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Researchers used Oxford Nanopore long-read sequencing to simultaneously analyze chromatin organization and RNA transcription in yeast lacking two chromatin remodeling proteins, ISW1 and CHD1. They developed EpiFLAIR, a computational tool that links chromatin states across entire genes to specific RNA isoforms at the single-molecule level. The study reveals that nucleosome positioning regulates which transcription start sites are used, affects RNA polymerase processivity, and influences splicing outcomes, demonstrating that chromatin structure controls multiple steps of gene expression to maintain transcriptional accuracy.
Why it matters
This work establishes a new method for connecting chromatin organization to gene expression at unprecedented resolution, revealing how disrupted chromatin remodeling can simultaneously activate some genes while silencing others. The findings have implications for understanding gene regulation in diseases where chromatin remodelers are mutated, and the long-read sequencing approach could be applied to study complex gene regulation in other organisms including humans.
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⚠️ Preprint – Noch nicht peer-reviewed
Dieser Artikel wurde noch nicht von unabhängigen Experten begutachtet. Die Ergebnisse sind vorläufig und sollten mit Vorsicht interpretiert werden.
Transcription and RNA processing are tightly coupled to chromatin organization, yet how nucleosome positioning is coordinated across the promoter and gene body to shape alternative isoform expression remains poorly understood. This question has been difficult to address because short-read chromatin profiling cannot simultaneously capture promoter and gene-body chromatin states on the same DNA molecule, and short-read RNA sequencing cannot resolve full-length transcripts without requiring computational assembly. To address this, we deleted two conserved chromatin remodelers, ISW1 and CHD1, in Saccharomyces cerevisiae and profiled chromatin fibers, nascent RNA, and full-length mature RNA using Oxford Nanopore long-read sequencing. We developed EpiFLAIR, a computational framework that assigns discrete long-range chromatin states across entire genes and integrates these states with isoform-level transcriptional outputs. Using EpiFLAIR, we show that single-molecule chromatin states together with sequence motifs are strong predictors of alternative TSS isoform expression. Loss of ISW1 and CHD1 produced divergent transcriptional changes by activating transcriptionally silenced promoters while repressing active ones. Single-molecule chromatin profiling suggested that this redistribution of transcriptional activity arose, in part, from an anticorrelation between gene-body and promoter chromatin accessibility along the same chromatin fiber, a finding uniquely enabled by long-read single-molecule resolution. Furthermore, disruption of regular nucleosome spacing impaired RNAPII processivity and co-transcriptional splicing, consequently altering mature RNA levels and splicing isoform composition. Together, our findings demonstrate that nucleosomes maintain transcriptional fidelity during initiation, elongation, and splicing to regulate isoform expression. More broadly, long-read single-molecule chromatin profiling represents a powerful approach for linking chromatin organization to isoform-level gene regulation.