Anders S. Hansen

The paper investigates Polycomb-mediated 3D chromatin interactions and finds that cPRC1 is not essential for their formation.

This paper introduces Swap-seq, a method to systematically delete and quantify the effects of enhancers, silencers, and topological elements on gene expression in human cells.

The paper identifies a cell-state-dependent pathway for degrading ER-retained 60S ribosomal subunits through UFMylation loss and the action of TLSD1.

This study shows that SAF-A/HNRNPU regulates euchromatin dynamics and is essential for maintaining nuclear envelope integrity through transcription-dependent mechanisms.

CTCF dimerization on stacked nucleosomes is resolved by cryo-EM through a ZnF6-7-8 interface. Disrupting it in mouse stem cells weakens CTCF-cohesin loops more than insulation and impairs germline differentiation.

The paper investigates how lipid modifications affect Hedgehog morphogen signaling and gradient formation, revealing a tradeoff between local enrichment and long-range diffusion.

The paper identifies 'matchmaker' cis-regulatory elements in erythropoiesis that strengthen loops between neighboring elements and are linked to gene expression and cohesin loading.

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

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

The paper tracks chromatin dynamics across seven orders of magnitude in human and mouse cells, finding strongly subdiffusive behavior with limited sensitivity to transcription and histone modifications.

The paper identifies ZNF654 and JMJD6 as novel factors defining TAD boundaries through in silico screens and experimental validation.

The paper develops a general AI model that integrates diverse genomic modalities and knowledge, showing strong performance across cell types and tissues.

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.

The paper generates a high-resolution Micro-C map of tomato, identifies two epigenetic classes of chromatin loops, and reveals their dual regulatory roles in gene expression.

The paper relocates promoter-reporter constructs to study the positional relationship between the Sox2 gene and its enhancer, revealing gene-mediated confinement of enhancer activity.

The paper introduces Cleopatra, a deep learning model that predicts high-resolution 3D genome maps across human cell types, revealing cell-type-specific loops and gene regulation patterns.

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.

The paper investigates how CTCF mutations affect chromatin accessibility, cohesin binding, and gene regulation through multivariate modeling and mutant perturbations.

This study shows LDB1 directly promotes enhancer-promoter loops and organizes multi-enhancer networks to activate transcription, independent of CTCF, cohesin, or YY1.

The paper shows ZNF143/ZFP143 is an essential transcription factor with no general looping function, functioning independently of CTCF and regulating mitochondrial and ribosomal genes.

The paper shows SCUBE1 expands Hedgehog gradients by enabling transient diffusion through cell gaps, revealing a topology-limited diffusion mechanism for morphogen signaling.

The paper uses high-resolution CTCF MNase HiChIP data to analyze chromatin loop structures and introduces FactorFinder, finding that fully extruded CTCF-CTCF loops are rare and that chromatin state affects cohesin extrusion dynamics.

The paper identifies 10 PTEN enhancers and proposes a new model of enhancer organization that includes spatial separation of functional and structural elements.

The paper introduces RCMC, a method to capture deep 3D genome structure, revealing microcompartments where enhancers and promoters coalesce.

The paper investigates how enhancer-promoter interactions and transcription are affected by acute loss of CTCF, cohesin, WAPL, and YY1, finding minimal effects on E-P interactions and gene expression despite 3D genome perturbations.

The paper analyzes how gene promoters exhibit different dynamic behaviors in response to varying transcription factor contexts using single-cell measurements and a statistical method.

The paper investigates how transcriptional regulatory elements influence the 3D organization of microTADs in mouse stem cells.

This study uses super-resolution imaging to reveal the 3D structure and organizing mechanism of accessible chromatin domains.

The paper shows that herpesvirus creates replication compartments that recruit RNA Polymerase II through DNA interactions, not phase separation, leading to local protein accumulations.

The paper shows CTCF binding and nucleosome positioning at CTCF sites change during the cell cycle, with loss of binding in prometaphase and rearrangement of chromatin structure.