Alistair Nicol Boettiger

Multiscale spatial analysis implicates chromosomal metaloops in gene patterning across the Drosophila brain

The paper identifies chromosomal metaloops in Drosophila brains and shows their role in organizing gene expression patterns through metadomains.

Single-cell chromatin state transitions during epigenetic memory formation

The paper investigates chromatin state transitions during epigenetic memory formation by analyzing single-cell gene expression and chromatin structure changes after repressor recruitment and release.

Loop Extrusion Accelerates Long-Range Enhancer-Promoter Searches in Living Embryos

The paper investigates how cohesin-mediated loop extrusion and tethering elements contribute to enhancer-promoter interactions in Drosophila embryos using imaging, genetics, and simulations.

The role of cohesin loading at enhancers in the flux of loop extrusion and long-range transcriptional control

This study shows that cohesin loading at enhancers does not significantly contribute to genome folding or long-range transcriptional control, as inhibiting cohesin recruitment near enhancers reduces target promoter transcription.

Enhancer activation from transposable elements in extrachromosomal DNA

The paper identifies enhancer-like elements on ecDNA in colorectal cancer that are derived from transposable elements and are functionally active in cancer cell fitness.

Promoter strength and position govern promoter competition via transcript-dependent insulation

This study investigates how promoter strength and position influence promoter competition by inserting diverse promoters into the Sox2 locus and measuring their effect on endogenous Sox2 expression.

Kinetic organization of the genome revealed by ultra-resolution, multiscale live imaging

This paper introduces TRACK-IT, a live imaging technique that reveals rapid, cohesin-dependent genomic motion across multiple scales, challenging previous assumptions about genome organization.

Long range regulation of transcription scales with genomic distance in a gene specific manner

The paper shows that enhancer-promoter communication scales with genomic distance in a gene-specific manner, independent of 3D contact frequency or chromatin state.

Super-enhancer interactomes from single cells link clustering and transcription

The paper maps single-cell super-enhancer interactomes, revealing that SEs form loose communities linked to transcriptional bursts.

Boundary stacking interactions enable cross-TAD enhancer-promoter communication during limb development

The paper investigates cross-TAD enhancer-promoter communication during limb development using ORCA and simulations, finding that boundary stacking enables such interactions and explains architectural stripes.

SnapFISH: a computational pipeline to identify chromatin loops from multiplexed DNA FISH data

SnapFISH identifies chromatin loops from multiplexed DNA FISH data with high sensitivity and accuracy in mouse embryonic stem cells.

Structural elements facilitate extreme long-range gene regulation at a human disease locus

The paper investigates how structural elements regulate SOX9 expression over long genomic distances in PRS patients by analyzing chromatin topology and modeling interactions.

Polycomb repression of Hox genes involves spatial feedback but not domain compaction or demixing

The paper challenges the repression-by-compaction model of Polycomb proteins by showing that PcG-bound chromatin remains repressed while exploring decompact states and mixing with neighboring chromatin.

Polycomb-mediated Genome Architecture Enables Long-range Spreading of H3K27 methylation

The paper investigates how Polycomb-mediated genome architecture facilitates long-range H3K27 methylation spreading in ESCs and iPSCs, revealing RNA-dependent DNA looping and developmental gene roles in chromatin organization.

mSWI/SNF promotes polycomb repression both directly and through genome-wide redistribution

This study shows that the BAF complex both antagonizes and promotes polycomb-mediated repression by redistributing polycomb complexes across the genome in embryonic stem cells.