Biology subjects

de Barbanson, B. A.

Publications and source records attributed to de Barbanson, B. A..

3 recordsLinked to original sources

bioRxiv2024

T-ChIC: multi-omic detection of histone modifications and full-length transcriptomes in the same single cell

Epigenetic mechanisms, including histone modifications, are key regulators of transcription and influence cellular differentiation. To uncover the interplay between histone modifications and transcription, we developed T-ChIC (Transcriptome + Chromatin ImmunoCleavage), which detects full-length transcripts and histone modifications in the same single cell. We applied T-ChIC to gastruloids, an in vitro model containing cell types derived from all three germ layers. During gastruloid development we observed a switch in transcription start site usage from multiple regions marked by H3K4me3 to one marked start site per gene. H3K27me3 coverage transitions from global marking of non-transcribed regions towards localised marking of repressive regions. Upon lineage commitment, bivalent regions are sequentially resolved towards a germ layer-specific state, where endoderm retains a high abundance of H3K27me3 while ectoderm displays a widespread loss. Together, we propose a model for a cell-intrinsic epigenetic timer, which ensures sequential perceptiveness of pluripotent cells to transcriptional activation of germ layer-specific genes.

genomics↗

bioRxiv2021

Hierarchical chromatin regulation during blood formation uncovered by single cell sortChIC

Post-translational histone modifications modulate chromatin packing to regulate gene expression. How chromatin states, at euchromatic and heterochromatic regions, underlie cell fate decisions in single cells is relatively unexplored. We develop sort assisted single-cell chromatin immunocleavage (sortChIC) and map active (H3K4me1 and H3K4me3) and repressive (H3K27me3 and H3K9me3) histone modifications in hematopoietic stem and progenitor cells (HSPCs), and mature blood cells in the mouse bone marrow. During differentiation, HSPCs acquire distinct active chromatin states that depend on the specific cell fate, mediated by cell type-specifying transcription factors. By contrast, most regions that gain or lose repressive marks during differentiation do so independent of cell fate. Joint profiling of H3K4me1 and H3K9me3 demonstrates that cell types within the myeloid lineage have distinct active chromatin but share similar myeloid-specific heterochromatin-repressed states. This suggests hierarchical chromatin regulation during hematopoiesis: heterochromatin dynamics define differentiation trajectories and lineages, while euchromatin dynamics establish cell types within lineages.

genomics↗

bioRxiv2021

Deconvolving multiplexed histone modifications in single cells

Recent advances have enabled mapping of histone modifications in single cells1-12, but current methods are constrained to profile only one histone modification per cell. Here we present an integrated experimental and computational framework, scChIX (single-cell chromatin immunocleavage and unmixing), to map multiple histone modifications in single cells. scChIX multiplexes two histone modification profiles together in single cells, then computationally deconvolves the signal using training data from respective histone modification profiles. We first validate this method using purified blood cells and show that although the two repressive marks, H3K27me3 and H3K9me3, are generally mutually exclusive, the transitions between the two regions can vary between cell types. Next we apply scChIX to a heterogenous cell population from mouse bone marrow to generate linked maps of active (H3K4me1) and repressive (H3K27me3) chromatin landscapes in single cells, where coordinates in the active modification map correspond to coordinates in the repressive map. Linked analysis reveals that immunoglobulin genes in the Igkv region are in a repressed chromatin state in pro-B cells, but become activated in B cells. Overall, scChIX unlocks systematic interrogation of the interplay between histone modifications in single cells.

genomics↗