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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. April 2026 36: 769-784; Published in Advance March 26, 2026, doi:10.1101/gr.281350.125
...expression and epigenetic landscapes at single-cell resolution. However, the application of these technologies remains limited owing to technical challenges and high costs. Computational approaches for cross-modality translation provide a promising solution to these limitations by enabling the inference...
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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
...of cell fates from single-cell snapshots. However, the study suggested that scRNA-seq fails to capture the heritable properties that guide fate determination, where additional studies such as chromatin accessibility or proteomics information may help to identify the hidden information (VanHorn and Morris...
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Method: Atlas-scale single-cell chromatin accessibility using nanowell-based combinatorial indexing
- Brendan L. O'Connell,
- Ruth V. Nichols,
- Dmitry Pokholok,
- Jerushah Thomas,
- Sonia N. Acharya,
- Andrew Nishida,
- Casey A. Thornton,
- Marissa Co,
- Andrew J. Fields,
- Frank J. Steemers,
- and Andrew C. Adey
Genome Res. February 2023 33: 208-217; Published in Advance February 15, 2023, doi:10.1101/gr.276655.122
...C, Steemers FJ, Mandel G, Adey AC. 2019. The accessible chromatin landscape of the murine hippocampus at single-cell resolution. Genome Res 29: 857–869. doi:10.1101/gr.243725.118 ↵Thornton CA, Mulqueen RM, Torkenczy KA, Nishida A, Lowenstein EG, Fields AJ, Steemers FJ, Zhang W, McConnell HL, Woltjer...
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Perspective: Tagmentation-based single-cell genomics
- Andrew C. Adey
Genome Res. October 2021 31: 1693-1705; doi:10.1101/gr.275223.121
...into a feature for single-cell ATAC assays) (Fiskin et al. 2020; Lareau et al. 2020), the original description of the assay was able to produce useful chromatin accessibility profiles from as few as 500 cells (Buenrostro et al. 2013), and the proportion of mitochondrial DNA was reduced by extensive protocol...
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Method: High-resolution spatial transcriptomics in fixed tissue using a cost-effective PCL-seq workflow
- Xue Dong,
- Mengzhu Hu,
- Xiaonan Cui,
- Wenjian Zhou,
- Jingtao Cai,
- Guangyao Mao,
- and Weiyang Shi
Genome Res. September 2025 35: 2052-2063; Published in Advance August 5, 2025, doi:10.1101/gr.279906.124
...in both frozen and FFPE tissues with subcellular resolution.With the advancement of single-cell sequencing technologies, it has become evident that spatial regulation of gene expression is critical for the proper functioning of biological systems (Delile et al. 2019; Hildebrandt et al. 2021; Chen et al...
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Method: Identification of bona fide B2 SINE retrotransposon transcription through single-nucleus RNA-seq of the mouse hippocampus
- Sara B. Linker,
- Lynne Randolph-Moore,
- Kalyani Kottilil,
- Fan Qiu,
- Baptiste N. Jaeger,
- Jerika Barron,
- and Fred H. Gage
Genome Res. November 2020 30: 1643-1654; Published in Advance October 29, 2020, doi:10.1101/gr.262196.120
...BonaFide-TEseq to examine SINE expression in the mouse hippocampus as a function of a brief exposure to a NE at single-neuron resolution. Together, these results show the utility of single-cell data for examining bona fide retrotransposon expression.ResultsDetection of bona fide SINE transcripts...
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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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Research: Dynamics of chromatin accessibility and long-range interactions in response to glucocorticoid pulsing
- Diana A. Stavreva,
- Antoine Coulon,
- Songjoon Baek,
- Myong-Hee Sung,
- Sam John,
- Lenka Stixova,
- Martina Tesikova,
- Ofir Hakim,
- Tina Miranda,
- Mary Hawkins,
- John A. Stamatoyannopoulos,
- Carson C. Chow,
- and Gordon L. Hager
Genome Res. June 2015 25: 845-857; Published in Advance February 12, 2015, doi:10.1101/gr.184168.114
.... Changes in chromatin accessibility at the MMTV array locus and at endogenous sites in response to pulsed and constant hormone stimulation. (A) High-resolutionmapping of the GR binding profile at theMMTV locus demonstrates an excellent concordance between the results obtained by single cell imaging (Fig. 1...
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Method: Simple and efficient profiling of transcription initiation and transcript levels with STRIPE-seq
- Robert A. Policastro,
- R. Taylor Raborn,
- Volker P. Brendel,
- and Gabriel E. Zentner
Genome Res. June 2020 30: 910-923; Published in Advance July 6, 2020, doi:10.1101/gr.261545.120
...an adapter sequence to the 5′ end of the cDNA (Zhu et al. 2001). TSS mapping methods incorporating TSRT include 5′ serial analysis of gene expression (5′ SAGE) (Zhang and Dietrich 2005), nano-cap analysis of gene expression (nanoCAGE 2010/2017) (Plessy et al. 2010; Poulain et al. 2017), single-cell tagged...
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Research: Somatic retrotransposition in the developing rhesus macaque brain
- Victor Billon,
- Francisco J. Sanchez-Luque,
- Jay Rasmussen,
- Gabriela O. Bodea,
- Daniel J. Gerhardt,
- Patricia Gerdes,
- Seth W. Cheetham,
- Stephanie N. Schauer,
- Prabha Ajjikuttira,
- Thomas J. Meyer,
- Cora E. Layman,
- Kimberly A. Nevonen,
- Natasha Jansz,
- Jose L. Garcia-Perez,
- Sandra R. Richardson,
- Adam D. Ewing,
- Lucia Carbone,
- and Geoffrey J. Faulkner
Genome Res. July 2022 32: 1298-1314; Published in Advance June 21, 2022, doi:10.1101/gr.276451.121
...primate germline. As revealed by case studies, the presently active human L1 subfamily can also mobilize during embryonic and brain development in vivo. It is unknown whether nonhuman primate L1s can similarly generate somatic insertions in the brain. Here we applied approximately 40× single-cell whole...
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