Leonid A. Mirny

Stepwise reorganization of chromosome conformation and nuclear organization during stem cell differentiation

The paper temporally maps nuclear reorganization during human stem cell differentiation and identifies three temporally ordered transitions in nuclear structure and function.

Smc5/6 - microtubules binding shapes pericentromeric chromatin

This study shows that Smc5/6 microtubule binding constrains chromatin dynamics and promotes pericentromeric folding in yeast, safeguarding genome stability during mitosis.

Genome-wide absolute quantification of chromatin looping

This study calibrates Micro-C with live imaging to determine absolute chromatin looping probabilities in mouse cells, finding most loops occur at low frequencies.

Live-cell imaging of enhancer-promoter dynamics reveals transient contact-driven gene activation

This study uses live-cell imaging to show that enhancer-promoter interactions drive gene activation through transient contacts of ~25-42 nanometers.

Cohesin bridging as a physical principle of enhancer-promoter communication

This study proposes that cohesin bridging, not spatial proximity, mediates enhancer-promoter communication and develops a model to validate this mechanism through engineered cell systems.

PDS5 proteins control genome architecture by limiting the lifetime of cohesin-NIPBL complexes

This study shows PDS5 proteins regulate genome architecture by stopping loop extrusion and strengthening CTCF boundaries through NIPBL dissociation from cohesin.

Condensin Accelerates Long-Range Intra-Chromosomal Interactions

This study measures chromosomal encounter times in budding yeast using CICI and finds that condensin accelerates long-range intra-chromosomal interactions compared to inter-chromosomal ones.

Extrusion fountains are hallmarks of chromosome organization emerging upon zygotic genome activation

The paper identifies 'fountains' as enhancer-specific chromosome organization elements emerging during zygotic genome activation in zebrafish and mouse.

Cohesin-mediated chromatin remodeling controls the differentiation and function of conventional dendritic cells

This study shows cohesin-mediated chromatin remodeling is essential for dendritic cell differentiation and function, particularly antigen cross-presentation and IL-12 secretion.

Unique territorial and compartmental organization of chromosomes in the holocentric silkworm

The paper discovers a novel chromatin folding structure, compartment S, in the silkworm Bombyx mori using Hi-C, showing unique loop extrusion and contact patterns.

HIRA defines early replication initiation zones independently of their genome compartment

The paper shows HIRA regulates early replication initiation zones independently of chromatin accessibility, histone marks, and 3D compartment organisation.

Dynamics of microcompartment formation at the mitosis-to-G1 transition

The paper uses Region Capture Micro-C to study microcompartment formation during mitosis-to-G1 transition, finding they form in prometaphase and are influenced by chromatin compaction and loop extrusion.

Rules of engagement for condensins and cohesins guide mitotic chromosome formation

In DT40 cells, condensins displace extrusive cohesin, bypass cohesive cohesin and stall against each other while extruding ~1-3 kb/sec, yielding irregular helical chromatids of consecutive loops.

HIRA-dependent provision of histone H3.3 in active chromatin ensures genome compartmentalisation

This study shows that HIRA-dependent histone H3.3 deposition maintains 3D genome compartmentalisation in active chromatin, independent of histone PTMs.

Mitotic chromosomes are self-entangled and disentangle through a Topoisomerase II-dependent two stage exit from mitosis

The paper shows mitotic chromosomes are self-entangled and disentangle through a Topoisomerase II-dependent two-stage process during mitotic exit.

Tunable DNMT1 degradation reveals cooperation of DNMT1 and DNMT3B in regulating DNA methylation dynamics and genome organization

This study uses tunable DNMT1 degradation to investigate DNA methylation dynamics and genome organization, revealing cooperative roles of DNMT1 and DNMT3B and their impact on heterochromatin and cell fitness.

Transcription shapes 3D chromatin organization by interacting with loop extrusion

The paper shows that transcribing RNA polymerases act as moving barriers to cohesin, altering chromatin organization near active genes.

Heterochromatin diversity modulates genome compartmentalization and loop extrusion barriers

The paper identifies three inactive chromatin states in HCT116 cells and shows how H3K9me3-HP1/β heterochromatin influences genome compartmentalization and loop extrusion barriers through DNA methylation.

The 4D Nucleome Data Portal: a resource for searching and visualizing curated nucleomics data

The paper introduces the 4DN Data Portal, a resource for searching and visualizing curated nucleomics data, including Hi-C and other chromosome architecture datasets.

Systematic evaluation of chromosome conformation capture assays

This study evaluates 3C-based assays to understand how experimental parameters affect chromatin interaction detection and quantification, leading to the development of Hi-C 3.0.

Molecular basis of CTCF binding polarity in genome folding

The paper investigates how CTCF binding polarity influences chromatin loop formation by showing that CTCF positions cohesin but does not control its binding dynamics.

Is tumor mutational burden predictive of response to immunotherapy?

This paper challenges the predictive value of tumor mutational burden (TMB) for immunotherapy response, finding little evidence of its association and suggesting previous studies had methodological flaws.

Ultrastructural details of mammalian chromosome architecture

This study improves chromosome architecture mapping by using Micro-C to achieve nucleosome-resolution insights in human cells, revealing new looping interactions and structural patterns.

The genome-wide, multi-layered architecture of chromosome pairing in early Drosophila embryos

A haplotype-resolved Hi-C approach reveals structured homolog pairing in early Drosophila embryos, correlated with Zelda-mediated chromatin accessibility.

Highly Structured Homolog Pairing Reflects Functional Organization of the Drosophila Genome

The paper uses haplotype-resolved Hi-C to reveal structured homolog pairing and its global impact on gene activity in hybrid Drosophila cells.

Cooler: scalable storage for Hi-C data andother genomically-labeled arrays

Cooler provides a scalable storage format for multidimensional genomic datasets, enabling efficient compression and random access for analysis.

Higher-Order Organization Principles of Pre-translational mRNPs

This study develops a method to probe mRNA 3D structures and finds that pre-translational mRNPs form linear rod-like structures without strong end interactions.

Condensin II inactivation in interphase does not affect chromatin folding or gene expression

This study shows that deleting Ncaph2 in mouse hepatocytes does not alter chromatin folding or gene expression, suggesting condensin II's role in interphase may be limited.

HiGlass: Web-based Visual Exploration and Analysis of Genome Interaction Maps

HiGlass, a web-based, containerized viewer, enables continuous multiscale navigation of Hi-C contact maps alongside genomic tracks using composable views linked by location and zoom.

Mitotic chromosomes fold by condensin-dependent helical winding of chromatin loop arrays

The paper shows mitotic chromosomes form through condensin-mediated disassembly of interphase chromatin and helical winding of loop arrays during prophase and prometaphase.