Searching journal content for articles similar to Yu et al. 23 (2): 352.

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  1. 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 ; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
    ...of transcription factor binding site co-occurrence. However, rigid arrangement of binding sites is not a common characteristic of the identified CRMs, suggesting more complex or individual grammatical rules. Overall, our analyses provide key insights into critical gene regulatory control during vertebrate endoderm...
  2. 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
    ...gene activity within cells and tissues. This is crucial for understanding the dynamics of gene regulation during cell growth, differentiation, and responses to stimuli (Zou and Bai 2019). When staining protocols do not require cells to be fixed, fluorescence microscopy imaging is not destructive...
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  3. Research: Genome-wide chromatin interaction profiling reveals a vital role of super-enhancers and rearrangements in host enhancer contacts during BmNPV infection
    • Shudi Zhao,
    • Yuedong Li,
    • Guanping Chen,
    • Xingyang Wang,
    • Nan Chen,
    • and Xiaofeng Wu
    Genome Res. November 2023 33: 1958-1974; Published in Advance October 23, 2023, doi:10.1101/gr.277931.123
    ...for investigation of the enhancer functions and to elaborate the dynamic changes in the host enhancer regulatory network during baculovirus infection.ResultsEpigenomic state and DNA interaction participate in regulating gene expressionIn eukaryotes, open chromatin regions and histone modifications are not uniformly...
  4. 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
    ...Fig. S6). As a general rule, we can thus confirm that contacts do not generally form between immediately neighboring promoters and enhancers (Smemo et al. 2014).To further test the presence of genuine regulatory interactions in the PCHi-C data, we evaluated the correlations between gene expression...
  5. Research: Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal
    • Juan L. Mateo,
    • Debbie L.C. van den Berg,
    • Maximilian Haeussler,
    • Daniela Drechsel,
    • Zachary B. Gaber,
    • Diogo S. Castro,
    • Paul Robson,
    • Q. Richard Lu,
    • Gregory E. Crawford,
    • Paul Flicek,
    • Laurence Ettwiller,
    • Joachim Wittbrodt,
    • François Guillemot,
    • and Ben Martynoga
    Genome Res. January 2015 25: 41-56; Published in Advance October 7, 2014, doi:10.1101/gr.173435.114
    ...analyzed (Fig. 1; Supplemental Table S1).View larger version: In this window In a new window Figure 1. Clustering analysis reveals multiple classes of epigenetically distinct gene regulatory regions in NS cells. (A) Schematic depicting the classification and regulatory annotation of DHS regions employed...
  6. Review: The superpowers of imprinting control regions
    • Bertille Montibus,
    • Franck Court,
    • and Philippe Arnaud
    Genome Res. January 2026 36: 1-19; Published in Advance December 10, 2025, doi:10.1101/gr.281215.125
    ...conserved genomic clusters, which contain two or more maternally and paternally expressed genes in large regions of up to several megabases in size (Table 1; Fig. 1).View larger version: In this window In a new window Figure 1. Schematic representation of the genomic organization of the 10 largest imprinted...
  7. Review: Advancements in prospective single-cell lineage barcoding and their applications in research
    • Xiaoli Zhang,
    • Yirui Huang,
    • Yajing Yang,
    • Qi-En Wang,
    • and Lang Li
    Genome Res. December 2024 34: 2147-2162; Published in Advance November 21, 2024, doi:10.1101/gr.278944.124
    ...and plasticity over extended periods of cell culture. This study revealed insightful findings, indicating that cell transcriptome states are not only inherited but also dynamically reshaped based on constrained rules encoded within the cell lineage. These were observed under various conditions, including basal...
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  8. Research: Distinctive regulatory architectures of germline-active and somatic genes in C. elegans
    • Jacques Serizay,
    • Yan Dong,
    • Jürgen Jänes,
    • Michael Chesney,
    • Chiara Cerrato,
    • and Julie Ahringer
    Genome Res. December 2020 30: 1752-1765; Published in Advance October 22, 2020, doi:10.1101/gr.265934.120
    ...tissues. We observe the 10-bp periodic WW signal at ubiquitous promoters in other animals, suggesting it is an ancient conserved signal. Our results show fundamental differences in regulatory architectures of germline and somatic tissue–specific genes, uncover regulatory rules for generating diverse gene...
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  9. Method: Chromatin module inference on cellular trajectories identifies key transition points and poised epigenetic states in diverse developmental processes
    • Sushmita Roy and
    • Rupa Sridharan
    Genome Res. July 2017 27: 1250-1262; Published in Advance April 19, 2017, doi:10.1101/gr.215004.116
    ...thatgainmultivalency in iPSCs froma repressed state inMEF. Gene names are provided on the left. The heatmaps show the enrichment of histonemarks compared to input in each cell type. (D) Chromatin module dynamics of genes identified using rules encoding patterns. The right panels providemodulemembership of genes in (I...
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  10. Resource: Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development
    • Michal Pawlak,
    • Katarzyna Z. Kedzierska,
    • Maciej Migdal,
    • Karim Abu Nahia,
    • Jordan A. Ramilowski,
    • Lukasz Bugajski,
    • Kosuke Hashimoto,
    • Aleksandra Marconi,
    • Katarzyna Piwocka,
    • Piero Carninci,
    • and Cecilia L. Winata
    Genome Res. March 2019 29: 506-519; Published in Advance February 13, 2019, doi:10.1101/gr.244491.118
    ...-seq) (Buenrostro et al. 2013) to capture the dynamics of regulatory landscape throughout the progression of heart morphogenesis in vivo therefore unravelling the gene regulatory network driving key processes of heart development.ResultsCM transcriptome reveals strong dynamics at early stages of heart morphogenesis...
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