Searching journal content for articles similar to Salas et al. 28 (9): 1285.

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  1. Method: High-fidelity bidirectional translation between single-cell transcriptomes and DNA methylomes with scBOND
    • Kehan Lang,
    • Chenyang Jia,
    • Siyu Li,
    • Yi Guo,
    • Dingjun Hu,
    • and Shengquan Chen
    Genome Res. March 26, 2026 ; Published in Advance March 26, 2026, doi:10.1101/gr.281350.125
    .....org G H C D Figure 4. Transcriptomic–epigenetic dynamics in the oligodendrocyte lineage. (A) UMAP visualization of RNA and predicted DNAm profiles on the HumanBrainB data set. (B–D) Scatter plots showing the relationship between gene expression and promoter-proximal DNA methylation levels across cell...
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  2. Method: RETrace: simultaneous retrospective lineage tracing and methylation profiling of single cells
    • Christopher Jen-Yue Wei and
    • Kun Zhang
    Genome Res. April 2020 30: 602-610; Published in Advance March 3, 2020, doi:10.1101/gr.255851.119
    ...tracing and cell type determination for single cells through the capture of both microsatellite and DNA methylation status from the same cells. We demonstrated that this approach successfully achieved higher resolution lineage trees than other published methods and allows for reliable identification...
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  3. 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
    ...to investigate cellular dynamics, fate determination, and the underlying molecular mechanisms. This review thoroughly examines the latest prospective lineage DNA barcode tracing technologies. It further highlights pivotal studies that leverage single-cell lentiviral integration barcoding technology to unravel...
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  4. Method: Single-cell methylation sequencing data reveal succinct metastatic migration histories and tumor progression models
    • Yuelin Liu,
    • Xuan Cindy Li,
    • Farid Rashidi Mehrabadi,
    • Alejandro A. Schäffer,
    • Drew Pratt,
    • David R. Crawford,
    • Salem Malikić,
    • Erin K. Molloy,
    • Vishaka Gopalan,
    • Stephen M. Mount,
    • Eytan Ruppin,
    • Kenneth D. Aldape,
    • and S. Cenk Sahinalp
    Genome Res. July 2023 33: 1089-1100; Published in Advance June 14, 2023, doi:10.1101/gr.277608.122
    ...in the data sets, which calls for data imputation or aggregation; on the other hand, tumor lineage inference using CNAs called from single-cell sequencing data often involves ambiguities in the determination of chromosomal breakpoints that may mislead the conclusion. DNA methylation, the addition of a methyl...
  5. Research: Evolutionary rewiring of the wheat transcriptional regulatory network by lineage-specific transposable elements
    • Yuyun Zhang,
    • Zijuan Li,
    • Yu'e Zhang,
    • Kande Lin,
    • Yuan Peng,
    • Luhuan Ye,
    • Yili Zhuang,
    • Meiyue Wang,
    • Yilin Xie,
    • Jingyu Guo,
    • Wan Teng,
    • Yiping Tong,
    • Wenli Zhang,
    • Yongbiao Xue,
    • Zhaobo Lang,
    • and Yijing Zhang
    Genome Res. December 2021 31: 2276-2289; Published in Advance September 9, 2021, doi:10.1101/gr.275658.121
    .... 2017; Zhao et al. 2018). The read density distributions for TFBSs in TEs and non-TE regions were very similar (Fig. 4B). Transposable elements are generally repressed by DNA methylation, with low chromatin accessibility. In this study, we observed that 40,807 collapsed TFBSs (with overlapping TFBSs...
  6. Research: Intrinsic DNA binding properties demonstrated for lineage-specifying basic helix-loop-helix transcription factors
    • Bradford H. Casey,
    • Rahul K. Kollipara,
    • Karine Pozo,
    • and Jane E. Johnson
    Genome Res. April 2018 28: 484-496; Published in Advance March 2, 2018, doi:10.1101/gr.224360.117
    ...compared their DNA binding properties when ectopically expressed in embryonic stem cells (Fig. 1C). Although the genomic binding pattern of this subset of bHLH factors has previously been compared in their respective lineages, their DNA binding behavior in a single, common cell type mitigates the influence...
  7. Research: Epigenetic analyses of planarian stem cells demonstrate conservation of bivalent histone modifications in animal stem cells
    • Anish Dattani,
    • Damian Kao,
    • Yuliana Mihaylova,
    • Prasad Abnave,
    • Samantha Hughes,
    • Alvina Lai,
    • Sounak Sahu,
    • and A. Aziz Aboobaker
    Genome Res. October 2018 28: 1543-1554; Published in Advance August 24, 2018, doi:10.1101/gr.239848.118
    ...that H3K4me3 and H3K36me3 levels correlate with gene expression in planarian NBsResearch into the epigenetic mechanisms governing stem cell pluripotency in planarian NBs is still in its infancy (Dattani et al. 2018). Previous work uncovered a lack of endogenous DNA methylation in the Schmidtea...
  8. Method: Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage
    • Lukas Chavez,
    • Justyna Jozefczuk,
    • Christina Grimm,
    • Jörn Dietrich,
    • Bernd Timmermann,
    • Hans Lehrach,
    • Ralf Herwig,
    • and James Adjaye
    Genome Res. October 2010 20: 1441-1450; Published in Advance August 27, 2010, doi:10.1101/gr.110114.110
    ...Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage Lukas Chavez 1 , 5 , Justyna Jozefczuk 1 , Christina Grimm 1 , Jörn Dietrich 1 , Bernd Timmermann 2...
  9. Research: Interplay of TRIM28 and DNA methylation in controlling human endogenous retroelements
    • Priscilla Turelli,
    • Nathaly Castro-Diaz,
    • Flavia Marzetta,
    • Adamandia Kapopoulou,
    • Charlène Raclot,
    • Julien Duc,
    • Vannary Tieng,
    • Simon Quenneville,
    • and Didier Trono
    Genome Res. August 2014 24: 1260-1270; Published in Advance May 30, 2014, doi:10.1101/gr.172833.114
    ...) upon TRIM28 KD. Turell i et al. 1264 Genome Research www..org roborates our observation that most TRIM28-bound SVAs are methylated in ES cells and suggests a role for tethering factors, the DNA binding of which is methylation-dependent, as for ZFP57 at ICRs. Establishment of naive human stem cells...
  10. Research: ZNF91 deletion in human embryonic stem cells leads to ectopic activation of SVA retrotransposons and up-regulation of KRAB zinc finger gene clusters
    • Nina L. Haring,
    • Elisabeth J. van Bree,
    • Whitney S. Jordaan,
    • Judith R.E. Roels,
    • Gonzalo Congrains Sotomayor,
    • Tiziana M. Hey,
    • Fred T.G. White,
    • Marc D. Galland,
    • Marten P. Smidt,
    • and Frank M.J. Jacobs
    Genome Res. April 2021 31: 551-563; Published in Advance March 15, 2021, doi:10.1101/gr.265348.120
    .... 2019; Farmiloe et al. 2020), and maintenance of DNA methylation at imprinting control regions (Li et al. 2008; Takahashi et al. 2015, 2019; Riso et al. 2016).In this study we focus on a primate-specific TE class, named after its composite domains: SINE-VNTR-Alu (SVA). There are approximately 2800 fixed...
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