Anton A. Goloborodko

Chromosome folding encodes mechanisms of cohesion maintenance

The paper shows how changes in sister chromatid folding over time encode mechanisms of cohesion maintenance, revealing how transient cofactor interactions regulate long-lived cohesin protection.

Conformational asymmetry of replicated human chromosomes

The paper reveals a genome-wide asymmetry in sister chromatid alignment due to replication fork asymmetry, maintained by cohesive cohesins.

Nested TAD hierarchy defines cohesion zones on replicated chromosomes

The paper shows cohesin function is partitioned within the TAD hierarchy to form cohesion zones and enable sister-chromatid cohesion while preserving loop folding.

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.

Pairtools: from sequencing data to chromosome contacts

Pairtools processes sequencing data into contact pairs for 3C+ analysis, offering high-performance and flexible tools for various protocols.

Cooltools: enabling high-resolution Hi-C analysis in Python

Cooltools provides scalable and flexible analysis tools for high-resolution Hi-C data, addressing challenges in storage, memory, and customization.

Bioframe: Operations on Genomic Intervals in Pandas Dataframes

Bioframe provides a Python library for efficient genomic interval operations using pandas dataframes, extending the data science stack for computational genomics.

A de novo transcription-dependent TAD boundary underpins critical multiway interactions during antibody class switch recombination

The paper shows that a de novo TAD boundary formed by transcriptional activity at acceptor S regions facilitates synapsis during antibody class switch recombination.

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.

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.

Two independent modes of chromosome organization are revealed by cohesin removal

This study shows that cohesin removal leads to loss of TADs and loops but preserves compartments, revealing two independent modes of chromosome organization.

Cohesin dependent compaction of mitotic chromosomes

This study investigates the roles of cohesin and condensin in mitotic chromosome organization in budding yeast using Hi-C and polymer modeling, revealing distinct functions for each complex.

Targeted degradation of CTCF decouples local insulation of chromosome domains from higher-order genomic compartmentalization

This study shows CTCF is essential for TAD organization but not for genome compartmentalization, revealing distinct mechanisms for chromatin folding and insulation.

Emerging Evidence of Chromosome Folding by Loop Extrusion

The paper reviews polymer models and experimental evidence supporting loop extrusion as a mechanism for chromosome folding, focusing on CTCF and cohesin perturbations in interphase.

Formation of Chromosomal Domains by Loop Extrusion

This paper proposes that loop extrusion by cohesins and boundary proteins like CTCF forms Topologically Associating Domains (TADs) through dynamic loop creation and stabilization.