UCNEbase – a database of ultra-conserved non-coding elements and genomic regulatory blocks

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Growing evidence indicates that transposable elements (TEs) play important roles in evolution by providing genomes with coding and non-coding sequences. Identification of TE-derived functional elements, however, has relied on TE annotations in individual s ...

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 ...

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 ...

Recently, Pham et al. used an array of model systems to uncover a role for the enzyme methionine adenosyltransferase (MAT) -1A, which is mainly expressed in liver, in both sensing formaldehyde and regulating transcriptional responses that protect against i ...

Analysis of single-cell datasets generated from diverse organisms offers unprecedented opportunities to unravel fundamental evolutionary processes of conservation and diversification of cell types. However, interspecies genomic differences limit the joint ...

Global change exposes ecosystems to changes in the frequency, magnitude, and concomitancy of disturbances, which impact the composition and functioning of these systems. Here, we experimentally evaluate the effects of salinity disturbances and eutrophicati ...

The adaptation of organisms to their environment depends on the innovative potential inherent to genetic variation. In complex organisms such as mammals, processes like development and immunity require tight gene regulation. Complex forms emerge more often ...

Cis-genetic effects are key determinants of transcriptional divergence in discrete tissues and cell types. However, how cis- and trans-effects act across continuous trajectories of cellular differentiation in vivo is poorly understood. Here, we quantify al ...

One of the primary causes of non-uniform snowfall deposition on the ground in mountainous regions is the preferential deposition of snow, which results from the interaction of near-surface winds with topography and snow particles. However, producing high-r ...

Background & Aims: Current therapies for the treatment of alcohol-related liver disease (ALD) have proven largely ineffective. Patients relapse and the disease progresses even after liver transplantation. Altered epigenetic mechanisms are characteristic of ...

Gene regulatory networks (GRNs) play a crucial role in an organism's response to changing environmental conditions. Cellular behaviors typically result from the integration of multiple gene outputs, and their regulation often demands precise control of num ...

BackgroundIt is generally accepted that most evolutionary transformations at the phenotype level are associated either with rearrangements of genomic regulatory elements, which control the activity of gene networks, or with changes in the amino acid conten ...

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 ...

Temporal activation of Hox genes in mouse pseudo-embryos in vitro initiates at the anterior part of the cluster and is accompanied by asymmetric loading of cohesin. Posterior CTCF sites then successively act as transient insulators, regulating the timed tr ...

Functional materials that enable many technological applications in our everyday lives owe their unique properties to defects that are carefully engineered and incorporated into these materials during processing. However, optimizing and characterizing thes ...

Long-term consumption of lipid-rich foods can contribute to common metabolic diseases and systemic low-grade inflammation. However, dietary responses and the development of non-communicable diseases are shaped by genetic factors and gene-by-environment int ...

DNA biosensors are promising candidates for the development of point-of-care diagnosis methods. They can be inserted in microfluidic platforms, are often non-expensive, and can be produced for a variety of targeted analytes. However, their development face ...

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 ...

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 ...

Mutations to gene regulatory networks can be maladaptive or a source of evolutionary novelty. Epistasis con-founds our understanding of how mutations affect the expression patterns of gene regulatory networks, a chal-lenge exacerbated by the dependence of ...

UCNEbase – a database of ultra-conserved non-coding elements and genomic regulatory blocks

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Ancestral genome reconstruction enhances transposable element annotation by identifying degenerate integrants

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

Decoding Chromatin Ubiquitylation: A Chemical Biology Perspective

Formaldehyde regulates one-carbon metabolism and epigenetics

Toward universal cell embeddings: integrating single-cell RNA-seq datasets across species with SATURN

The cost of adaptability: resource availability constrains functional stability under pulsed disturbances

Meeting our Makers: Uncovering the cis-regulatory activity of transposable elements using statistical learning

The dynamic genetic determinants of increased transcriptional divergence in spermatids

Snowfall deposition in mountainous terrain: a statistical downscaling scheme from high-resolution model data on simulated topographies

Anti-miR-873-5p improves alcohol-related liver disease by enhancing hepatic deacetylation via SIRT1

Quantitative characterization of the inorganic phosphate gene regulatory networks in S. cerevisiae and bottom up engineering an orthogonal gene network

Wide-scale identification of novel/eliminated genes responsible for evolutionary transformations

Chromatin modules and their implication in genomic organization and gene regulation

Sequential and directional insulation by conserved CTCF sites underlies the Hox timer in stembryos

AiiDA-defects: an automated and fully reproducible workflow for the complete characterization of defect chemistry in functional materials

Identifying genetic and dietary modulators of metabolic disorders using systems genetics

Tailoring the Hybridization Density of DNA Biosensors through Tunable Surface Functionalization

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

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

Environment-dependent epistasis increases phenotypic diversity in gene regulatory networks