EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era

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Circular RNAs (circRNAs) are covalently closed back‐splicing products involved in the regulation of different cellular processes, and their dysregulation has been frequently observed in cancer cells. CircCDYL, a circRNA derived from the back‐splicing of CD ...

Chromatin-modifying enzymes target distinct residues within histones to finetune gene expression profiles. SIRT7 is an NAD+-dependent deacylase often deregulated in cancer, which deacetylates either H3 lysine 36 (H3K36) or H3K18 with high specificity withi ...

Wastewater resulting from human activities must be treated to minimize the impact on the receiving ecosystems. One of such potential impacts in lakes and other water bodies is eutrophication, an excessive increase in their nitrogen and phosphorus content. ...

The precise control of transcription factor (TF) concentrations is crucial for While TF concentration gradients are well-characterized in model organisms like Drosophila and Caenorhabditis elegans, their quantitative relationship with genomic occupancy in ...

Telomeres are the nucleoprotein structures at chromosome ends. Telomeres are particularly sensitive to oxidative stress, which can induce telomere damage, shortening, and premature cellular senescence. How oxidative damage influences telomere structure has ...

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 ...

The control of eukaryotic gene expression is intimately connected to highly dynamic chromatin structures. Gene regulation relies on activator and repressor transcription factors (TFs) that induce local chromatin opening and closing. However, it is unclear ...

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 ...

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 ...

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 ...

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 ...

Viral metagenomics is a useful tool for detecting multiple human viruses in urban sewage. However, more refined protocols are required for its effective use in disease surveillance. In this study, we investigated the performance of three different preampli ...

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 ...

How chronic mutational processes and punctuated bursts of DNA damage drive evolution of the cancer genome is poorly understood. Here, we demonstrate a strategy to disentangle and quantify distinct mechanisms underlying genome evolution in single cells, dur ...

Vibrio cholerae has caused seven cholera pandemics in the past two centuries. The seventh and ongoing pandemic has been particularly severe on the African continent. Here, we report long read-based genome sequences of six V. cholerae strains isolated in th ...

Light-controlled transcriptional activation is a commonly used optogenetic strategy that allows researchers to regulate gene expression with high spatiotemporal precision. The vast majority of existing tools are, however, limited to light-triggered inducti ...

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 ...

High-throughput transcriptomics is of increasing fundamental biological and clinical interest. The generation of molecular data from large collections of samples, such as biobanks and drug libraries, is boosting the development of new biomarkers and treatm ...

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 ...

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 ( ...

EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era

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CircCDYL Association With hnRNPL Modulates CDYL Isoform Switching in Breast Cancer Cells

Structural basis of SIRT7 nucleosome engagement and substrate specificity

Modelling the metabolism of the polyphosphate-accumulating organism Candidatus Accumulibacter

The Regulation of Transcription Factors Binding Site Occupancies by Their Concentrations

Oxidative stress at telomeres triggers internal DNA loops, TRF1 dissociation, and TRF2-dependent R-loops

Ancestral genome reconstruction enhances transposable element annotation by identifying degenerate integrants

Individual transcription factors modulate both the micromovement of chromatin and its long-range structure

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

Decoding Chromatin Ubiquitylation: A Chemical Biology Perspective

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

Formaldehyde regulates one-carbon metabolism and epigenetics

Comparison of Three Viral Nucleic Acid Preamplification Pipelines for Sewage Viral Metagenomics

The dynamic genetic determinants of increased transcriptional divergence in spermatids

Single-mitosis dissection of acute and chronic DNA mutagenesis and repair

Genome sequences of Vibrio cholerae strains isolated in the DRC between 2009 and 2012

A modular toolbox for the optogenetic deactivation of transcription

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

Multi-well plate lid for single-step pooling of 96 samples for high-throughput barcode-based sequencing

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

Inheritance of H3K9 methylation regulates genome architecture in Drosophila early embryos