Systems Chronobiology: Global Analysis of Gene Regulation in a 24-Hour Periodic World

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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 ...

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 ...

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 ...

Earth rotation around its axis imposes a 24-hour rhythmicity to all life on the planet. Rather than passively responding to these periodic changes, nature has given us an internal timekeeper, the circadian clock, to anticipate to our advantage the fluctuat ...

The circadian clock modulates human physiology. However, the organization of tissue-specific gene expression rhythms and how these depend on age and sex is not defined in humans. We combined data from the Genotype-Tissue Expression (GTEx) project with an a ...

The synchronization of circadian clock depends on a central pacemaker located in the suprachiasmatic nuclei. However, the potential feedback of peripheral signals on the central clock remains poorly characterized. To explore whether peripheral organ circad ...

Wearable biosensors and smartphone applications can measure physiological variables over multiple days in free-living conditions. We measure food and drink ingestion, glucose dynamics, physical activity, heart rate (HR), and heart rate variability (HRV) in ...

Nerve injuries cause permanent neurological disability due to limited axonal regeneration. Injury-dependent and-independent mechanisms have provided important insight into neuronal regeneration, however, common denominators underpinning regeneration remain ...

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 ...

Efficient numerical simulations of coupled multi-component systems can be particularly challenging. This is mostly due to the complexity of their solutions, as mutual interactions may cause emergent behaviors, including synchronization and instabilities. V ...

Background: Transposable elements (TEs) have colonized the genomes of most metazoans, and many TE-embedded sequences function as cis-regulatory elements (CREs) for genes involved in a wide range of biological processes from early embryo- genesis to innate ...

Aging is characterized by a decline in tissue function, but the underlying changes at cellular resolution across the organism remain unclear. Here, we present the Aging Fly Cell Atlas, a single-nucleus transcriptomic map of the whole aging Drosophila. We c ...

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 ...

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 ...

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, ...

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 ...

The ipRGCs in the human eye mediate several effects on people, such as alertness and circadian rhythms. The spectral, temporal and spatial characteristics of light influence the magnitude of these effects. To facilitate the anticipation of the ipRGC-influe ...

In eukaryotes, RNA is synthesised in the nucleus, spliced, and exported to the cytoplasm where it is translated and finally degraded. Any of these steps could be subject to temporal regulation during the circadian cycle, resulting in daily fluctuations of ...

Enhancing lighting conditions in institutions for individuals with dementia improves their sleep, circadian rhythms and well-being. Here, we report first findings that exposure to brighter light during daytime may support the immune response to the annual ...

Systems Chronobiology: Global Analysis of Gene Regulation in a 24-Hour Periodic World

Chattez avec Graph Search

Decoding Chromatin Ubiquitylation: A Chemical Biology Perspective

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

The dynamic genetic determinants of increased transcriptional divergence in spermatids

Formaldehyde regulates one-carbon metabolism and epigenetics

Statistical physics of periodic biological processes

Sex-dimorphic and age-dependent organization of 24-hour gene expression rhythms in humans

Mice with humanized livers reveal the role of hepatocyte clocks in rhythmic behavior

Uncovering personalized glucose responses and circadian rhythms from multiple wearable biosensors with Bayesian dynamical modeling

The circadian clock time tunes axonal regeneration

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

Reduced order models for coupled systems

Statistical learning quantifies transposable element-mediated cis-regulation

Aging Fly Cell Atlas identifies exhaustive aging features at cellular resolution

Chromatin modules and their implication in genomic organization and gene regulation

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

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

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

A simulation tool for building and lighting design considering ipRGC-influenced light responses

Comprehensive analysis of the circadian nuclear and cytoplasmic transcriptome in mouse liver

Preliminary evidence that daily light exposure enhances the antibody response to influenza vaccination in patients with dementia