Anderson et al. compare brain gene regulation across nine mammals, revealing that enhancer conservation extends beyond DNA sequence to include cell-type specificity and gene targets. Functional assays...

Alzheimer’s disease (AD) exhibits region- and cell-type–specific vulnerability, yet the underlying regulatory mechanisms remain poorly defined. We performed integrated single-nucleus RNA-seq and ATAC-...

ATAC-seq library quality depends on sample preparation, Tn5 insertion preferences, and downstream DNA processing. Understanding these factors helps researchers interpret weak regulatory signals and...

Acute myeloid leukaemia (AML) is an aggressive blood cancer characterized by the unregulated proliferation of immature myeloblasts. Gene mutations have been shown to have a large effect on pathogenesis, inter-tumour heterogeneity and clinical outcomes in AML1–8; however, the role of epigenetic alterations in these respects has been investigated less extensively. Here we use ATAC-seq (assay for transposase-accessible chromatin with sequencing) in a cohort of 1,563 individuals with a recent diagnosis of AML (the ‘eCHROMA’ cohort) to show that AML can be classified into 16 subgroups on the basis of chromatin accessibility profiles. Multiomics analyses of gene mutations, the transcriptome, DNA methylation and histone marks show that these ATAC subgroups exhibit distinct driver mutations, differentiation states, gene expression, DNA methylation and super-enhancer profiles, and are also associated with clinical outcomes. These findings were validated in independent cohorts. Single-cell ATAC

Rebuilding human naïve pluripotency from primed stem cells is essential for generating pre-implantation epiblast-like cells, a key source for regenerative medicine. Here we present a defined, feeder-free protocol that efficiently converts primed human pluripotent stem cells (hPSCs) to a naïve-like state within 12 days. Integrated ATAC-seq, RNA-seq and miRNA-seq analyses reveal a rapid chromatin rewiring marked by increased accessibility at OCT/KLF motifs, closure at ZIC/RFX/NFκB sites, upregulation of miR-372/373 and miR-182/183, and downregulation of miR-302 and miR-363/106 clusters. Functional assays demonstrate that the inflammatory transcription factor NFκB/RELA blocks naïve induction by activating peri-implantation barrier genes, including IKBKE and VEGFR1. Conversely, enforced miR-372/373 expression accelerates conversion by directly targeting RELA. These data delineate an NFκB/RELA axis that orchestrates the epigenetic switch to human naïve pluripotency, offering a tractable fra

This post references AWS ParallelCluster. Check out AWS Parallel Computing Service (AWS PCS), our new managed Slurm service for running HPC and AI workloads on AWS. Regeneron Pharmaceuticals processes thousands of genomic samples each week, using Nextflow as a core part of its scientific computing infrastructure. When its genomics workloads like ATAC-seq (Assay for Transposase-Accessible [...]

B cells sustain both a functional immune system and immune-mediated diseases. Here, the authors use bulk RNA-seq, CITE-seq, and ATAC-seq to profile B cells from healthy donors upon stimulation with di...