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Research: Copy number variation alters local and global mutational tolerance
- Grace Avecilla,
- Pieter Spealman,
- Julia Matthews,
- Elodie Caudal,
- Joseph Schacherer,
- and David Gresham
Genome Res. August 2023 33: 1340-1353; Published in Advance August 31, 2023, doi:10.1101/gr.277625.122
...in novel genetic interactions with unlinked genes. We validated a novel genetic interaction between different CNVs and BMH1 that was common to multiple strains. We also analyzed global gene expression and found that transcriptional dosage compensation does not affect most genes amplified by CNVs, although...
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Research: Ancestral aneuploidy and stable chromosomal duplication resulting in differential genome structure and gene expression control in trypanosomatid parasites
- João L. Reis-Cunha,
- Samuel A. Pimenta-Carvalho,
- Laila V. Almeida,
- Anderson Coqueiro-dos-Santos,
- Catarina A. Marques,
- Jennifer A. Black,
- Jeziel Damasceno,
- Richard McCulloch,
- Daniella C. Bartholomeu,
- and Daniel C. Jeffares
Genome Res. March 2024 34: 441-453; Published in Advance April 11, 2024, doi:10.1101/gr.278550.123
...of having unbalanced gene copies and the potential fitness gained from an increased dosage of specific advantageous genes (Pompei and Cosentino Lagomarsino 2023). Most aneuploidy studies have focused on cancer or yeast, in which aneuploidy has been linked with loss of cell cycle control, survival...
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Resource: Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562
- Bo Zhou,
- Steve S. Ho,
- Stephanie U. Greer,
- Xiaowei Zhu,
- John M. Bell,
- Joseph G. Arthur,
- Noah Spies,
- Xianglong Zhang,
- Seunggyu Byeon,
- Reenal Pattni,
- Noa Ben-Efraim,
- Michael S. Haney,
- Rajini R. Haraksingh,
- Giltae Song,
- Hanlee P. Ji,
- Dimitri Perrin,
- Wing H. Wong,
- Alexej Abyzov,
- and Alexander E. Urban
Genome Res. March 2019 29: 472-484; Published in Advance February 8, 2019, doi:10.1101/gr.234948.118
...,D). These observations made by integrating our K562 linked-read data and ENCODE RNA expression data provide novel insights into gene regulatory mechanisms in terms of ectopic expression and dosage compensation, which also raises important questions regarding the history of the K562 cell line in terms of mutations...
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Research: DNA replication and transcription programs respond to the same chromatin cues
- Yoav Lubelsky,
- Joseph A. Prinz,
- Leyna DeNapoli,
- Yulong Li,
- Jason A. Belsky,
- and David M. MacAlpine
Genome Res. July 2014 24: 1102-1114; Published in Advance July 1, 2014, doi:10.1101/gr.160010.113
...; Schwaiger et al. 2009) are dependent on the dosage compensation complex (DCC) and that a single histone modification is sufficient to alter the replication timing of an entire chromosome. Results Replication timing profiles of three Drosophila cell lines The modENCODE Consortium has extensively...
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Method: Chromosome engineering to correct a complex rearrangement on Chromosome 8 reveals the effects of 8p syndrome on gene expression and neural differentiation
- Sophia N. Lee,
- Erin C. Banda,
- Lu Qiao,
- Sarah L. Thompson,
- Karan Singh,
- Ryan A. Hagenson,
- Teresa Davoli,
- Stefan F. Pinter,
- and Jason M. Sheltzer
Genome Res. March 2026 36: 547-560; Published in Advance January 12, 2026, doi:10.1101/gr.280425.125
..., by inhibiting the function of a dosage-sensitive protein encoded in a triplicated region, have not proven to be successful (Jiang et al. 2013). The failure of targeted therapies to produce clinical benefit raises the possibility that other interventions may best be able to correct the underlying genetic...
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Method: RNA-seq as a tool for evaluating human embryo competence
- Abigail F. Groff,
- Nina Resetkova,
- Francesca DiDomenico,
- Denny Sakkas,
- Alan Penzias,
- John L. Rinn,
- and Kevin Eggan
Genome Res. October 2019 29: 1705-1718; Published in Advance September 23, 2019, doi:10.1101/gr.252981.119
..., the X-linked gene that is responsible for dosage compensation and that is commonly used to identify females in genotyping assays (Disteche and Berletch 2015), is expressed in both XX and XY embryos (Supplemental Fig. S2A; Daniels et al. 1997; Nichols et al. 2009; Briggs et al. 2015; Petropoulos et al...
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