Bas van Steensel

Local chromatin, 3D genome folding and transposon cargo shape Sleeping Beauty transposition

This study identifies factors influencing Sleeping Beauty transposition, showing chromatin context, cargo size, and transcriptional activity affect efficiency and reintegration patterns.

Systematic comparison of estimates of transcription factor activity by ATAC-seq and multiplexed reporter assays

This study compares ATAC-seq-based estimates of transcription factor activity with multiplexed reporter assays across perturbations, finding overlap but also discrepancies in their sensitivity to different TF types.

Transcription controls chromatin-nuclear lamina contacts through distinct Lamin A and LBR tethering mechanisms

This study shows that transcription inhibition rapidly and reversibly rewires chromatin-nuclear lamina contacts through distinct Lamin A and LBR tethering mechanisms.

Effects of CTCF on the regulatory landscape of the mouse Sox2 locus

The paper investigates how CTCF binding sites affect the regulatory landscape of the mouse Sox2 locus by relocating them and measuring their impact on gene expression.

An integrated view of the structure and function of the human 4D nucleome

The paper integrates 4D Nucleome data to analyze 3D genome structure and function in human cells, revealing chromatin domains, loops, and interactions, and showing how genetic variants affect genome folding.

Coordinated control of genome-nuclear lamina interactions by Topoisomerase 2B and Lamin B receptor

The paper identifies TOP2B as a regulator of genome-nuclear lamina interactions, showing its role in partitioning genomic regions between the nuclear lamina and interior, with LBR playing a complementary role.

Functional maps of a genomic locus reveal confinement of an enhancer by its target gene.

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.

Genome - nuclear lamina interactions are multivalent and cooperative

The paper investigates how genomic regions called LADs interact with the nuclear lamina, finding that these interactions are multivalent and cooperative, with some subregions having stronger affinity and influencing neighboring sequences.

Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks

The paper shows that DSBs in LADs cause megabase-scale detachment from the nuclear lamina, which is necessary for efficient repair.

Rapid depletion of CTCF and cohesin proteins reveals dynamic features of chromosome architecture.

This study shows that cohesin accumulates at CTCF-bound loop anchors after WAPL depletion, and active genes form long-range clusters independent of cohesin.

Identification of (ultra-)rare functional promoter mutations in cancer using sequence-based deep learning models

This study uses sequence-based deep learning models to identify functional promoter mutations in cancer, finding enrichment in known and novel cancer genes.

Beyond A and B Compartments: how major nuclear locales define nuclear genome organization and function

The paper examines genome organization in human cells relative to nuclear locales, finding that gene expression and replication timing correlate with different nuclear structures and that LADs and iLADs compete for lamina attachment.

Transcription can be sufficient, but is not necessary, to advance replication timing

The paper manipulates transcription to show it can advance replication timing but is not required for the switch to early replication.

Optimized reporters for multiplexed detection of transcription factor activity

The paper systematically optimizes transcriptional reporters for 86 transcription factors and identifies 60 highly sensitive and specific reporters.

Large-scale analysis of the integration of enhancer-enhancer signals by promoters

The paper tests how enhancer pairs combine to activate promoters in mouse cells, finding near-additive behavior with non-linear scaling depending on promoter strength.

Chromatin protein complexes involved in gene repression in lamina-associated domains

The paper identifies chromatin regulators involved in gene repression in lamina-associated domains (LADs) through genetic screens, showing that transcription elongation and chromatin remodeling factors, not nuclear lamina proteins, mediate repression.

The regulatory grammar of human promoters uncovered by MPRA-trained deep learning

This paper introduces PARM, a deep learning model trained on MPRA data to predict human promoter activity and identify TF binding preferences, revealing positional and functional differences in regulatory grammar.

Widespread chromatin context-dependencies ofDNA double-strand break repair proteins

A multiplexed screen reveals how dozens of proteins sense the local chromatin context to tune the balance between two DNA repair pathways.

Chromatin context-dependent effects of epigenetic drugs on CRISPR-Cas9 editing

This study identifies 67 epigenetic drugs that modulate CRISPR-Cas9 editing efficiency and repair outcomes based on chromatin context in human cells.

Predicting prime editing efficiency across diverse edit types and chromatin contexts with machine learning

Perturbations in 3D genome organization can promote acquired drug resistance

The paper shows that disrupting nuclear lamina association promotes ABCB1 gene derepression and taxol resistance in RPE cells.

Optimisation of TP53 reporters by systematic dissection of synthetic TP53 response elements

The paper systematically examines how TP53 binding site architecture affects transcriptional output and develops a model to predict reporter activity.

Dynamic chromosomal interactions and control of heterochromatin positioning by Ki67

The paper investigates Ki67's role in chromatin organization by analyzing its genomic interactions and dynamics during the cell cycle in human cells.

CTCF and cohesin promote focal detachment of DNA from the nuclear lamina

The paper investigates the role of CTCF and cohesin in LAD positioning, finding they reinforce borders but do not position LADs, and mediate fine-tuning of nuclear lamina interactions.

Systematic analysis of intrinsic enhancer-promoter compatibility in the mouse genome.

The paper systematically analyzes enhancer-promoter compatibility in the mouse genome using high-throughput assays, finding significant promoter selectivity and diverse compatibility patterns.

Nonlinear control of transcription through enhancer-promoter interactions

The paper quantifies how enhancer-promoter interactions influence transcription through nonlinear relationships and reveals mechanisms of transcriptional control via chromosome structure.

Impact of chromatin context on Cas9-induced DNA double-strand break repair pathway balance

The paper measures how chromatin context influences the balance between DNA repair pathways after Cas9-induced breaks in over 1,000 genomic locations.

SPIN reveals genome-wide landscape of nuclear compartmentalization

The paper introduces SPIN, a method to identify genome-wide nuclear spatial localization patterns by integrating nuclear compartment mapping and chromatin interaction data.

Cell cycle dynamics of lamina associated DNA

The paper develops pA-DamID to study LAD-NL contacts during interphase, finding rapid early G1 establishment and differential dynamics between distal and centromere-proximal LADs.

Local rewiring of genome - nuclear lamina interactions by transcription.

The paper investigates how gene activation affects nuclear lamina interactions and shows that transcription can locally rewire these interactions without broadly altering chromosomal regions.