Easy-Multiome, a streamlined single-cell multiomic workflow that integrates a single in situ reverse transcription step into the standard droplet-based scATAC-seq protocol, is presented, demonstrating that robust and efficient joint profiling of plant gene expression and chromatin accessibility while requiring only minimal modifications to existing droplet-based scATAC-seq workflows.
Abstract
Gene expression and chromatin accessibility provide complementary insights into the regulatory mechanisms that define cell states. Although methods for jointly profiling these modalities exist, plant applications remain limited because of complex workflows, inconsistent performance, and prohibitive costs. Here, we present easy-Multiome, a streamlined single-cell multiomic workflow that integrates a single in situ reverse transcription step into the standard droplet-based scATAC-seq protocol. Using easy-Multiome, we profiled more than 20,000 nuclei from maize seedlings generating paired gene expression and chromatin accessibility data, with approximately 90% of nuclei containing both high-quality RNA and chromatin accessibility profiles. The resulting transcriptome data resolved 16 clusters corresponding to nine major maize seedling cell types and enabled direct characterization of cell-type-specific chromatin accessibility from the same nuclei. Furthermore, easy-Multiome simultaneously captured cell-type-specific transcription factor expression and the accessibility of their cognate DNA-binding motifs, providing direct links between transcriptional programs and regulatory landscapes. Together, these results demonstrate that easy-Multiome enables robust and efficient joint profiling of plant gene expression and chromatin accessibility while requiring only minimal modifications to existing droplet-based scATAC-seq workflows.
Fiber-seq simultaneously profiles chromatin accessibility, DNA methylation, protein footprints, and genetic variation on single molecules at near—base-pair resolution, revealing how genetic and epigenetic features interact to regulate gene expression and provides a powerful new framework for dissecting immune cell function and disease mechanisms.
Emily A. Madden, James T. Anderson, M. Cowles et al.· Journal of Immunology· 0 citations
Cellular senescence is accompanied by widespread chromatin and transcriptional remodeling, but datasets that capture these changes across intermediate stages of replicative senescence remain limited. Here, we present an integrated bulk RNA-seq and ATAC-seq resource generated from primary human colonic fibroblasts spanning three replicative states: early-passage young cells, intermediate pre-senescent cells, and late-passage senescent cells. This serial design enables not only endpoint comparison between young and senescent cells but also stepwise evaluation of molecular changes during senescence progression. Bulk RNA-seq profiles captured transcriptome-wide alterations across the three states, while ATAC-seq defined corresponding changes in chromatin accessibility. By integrating promoter-associated accessibility with gene expression, we generated a gene-level multi-omic resource for evaluating concordant and discordant chromatin-transcription relationships across senescence transitions. The dataset also supports downstream analyses including pathway enrichment and transcription factor activity inference. Together, this dataset provides a useful resource for studying chromatin accessibility, transcriptional regulation, and their coupling during the progression of replicative senescence in human colonic fibroblasts.
Won Kang, Young-Kyoung Lee, Min-Jung Sung et al.· Scientific Data· 0 citations
Understanding how immune cells develop and function requires insight into the epigenomic mechanisms that regulate gene expression. While many genomic studies focus on transcriptional outputs, changes in the chromatin landscape play a central role in shaping lineage commitment. The mammalian immune system is composed of highly diverse and dynamic cell types, but detailed epigenomic studies have been severely limited by technical challenges in profiling rare cell populations.
We developed and validated a low-input, automated CUT&RUN workflow that incorporates standardized sample preparation to ensure reliable generation of data at the consortium scale. This method minimizes sample handling and applies internal controls to monitor assay performance during experimental and sequencing stages.
Extensive optimization of assay conditions and antibody reagents enabled robust mapping of histone post-translational modifications (PTMs) from as few as 10,000 cells per reaction. Applying this approach, we profiled >170 immune subpopulations collected from 11 ImmGen consortium labs over two years.
These innovations establish a scalable, high-resolution platform for profiling chromatin landscapes from minimal cell inputs. Our automated CUT&RUN pipeline enables standardized, reproducible analysis across diverse immune cell types and can distinguish technical issues from true biological insights. Together, these advances lay the foundation for a companion study presenting the first comprehensive epigenomic atlas of immune lineages and provide a framework for studying chromatin regulation in rare or limited samples across the life sciences.
NIH R44 AI167215
Technological Innovations in Immunology (TECH)
Aaron J. Alcala, M. Marunde, C. L. Windham et al.· Journal of Immunology· 0 citations
A detailed protocol for flap-enabled next-generation capture (FENGC), a cost-effective method for targeted, multiplexed enrichment of DNA sequences for epigenetic and genetic analysis.
Mingqi Zhou, Marie-Pierre L. Gauthier, N. Nabilsi et al.· Methods in molecular biology· 0 citations
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