Searching journal content for articles similar to Müller and Nieduszynski 22 (10): 1953.

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  1. 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
    ...gene-specific transcriptional dosage compensation does occur for ∼12% of amplified genes. Furthermore, we find that CNV strains do not show previously described transcriptional signatures of aneuploidy. Our study reveals the extent to which local and global mutational tolerance is modified by CNVs...
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  2. Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
    • Daniela M Riley,
    • Randa Elsayed,
    • Mark D Walsh,
    • Simaran Johal,
    • Ying Lin,
    • Harry Walton,
    • Till Bretschneider,
    • Sascha Ott,
    • and Andrew C Nelson
    Genome Res. March 4, 2026 gr.280838.125; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
    ...1 Functional genomics analysis of developing zebrafish and human endoderm reveals 1 highly conserved cis-regulatory modules acting during vertebrate organogenesis 2 3 Daniela M. Riley1,†, Randa Elsayed1,†, Mark D. Walsh2,†, Simaran Johal2, Ying Lin3,4, Harry 4 Walton1, Till Bretschneider5, Sascha...
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  3. Research: Proteome-wide structural analysis quantifies structural conservation across distant species
    • Shijie Zhang,
    • Teng Zhang,
    • and Yuan Fu
    Genome Res. November 2023 33: 1975-1993; Published in Advance November 22, 2023, doi:10.1101/gr.277771.123
    ...) and that the structures determine the biological functions of proteins. As Rossman and Liljas noted half a century ago, “the preservation of structure may originate in the three-dimensional requirement for the conservation of essential functions” (Rossman and Liljas 1974). Proteins related by evolution can have similar...
  4. Method: Long-read RNA sequencing reveals allele-specific N6-methyladenosine modifications
    • Dayea Park and
    • Can Cenik
    Genome Res. April 2025 35: 999-1011; Published in Advance October 29, 2024, doi:10.1101/gr.279270.124
    ...-methyladenosine (m6A) modifications in native mRNA. We used human and mouse cells with known genetic variants to assign the allelic origin of each mRNA molecule combined with a supervised machine learning model to detect read-level m6A modification ratios. Our analyses reveal the importance of sequences adjacent...
  5. Research: Replication timing networks reveal a link between transcription regulatory circuits and replication timing control
    • Juan Carlos Rivera-Mulia,
    • Sebo Kim,
    • Haitham Gabr,
    • Abhijit Chakraborty,
    • Ferhat Ay,
    • Tamer Kahveci,
    • and David M. Gilbert
    Genome Res. September 2019 29: 1415-1428; Published in Advance August 21, 2019, doi:10.1101/gr.247049.118
    ...of duplication, known as the replication timing (RT) program (Hiratani et al. 2008, 2010; Rivera-Mulia et al. 2015, 2018a). Spatiotemporal control of RT is conserved in all eukaryotes (Rivera-Mulia and Gilbert 2016a; Solovei et al. 2016; Zhao et al. 2017), and alterations in the RT program are associated...
  6. 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
    ...that emerge consistently in multiple experimental contexts and to conservatively estimate the degree of sharing among those conditions (Panousis et al. 2023; Natri et al. 2024; Popp et al. 2024).Across 13 cell types, we tested a total of 9469 genes and found 2438 cis eQTLs in 1778 genes (local false sign rate...
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  7. Resource: Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise
    • Aliza B. Rubenstein,
    • Gregory R. Smith,
    • Zidong Zhang,
    • Xi Chen,
    • Toby L. Chambers,
    • Frederique Ruf-Zamojski,
    • Natalia Mendelev,
    • Wan Sze Cheng,
    • Michel Zamojski,
    • Mary Anne S. Amper,
    • Venugopalan D. Nair,
    • Andrew R. Marderstein,
    • Stephen B. Montgomery,
    • Olga G. Troyanskaya,
    • Elena Zaslavsky,
    • Todd Trappe,
    • Scott Trappe,
    • and Stuart C. Sealfon
    Genome Res. July 2025 35: 1664-1677; Published in Advance May 20, 2025, doi:10.1101/gr.280051.124
    .... 2023). The molecular responses stimulated during each endurance exercise bout lead, over time, to functional and structural adaptations (i.e., improvements in aerobic fitness, exercise performance, and increase in lipid oxidation) as well as improved overall health (Williams and Neufer 1996; Egan...
  8. Research: Meta-analysis of activated neurons reveals dynamic regulation of diverse classes of alternative splicing
    • Keegan S. Krick,
    • Marissa Maroni,
    • Erica Korb,
    • Kristen W. Lynch,
    • and Elizabeth A. Heller
    Genome Res. June 2025 35: 1301-1312; Published in Advance April 24, 2025, doi:10.1101/gr.280082.124
    ..., and it functions by initiating conserved calcium-dependent signaling cascades to activate activity-dependent gene networks (West et al. 2001; Rienecker et al. 2020, 2022). Despite this, the paradigm cannot recapitulate the temporal kinetics of variable stimuli or uncouple localized depolarization, for example...
  9. Research: Loss of histone H3.3 results in DNA replication defects and altered origin dynamics in C. elegans
    • Maude Strobino,
    • Joanna M. Wenda,
    • Laura Padayachy,
    • and Florian A. Steiner
    Genome Res. December 2020 30: 1740-1751; Published in Advance November 10, 2020, doi:10.1101/gr.260794.120
    ...replication. We therefore aimed to investigate the role of H3.3 in DNA replication and origin firing and to adapt tools to study these processes to the C. elegans model system.ResultsGenome-wide replication timing in C. elegans embryosWe first determined whether loss of H3.3 causes global changes...
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  10. Research: Comprehensive functional annotation of ESR1-driven enhancers in breast cancer reveals hierarchical activity independent of genomic and epigenomic contexts
    • Yanis Zekri,
    • Sebastian Gregoricchio,
    • Elif Yapıcı,
    • Chia-Chi Flora Huang,
    • Tunç Morova,
    • Umut Berkay Altıntaş,
    • Gozde Korkmaz,
    • Nathan A. Lack,
    • and Wilbert Zwart
    Genome Res. July 2025 35: 1530-1543; Published in Advance June 10, 2025, doi:10.1101/gr.280320.124
    ...[GEO; https://www.ncbi.nlm.nih.gov/geo/] under accession number GSE54855) (Guertin et al. 2014) revealed similar time kinetics across ERBS categories, but induced sites showed stronger signal (Fig. 1F). Whereas 80% of induced ERBS sequence matched the consensus ESR1 motif, only 25%–30% of constitutive...
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