, reveal the extent of clock control of alternative splicing and RNA editing, and provide a novel, -wide map of splicing in Drosophila brain. [Supplemental material is available for this article...
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Review: Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics
- Natan Belchikov,
- Justine Hsu,
- Xiang Jennie Li,
- Julien Jarroux,
- Wen Hu,
- Anoushka Joglekar,
- and Hagen U. Tilgner
Genome Res. November 2024 34: 1735-1746; doi:10.1101/gr.279640.124
...of Biomedical Informatics, Columbia University, New York, New York 10032, USA Corresponding author: hagen.u.tilgner@gmail.comAbstractRNA isoform diversity, produced via alternative splicing, and alternative usage of transcription start and poly(A) sites, results in varied transcripts being derived from the same...
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Research: Mosaic loss of Chromosome Y in aged human microglia
- Michael C. Vermeulen,
- Richard Pearse,
- Tracy Young-Pearse,
- and Sara Mostafavi
Genome Res. October 2022 32: 1795-1807; Published in Advance August 30, 2022, doi:10.1101/gr.276409.121
...age-related diseases, including Alzheimer's disease (AD). The molecular basis of LOY in brain cells has not been systematically investigated. Here, we present a large-scale analysis of single-cell and single-nuclei RNA brain data sets, yielding 851,674 cells, to investigate the cell type...
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Research: Widespread intron retention impairs protein homeostasis in C9orf72 ALS brains
- Qingqing Wang,
- Erin G. Conlon,
- James L. Manley,
- and Donald C. Rio
Genome Res. December 2020 30: 1705-1715; Published in Advance October 14, 2020, doi:10.1101/gr.265298.120
.... The repetitive RNA derived from the C9 repeat is known to sequester hnRNPH, a splicing regulator, into insoluble aggregates, resulting in aberrant alternative splicing. Furthermore, hnRNPH insolubility and altered splicing of a robust set of targets have been observed to correlate in C9 and sporadic ALS...
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Letter: Repertoire and evolution of miRNA genes in four divergent nematode species
- Elzo de Wit,
- Sam E.V. Linsen,
- Edwin Cuppen,
- and Eugene Berezikov
Genome Res. November 2009 19: 2064-2074; Published in Advance September 15, 2009, doi:10.1101/gr.093781.109
...expansion through gene duplication. In addition, we identified a novel mode of miRNA evolution, termed “hairpin shifting,” in which an alternative hairpin is formed with up- or downstream sequences, leading to shifting of the hairpin and creation of novel miRNA* species. Finally, we identified 21U...

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