Tcf1 is essential for initiation of oncogenic Notch1-driven chromatin topology in T-ALL

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Allele-specific expression (ASE) is pivotal in understanding the genetic underpinnings of phenotypic variation within species, differences in disease susceptibility, and responses to environmental factors. We processed 11 different tissue types collected f ...

Regulatory elements, such as enhancers and silencers, control transcription by establishing physical proximity to target gene promoters. Neurons in flies and mammals exhibit long-range three-dimensional genome contacts, proposed to connect genes with dista ...

In natural habitats, nutrient availability limits bacterial growth. We discovered that bacteria can overcome this limitation by acquiring nutrients by lysing neighboring cells through contact-dependent antagonism. Using single-cell live imaging and isotopi ...

It is well-established that symptomatic cancers evade immune destruction by coalescing tumor microenvironments to suppress adaptive immunity. Additionally, mouse models of cervical and other cancers have revealed a capability of tumors to systemically indu ...

Apoptosis controls cell fate, ensuring tissue homeostasis and promoting disease when dysregulated. The rate-limiting step in apoptosis is mitochondrial poration by the effector B cell lymphoma 2 (BCL-2) family proteins BAK and BAX, which are activated by i ...

Motivation Many machine learning (ML) models developed to classify phenotype from gene expression data provide interpretations for their decisions, with the aim of understanding biological processes. For many models, including neural networks, interpretati ...

Two fundamental properties of embryonic stem cells (ESCs) are their ability to self-renew and differentiate into all somatic cell types. Maintenance of their identity faces major challenges when transitioning through mitosis, as most DNA-binding proteins a ...

5-Methylcytosine (5mC) is a widespread silencing mechanism that controls genomic parasites. In eukaryotes, 5mC has gained complex roles in gene regulation beyond parasite control, yet 5mC has also been lost in many lineages. The causes for 5mC retention an ...

Whole-genome doubling (WGD) is a recurrent event in human cancers and it promotes chromosomal instability and acquisition of aneuploidies(1-8). However, the three-dimensional organization of chromatin in WGD cells and its contribution to oncogenic phenotyp ...

Cell fate progression of pluripotent progenitors is strictly regulated, resulting in high human cell diversity. Epigenetic modifications also orchestrate cell fate restriction. Unveiling the epigenetic mechanisms underlying human cell diversity has been di ...

Regulation of gene expression is a complex but highly guided process. While genomic technologies and computational approaches have allowed high-throughput mapping of cis-regulatory elements (CREs) and their interactions in 3D, their precise role in regulat ...

Many enhancers control gene expression by assembling regulatory factor clusters, also referred to as condensates. This process is vital for facilitating enhancer communication and establishing cellular identity. However, how DNA sequence and transcription ...

Since Strahl and Allis proposed the "language of covalent histone modifications", a host of experimental studies have shed light on the different facets of chromatin regulation by epigenetic mechanisms. Initially proposed as a concept for controlling gene ...

DNA methylation (DNAm) is one of the most frequently studied epigenetic mechanisms facilitating the interplay of genomic and environmental factors, which can contribute to externalizing behaviours and related psychiatric disorders. Previous epigenome-wide ...

Genomic instability enhances cancer progression by favoring clonal diversity, yet uncontrolled replicative stress can lead to mitotic catastrophe and inflammatory responses promoting immune rejection. KRAB-containing zinc finger proteins (KZFPs) are epigen ...

Constitutive heterochromatin is essential for transcriptional silencing and genome integrity. The establishment of constitutive heterochromatin in early embryos and its role in early fruitfly development are unknown. Lysine 9 trimethylation of histone H3 ( ...

The efficacy of anti-cancer therapies depends on the genomic composition of the tumor, its microenvironment, spatial organization, and intra-tumor heterogeneity. B-cell lymphomas are a heterogeneous group of tumors emerging from B-cells at different stages ...

Co-expression of two or more genes at the single-cell level is usually associated with functional co-regulation. While mRNA co-expression-measured as the correlation in mRNA levels-can be influenced by both transcriptional and post-transcriptional events, ...

Still displaying characteristics of their bacterial origin, such as autonomous division, motility, and their own genome, mitochondria remain an elusive component of modern eukaryotes. They produce most of the cell's energy in the form of adenosine triphosp ...

Human papillomavirus (HPV) infections are the primary drivers of cervical cancers, and often HPV DNA gets integrated into the host genome. Although the oncogenic impact of HPV encoded genes is relatively well known, the cis-regulatory effect of integrated ...

Tcf1 is essential for initiation of oncogenic Notch1-driven chromatin topology in T-ALL

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Genome-wide allele-specific expression in multi-tissue samples from healthy male baboons reveals the transcriptional complexity of mammals

A boundary-defining protein facilitates megabase-scale regulatory chromosomal loop formation in Drosophila neurons

Antagonism as a Foraging Strategy in Microbial Communities

HPV16-Expressing Tumors Release Multiple IL-1 Ligands to Orchestrate Systemic Immunosuppression Whose Disruption Enables Efficacy of a Therapeutic Vaccine

Structural basis of BAK sequestration by MCL-1 in apoptosis

A comparative analysis of gene expression profiling by statistical and machine learning approaches

Deciphering the molecular events leading to the global restoration of the chromatin landscape during mitotic exit

DNA methylation enables recurrent endogenization of giant viruses in an animal relative

Whole-genome doubling drives oncogenic loss of chromatin segregation

Single-cell epigenomic reconstruction of developmental trajectories from pluripotency in human neural organoid systems

Chromatin modules and their implication in genomic organization and gene regulation

Context transcription factors establish cooperative environments and mediate enhancer communication

Decoding Chromatin Ubiquitylation: A Chemical Biology Perspective

Epigenome-wide DNA methylation in externalizing behaviours: A review and combined analysis

KRAB zinc finger proteins link heterochromatin maintenance to replicative stress and inflammation in diffuse large B-cell lymphoma

Inheritance of H3K9 methylation regulates genome architecture in Drosophila early embryos

Development of patient-derived lymphomoids with preserved tumor architecture for lymphoma therapy screening

Exploring the role of transcriptional and post-transcriptional processes in mRNA co-expression

Unraveling mitochondrial dynamics: exploring asymmetries and function through advanced microscopy

Cis-regulatory effect of HPV integration is constrained by host chromatin architecture in cervical cancers