Biology subjects

Bryson, T. D.

Publications and source records attributed to Bryson, T. D..

4 recordsLinked to original sources

bioRxiv2026

Elevated polyadenylated histone gene transcription in human cancer

Histone production is tightly restricted to S-phase to prevent genomic instability, yet human cancers with an overabundance of RNA Polymerase II (RNAPII) at histone genes are associated with aggressive cancers. To better understand histone gene overexpression in cancer, we applied a quantitative PCR assay to measure total replication-coupled histone output across the histone gene clusters using cell line models. We observed pervasive accumulation of polyadenylated histone transcripts, supported by analysis of >1,400 RNA-sequencing datasets in human cancers, with more than 70% of patients showing tumor specific increases. This alternative processing preferentially enriches for histone H2B, which lacks replication independent variants, across >8,300 tumors comprising diverse cancer types and transcriptional subtypes. We also found that disruption of nuclear components required to maintain RNAPII levels at the histone genes increased polyadenylated histone transcripts. Our results suggest that S-phase-dependent histone genes are subject to unscheduled gap phase transcription in human cancer.

cancer biology↗

bioRxiv2022

A giant virus genome is densely packaged by stable nucleosomes

The two doublet histones of Marseillevirus are distantly related to the four eukaryotic core histones and wrap 121 basepairs of DNA to form remarkably similar nucleosomes. By permeabilizing Marseillevirus virions and performing genome-wide nuclease digestion, chemical cleavage and mass spectrometry assays, we find that the higher-order organization of Marseillevirus chromatin fundamentally differs from that of eukaryotes. Marseillevirus nucleosomes fully protect DNA within virions as closely abutted 121-bp DNA wrapped cores without linker DNA or phasing along genes. Likewise, we observed that a large fraction of the nucleosomes reconstituted onto multi-copy tandem repeats of a nucleosome positioning sequence are tightly packed. Dense promiscuous packing of fully wrapped nucleosomes rather than "beads-on-a-string" with genic punctuation represents a new mode of DNA packaging by histones. We suggest that doublet histones have evolved for viral genome protection and may resemble an early stage of histone differentiation leading to the eukaryotic octameric nucleosome.

evolutionary biology↗

bioRxiv2019

CUT&Tag for efficient epigenomic profiling of small samples and single cells

Many chromatin features play critical roles in regulating gene expression. A complete understanding of gene regulation will require the mapping of specific chromatin features in small samples of cells at high resolution. Here we describe Cleavage Under Targets and Tagmentation (CUT&Tag), an enzyme-tethering strategy that provides efficient high-resolution sequencing libraries for profiling diverse chromatin components. In CUT&Tag, a chromatin protein is bound in situ by a specific antibody, which then tethers a protein A-Tn5 transposase fusion protein. Activation of the transposase efficiently generates fragment libraries with high resolution and exceptionally low background. All steps from live cells to sequencing-ready libraries can be performed in a single tube on the benchtop or a microwell in a high-throughput pipeline, and the entire procedure can be performed in one day. We demonstrate the utility of CUT&Tag by profiling histone modifications, RNA Polymerase II and transcription factors on low cell numbers and single cells.

genomics↗

bioRxiv2019

A streamlined protocol and analysis pipeline for CUT&RUN chromatin profiling

We previously described a novel alternative to Chromatin Immunoprecipitation, Cleavage Under Targets & Release Using Nuclease (CUT&RUN), in which unfixed permeabilized cells are incubated with antibody, followed by binding of a Protein A-Micrococcal Nuclease (pA/MNase) fusion protein (1). Upon activation of tethered MNase, the bound complex is excised and released into the supernatant for DNA extraction and sequencing. Here we introduce four enhancements to CUT&RUN: 1) a hybrid Protein A-Protein G-MNase construct that expands antibody compatibility and simplifies purification; 2) a modified digestion protocol that inhibits premature release of the nuclease-bound complex; 3) a calibration strategy based on carry-over of E. coli DNA introduced with the fusion protein; and 4) a novel peak-calling strategy customized for the low-background profiles obtained using CUT&RUN. These new features, coupled with the previously described low-cost, high efficiency, high reproducibility and high-throughput capability of CUT&RUN make it the method of choice for routine epigenomic profiling.

molecular biology↗