Biology subjects

Felton, C.

Publications and source records attributed to Felton, C..

3 recordsLinked to original sources

bioRxiv2026

Multi-omic long-read sequencing reveals nucleosome control of transcriptional fidelity at the isoform level

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.

genomics↗

bioRxiv2023

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

AbstractThe Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP) Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. The consortium generated over 427 million long-read sequences from cDNA and direct RNA datasets, encompassing human, mouse, and manatee species, using different protocols and sequencing platforms. These data were utilized by developers to address challenges in transcript isoform detection and quantification, as well as de novo transcript isoform identification. The study revealed that libraries with longer, more accurate sequences produce more accurate transcripts than those with increased read depth, whereas greater read depth improved quantification accuracy. In well-annotated genomes, tools based on reference sequences demonstrated the best performance. When aiming to detect rare and novel transcripts or when using reference-free approaches, incorporating additional orthogonal data and replicate samples are advised. This collaborative study offers a benchmark for current practices and provides direction for future method development in transcriptome analysis.

genomics↗

bioRxiv2022

Intermittent systemic exposure to lipopolysaccharide-induced inflammation disrupts hippocampal long-term potentiation and impairs cognition in aging male mice

Age-related cognitive decline, a common component of the brain aging process, is associated with significant impairment in daily functioning and quality of life among geriatric adults. While the complexity of mechanisms underlying cognitive aging are still being elucidated, microbial exposure and the multifactorial inflammatory cascades associated with systemic infections is emerging as a potential driver of neurological senescence. The negative cognitive and neurobiological consequences of a single pathogen-associated inflammatory experience, such as that modeled through treatment with lipopolysaccharide (LPS), are well documented. Yet, the brain aging impacts of repeated, intermittent inflammatory challenges are less well studied. To extend the emerging literature assessing the impact of infection burden on cognitive function among normally aging mice, here, we repeatedly exposed adult mice to intermittent LPS challenges during the aging period. Male 10-month-old C57BL6 mice were systemically administered escalating doses of LPS once every two weeks for 2.5 months. We evaluated cognitive consequences using the non-spatial step-through inhibitory avoidance task and both spatial working and reference memory versions of the Morris water maze. We also probed several potential mechanisms, including cortical and hippocampal cytokine/chemokine gene expression as well as hippocampal neuronal function via extracellular field potential recordings. Though there was limited evidence for an ongoing inflammatory state in cortex and hippocampus, we observed impaired learning and memory and a disruption of hippocampal long-term potentiation. These data suggest that a history of intermittent exposure to LPS-induced inflammation is associated with a subtle but significantly accelerated trajectory of cognitive decline. The broader impact of these findings may have important implications for standard of care involving infections in aging individuals or populations at-risk for dementia.

neuroscience↗