Searching journal content for articles similar to Ouyang and Boyle 30 (7): 1040.

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  1. Research: The chromatin landscape of the histone-possessing Bacteriovorax bacteria
    • Georgi K. Marinov,
    • Benjamin Doughty,
    • Anshul Kundaje,
    • and William J. Greenleaf
    Genome Res. January 2025 35: 109-123; Published in Advance November 21, 2024, doi:10.1101/gr.279418.124
    ...of chromatin biology: transcription, gene regulation, DNA repair, DNA replication, mitosis and meiosis, and many others) (Jenuwein and Allis 2001), which are almost universally invariant across all eukaryotes.Eukaryotic histones trace their ancestry to Archaea (Woese and Fox 1977), which is the half...
  2. Research: Regeneration alters open chromatin and cis-regulatory landscape of erythroid precursors
    • Yichao Zhou,
    • Venkatasai Rahul Dogiparthi,
    • Hannah L. Harris,
    • Suhita Ray,
    • Avik Choudhuri,
    • Song Yang,
    • Yi Zhou,
    • Leonard I. Zon,
    • M. Jordan Rowley,
    • and Kyle J. Hewitt
    Genome Res. July 2025 35: 1518-1529; Published in Advance June 2, 2025, doi:10.1101/gr.279949.124
    ...driving this accelerated rate and phenotypic diversity of anemia responses are poorly understood. To identify DNA elements controlling increased regenerative activities involved in recovery from acute anemia, we profiled chromatin accessibility in populations of cells enriched for RBC precursors (LIN...
  3. Research: Revisiting chromatin packaging in mouse sperm
    • Qiangzong Yin,
    • Chih-Hsiang Yang,
    • Olga S. Strelkova,
    • Jingyi Wu,
    • Yu Sun,
    • Sneha Gopalan,
    • Liyan Yang,
    • Job Dekker,
    • Thomas G. Fazzio,
    • Xin Zhiguo Li,
    • Johan Gibcus,
    • and Oliver J. Rando
    Genome Res. December 2023 33: 2079-2093; Published in Advance December 21, 2023, doi:10.1101/gr.277845.123
    ..., allowing relatively free access to gene regulatory elements in the face of extensive physical compaction. In eukaryotes, the key principles of chromatin organization have been elucidated over the past half-century: A repeating nucleoprotein complex known as the nucleosome serves to compact ∼150 bp of DNA...
  4. Resource: Comprehensive characterization of tissue-specific chromatin accessibility in L2 Caenorhabditis elegans nematodes
    • Timothy J. Durham,
    • Riza M. Daza,
    • Louis Gevirtzman,
    • Darren A. Cusanovich,
    • Olubusayo Bolonduro,
    • William Stafford Noble,
    • Jay Shendure,
    • and Robert H. Waterston
    Genome Res. October 2021 31: 1952-1969; Published in Advance April 22, 2021, doi:10.1101/gr.271791.120
    ...in other single-cell genomics technologies can now also characterize the regulatory context of the that gives rise to these gene expression levels at a single-cell resolution. To explore the regulatory DNA of individual cell types in C. elegans, we collected single-cell chromatin accessibility data using...
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  5. Review: Artificial intelligence and machine learning in cell-free-DNA-based diagnostics
    • W.H. Adrian Tsui,
    • Spencer C. Ding,
    • Peiyong Jiang,
    • and Y.M. Dennis Lo
    Genome Res. January 2025 35: 1-19; doi:10.1101/gr.278413.123
    ...of origin of cfDNA. In this regard, many studies have demonstrated that methylation analysis of plasma cfDNA allows tissue-of-origin tracing of cfDNA in plasma (Luo et al. 2021; Oberhofer et al. 2022). These studies reveal that cfDNA is derived from a variety of tissues and cell types in which the major...
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  6. Research: Genomic origin, fragmentomics, and transcriptional properties of long cell-free DNA molecules in human plasma
    • Huiwen Che,
    • Peiyong Jiang,
    • L.Y. Lois Choy,
    • Suk Hang Cheng,
    • Wenlei Peng,
    • Rebecca W.Y. Chan,
    • Jing Liu,
    • Qing Zhou,
    • W.K. Jacky Lam,
    • Stephanie C.Y. Yu,
    • So Ling Lau,
    • Tak Y. Leung,
    • John Wong,
    • Vincent Wai-Sun Wong,
    • Grace L.H. Wong,
    • Stephen L. Chan,
    • K.C. Allen Chan,
    • and Y.M. Dennis Lo
    Genome Res. February 2024 34: 189-200; Published in Advance February 26, 2024, doi:10.1101/gr.278556.123
    ...with a dominant peak ∼166 bp, with 10-bp periodicities below 150 bp, suggesting a nucleosomal origin (Lo et al. 2010; Ivanov et al. 2015). Thus, cfDNA is generally believed to be a population of short DNA molecules. Moreover, cfDNA fragments from different tissues may bear information tracing to their tissues...
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  7. Research: Dynamic DNA N6-adenine methylation (6mA) governs the encystment process, showcased in the unicellular eukaryote Pseudocohnilembus persalinus
    • Yongqiang Liu,
    • Junhua Niu,
    • Fei Ye,
    • Therese Solberg,
    • Borong Lu,
    • Chundi Wang,
    • Mariusz Nowacki,
    • and Shan Gao
    Genome Res. February 2024 34: 256-271; Published in Advance March 12, 2024, doi:10.1101/gr.278796.123
    ...that 6mA, a mark of active transcription, is involved in altering the expression of encystment-related genes through changes in 6mA levels and 6mA symmetric-to-asymmetric conversion. Most importantly, we show that reducing 6mA levels by knocking down the DNA 6mA methyltransferase PpAMT1 accelerates cyst...
  8. Method: Evidence of widespread, independent sequence signature for transcription factor cobinding
    • Manqi Zhou,
    • Hongyang Li,
    • Xueqing Wang,
    • and Yuanfang Guan
    Genome Res. February 2021 31: 265-278; Published in Advance December 10, 2020, doi:10.1101/gr.267310.120
    ...the mechanisms underlying gene expression and human diseases is how to analyze and delineate the -wide landscape of multiple characteristic biochemical signatures. An important aspect is the regulation of transcription factors (TFs), which bind to DNAs and drive the expression or suppression of genes. TFs do...
  9. Method: Comprehensive determination of transcription start sites derived from all RNA polymerases using ReCappable-seq
    • Bo Yan,
    • George Tzertzinis,
    • Ira Schildkraut,
    • and Laurence Ettwiller
    Genome Res. January 2022 32: 162-174; Published in Advance November 23, 2021, doi:10.1101/gr.275784.121
    ...the differential positioning of chromatin marks and DNA-interacting proteins relative to both TSS classes. For this, we compared ReCappable-seq TSSs with published ChIP-seq from ENCODE data performed on A549 cells to identify potentially interesting differential chromatin marks associated with Pol II and non...
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  10. Method: Sequence-targeted nucleosome sliding in vivo by a hybrid Chd1 chromatin remodeler
    • Jeffrey N. McKnight,
    • Toshio Tsukiyama,
    • and Gregory D. Bowman
    Genome Res. May 2016 26: 693-704; Published in Advance March 18, 2016, doi:10.1101/gr.199919.115
    ...@fredhutch.org, gdbowman@jhu.edu AbstractATP-dependent chromatin remodelers regulate chromatin dynamics by modifying nucleosome positions and occupancy. DNA-dependent processes such as replication and transcription rely on chromatin to faithfully regulate DNA accessibility, yet how chromatin remodelers achieve well...
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