Effie Apostolou

KAT6 and KAT7 actively maintain mitotic chromatin composition and acetylation to preserve developmental competence

This study shows KAT6 and KAT7 maintain mitotic chromatin acetylation and composition, supporting postmitotic transcriptional memory and developmental competence in stem cells.

Developmental rewiring of EHMT1 function during human cortical neurogenesis

This study shows EHMT1's functional rewiring during human cortical neurogenesis, revealing its shift from restraining pluripotency to supporting neuronal programs and its resilience to prolonged depletion.

Discovery of Competent Chromatin Regions in Human Embryonic Stem Cells

The paper identifies pre-established chromatin regions in human ESCs that enable rapid activation of lineage-specific genes during differentiation.

TAD hierarchy restricts poised LTR activation and loss of TAD hierarchy promotes LTR co-option in cancer

The paper shows that TAD hierarchy restricts LTR activation, and its loss in cancer allows LTRs to act as alternative promoters, driving oncogene activation and transcriptional diversity.

Three-dimensional regulatory hubs support oncogenic programs in glioblastoma

This study identifies 3D regulatory hubs in glioblastoma stem cells and shows their role in oncogenic programs through computational and experimental analysis.

Genetic variation modulates susceptibility to aberrant DNA hypomethylation and imprint deregulation in naive pluripotent stem cells

The paper identifies genetic variants that influence DNA methylation stability and imprint deregulation in naive pluripotent stem cells across different mouse strains.

Post-mitotic transcriptional activation and 3D regulatory interactions show locus- and differentiation-specific sensitivity to cohesin depletion

This study shows that cohesin depletion affects locus- and differentiation-specific transcriptional activation and regulatory interactions in mouse ESCs, with some loops and genes being more sensitive than others.

Coordinated repression of totipotency-associated gene loci by histone methyltransferase EHMT2 through binding to LINE-1 regulatory elements

The paper identifies EHMT2's role in repressing totipotency-associated gene loci in mESCs by binding to LINE-1 elements and modulating gene expression during the mESC-to-2CLC transition.

ChromaFold predicts the 3D contact map from single-cell chromatin accessibility

ChromaFold predicts 3D chromatin contact maps from scATAC-seq data, outperforming bulk-based methods and enabling cell-type-specific interaction analysis.

CRISPR Screening Uncovers a Long-Range Enhancer for ONECUT1 in Pancreatic Differentiation and Links a Diabetes Risk Variant

The paper identifies a long-range enhancer for ONECUT1 involved in pancreatic differentiation and links a diabetes risk variant to disrupted transcription factor binding.

Transcriptional remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm

This study identifies OTX2 as a critical regulator of definitive endoderm specification and gut patterning through chromatin remodeling and signaling pathway regulation.

Systematic mapping and modeling of 3D enhancer-promoter interactions in early mouse embryonic lineages reveal regulatory principles that determine the levels and cell-type specificity of gene expression

Dynamic network-guided CRISPRi screen reveals CTCF loop-constrained nonlinear enhancer-gene regulatory activity in cell state transitions

The paper uses a CRISPRi screen in hESC differentiation to identify enhancers with nonlinear regulatory activity, revealing a CTCF loop-constrained model for improved enhancer prediction.

Single-cell analysis of bidirectional reprogramming between early embryonic states reveals mechanisms of differential lineage plasticities

The paper uses single-cell RNA and ATAC-seq to study bidirectional reprogramming between embryonic states, revealing differences in lineage plasticity.

A bipartite element with allele-specific functions safeguards DNA methylation imprints at the Dlk1-Dio3 locus

The paper identifies a bipartite imprinting control region at the Dlk1-Dio3 locus that maintains imprint stability through allele-specific regulation of DNA methylation and chromatin structure.

Mitotic retention of H3K27 acetylation promotes rapid topological and transcriptional resetting of stem cell-related genes and enhancers upon G1 entry

This study shows that H3K27 acetylation retention during mitosis accelerates transcriptional and topological resetting of stem cell genes in mouse pluripotent stem cells upon G1 entry.

EpiMethylTag simultaneously detects ATAC-seq or ChIP-seq signals with DNA methylation

EpiMethylTag combines ATAC-seq or ChIP-seq with bisulfite conversion to simultaneously assess chromatin accessibility/TF binding and DNA methylation.

Context-dependent requirement of H3K9 methyltransferase activity during cellular reprogramming to iPSCs

This study shows that reducing EHMT1/2 activity during reprogramming with ascorbic acid impairs iPSC formation and viability, highlighting the role of H3K9 methylation in reprogramming efficiency.

KLF4 is involved in the organization and regulation of pluripotency-associated 3D enhancer networks

This study investigates the role of KLF4 in chromatin reorganization and 3D enhancer rewiring during reprogramming of mouse embryonic fibroblasts to pluripotent stem cells.