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Showing 1–25 of 25 results
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  • Single-cell DNA methylome profiling allows the study of epigenomic heterogeneity in tissues but has been impeded by library quality. Here the authors demonstrate snmC-seq2 which improves mapping, throughput and library complexity.

    • Chongyuan Luo
    • Angeline Rivkin
    • Joseph R. Ecker
    ResearchOpen Access
    Nature Communications
    Volume: 9, P: 1-6

  • Post-drought rehydration triggers a preventive immune response in plants, revealing targets to enhance crop resilience by linking drought stress recovery with improved pathogen resistance.

    • Natanella Illouz-Eliaz
    • Jingting Yu
    • Joseph R. Ecker
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-15

  • A single-cell multiomics analysis of over 200,000 cells of the primary motor cortex of human, macaque, marmoset and mouse shows that divergence of transcription factor expression corresponds to species-specific epigenome landscapes, and conserved and divergent gene regulatory features are reflected in the evolution of the three-dimensional genome.

    • Nathan R. Zemke
    • Ethan J. Armand
    • Bing Ren
    ResearchOpen Access
    Nature
    Volume: 624, P: 390-402

  • The pituitary gland plays important roles in the regulation of key physiological functions. Here the authors provide a multiomics atlas including transcriptome, chromatin accessibility, and methylation status of over 70,000 single nuclei (sn) from mouse pituitaries.

    • Frederique Ruf-Zamojski
    • Zidong Zhang
    • Stuart C. Sealfon
    ResearchOpen Access
    Nature Communications
    Volume: 12, P: 1-20

  • Methylome-based clustering and cross-modality integration with companion datasets from the BRAIN Initiative Cell Census Network enabled the construction of a 3D multi-omic genome atlas of the adult mouse brain featuring thousands of cell-type-specific profiles.

    • Hanqing Liu
    • Qiurui Zeng
    • Joseph R. Ecker
    ResearchOpen Access
    Nature
    Volume: 624, P: 366-377

  • This study uses epi-retro-seq to link single-cell epigenomes and cell types to long-distance projections for neurons dissected from different regions projecting to different targets across the whole mouse brain.

    • Jingtian Zhou
    • Zhuzhu Zhang
    • Edward M. Callaway
    ResearchOpen Access
    Nature
    Volume: 624, P: 355-365

  • An examination of motor cortex in humans, marmosets and mice reveals a generally conserved cellular makeup that is likely to extend to many mammalian species, but also differences in gene expression, DNA methylation and chromatin state that lead to species-dependent specializations.

    • Trygve E. Bakken
    • Nikolas L. Jorstad
    • Ed S. Lein
    ResearchOpen Access
    Nature
    Volume: 598, P: 111-119

  • A comprehensive survey of the epigenome from 45 regions of the mouse cortex, hippocampus, striatum, pallidum and olfactory areas using single-nucleus DNA methylation sequencing enables identification of 161 cell clusters with distinct locations and projection targets and provides insights into the regulatory landscape underlying neuronal diversity and spatial regulation.

    • Hanqing Liu
    • Jingtian Zhou
    • Joseph R. Ecker
    ResearchOpen Access
    Nature
    Volume: 598, P: 120-128

  • Quantitative analysis of the methylation of mouse cortical neurons that project to different cortical and subcortical target regions provides insight into genetic mechanisms that contribute to differences in cell function.

    • Zhuzhu Zhang
    • Jingtian Zhou
    • Edward M. Callaway
    ResearchOpen Access
    Nature
    Volume: 598, P: 167-173

  • Analysis of 168 methylomes from 12 mouse tissues at 9 developmental stages sheds light on the epigenetic and regulatory landscape during mammalian fetal development.

    • Yupeng He
    • Manoj Hariharan
    • Joseph R. Ecker
    ResearchOpen Access
    Nature
    Volume: 583, P: 752-759

  • Genome-wide analysis of matched human IVF embryonic stem cells (IVF ES cells), induced pluripotent stem cells (iPS cells) and nuclear transfer ES cells (NT ES cells) derived by somatic cell nuclear transfer (SCNT) reveals that human somatic cells can be faithfully reprogrammed to pluripotency by SCNT; NT ES cells and iPS cells derived from the same somatic cells contain comparable numbers of de novo copy number variations, but whereas DNA methylation and transcriptome profiles of NT ES cells and IVF ES cells are similar, iPS cells have residual patterns typical of parental somatic cells.

    • Hong Ma
    • Robert Morey
    • Shoukhrat Mitalipov
    Research
    Nature
    Volume: 511, P: 177-183

  • Reprogramming of somatic cells to induce pluripotent cellular properties that closely resemble those of embryonic stem (ES) cells has important therapeutic potential. The first whole genome single-base resolution profiling of the DNA methylomes of several human ES cell, induced pluripotent stem cell (iPSC) and somatic progenitor lines shows that iPSCs are fundamentally distinct from ES cells, insofar as they manifest common, quantifiable epigenomic differences. These 'hotspots of aberrant reprogramming' might be potentially useful as diagnostic markers for incomplete iPSC reprogramming, for the characterization of the efficacy of different reprogramming techniques, and for screening the potential propagation of altered methylation states into derivative differentiated cells.

    • Ryan Lister
    • Mattia Pelizzola
    • Joseph R. Ecker
    Research
    Nature
    Volume: 471, P: 68-73

  • CrY2H-seq, a Cre recombinase reporter-mediated yeast two-hybrid method coupled with next-generation sequencing, enables ultra-high-throughput screening of transcription factor interactions in Arabidopsis thaliana.

    • Shelly A Wanamaker
    • Renee M Garza
    • Joseph R Ecker
    Research
    Nature Methods
    Volume: 14, P: 819-825

  • The authors summarize the data produced by phase III of the Encyclopedia of DNA Elements (ENCODE) project, a resource for better understanding of the human and mouse genomes.

    • Federico Abascal
    • Reyes Acosta
    • Zhiping Weng
    ResearchOpen Access
    Nature
    Volume: 583, P: 699-710

  • The BRAIN Initiative Cell Census Network has constructed a multimodal cell census and atlas of the mammalian primary motor cortex in a landmark effort towards understanding brain cell-type diversity, neural circuit organization and brain function.

    • Edward M. Callaway
    • Hong-Wei Dong
    • Susan Sunkin
    ResearchOpen Access
    Nature
    Volume: 598, P: 86-102

  • The authors summarize the history of the ENCODE Project, the achievements of ENCODE 1 and ENCODE 2, and how the new data generated and analysed in ENCODE 3 complement the previous phases.

    • Federico Abascal
    • Reyes Acosta
    • Richard M. Myers
    Reviews
    Nature
    Volume: 583, P: 693-698