Methods we have built and shared for seeing chromatin in single cells and single molecules. Each links to the paper that describes it.
Assays that read chromatin state, accessibility and methylation from the same molecules.
Clusters single long-read molecules and stitches overlapping reads to cover long regulatory neighborhoods. This links CTCF binding states, nucleosome occupancy and long-range interactions directly to transcription.
Use it to study cell-to-cell variation in chromatin state at specific loci.
Measures ATAC-seq or ChIP-seq signal together with DNA methylation from the same material.
Use it to ask whether accessibility or factor binding and methylation coexist at the same sites.
Ways of watching loci move, contract and pair inside the nucleus.
Standardized workflows to measure locus position, contraction and decontraction, and higher-order architecture in fixed cells.
Used throughout our work on antigen-receptor loci and CTCF-mediated folding.
CRISPR-dCas9 with sgRNA scaffolds tracks repeats and repeat-enriched individual loci in two colours in living cells.
Use it to follow locus dynamics in real time.
Analysis frameworks for chromatin contacts, methylation and regulatory networks.
Builds methylation-anchored networks across patient cohorts to find distal regulatory hubs and the genes they control.
Use it to find regulatory hubs in cancer cohorts.
Calls interactions from 4C-seq experiments reproducibly, using a hidden Markov model that accounts for distance from the viewpoint.
Use it to identify genome-wide contacts of a single viewpoint.
Identifies simultaneous interactions among several loci from 4C-seq data, revealing multi-contact hubs.
Use it to test whether contacts happen together rather than separately.
Genome-wide 3D analysis that nominates host genes likely to be regulated by transposable elements.
Use it to connect transposable elements to the genes they contact.
