Virulence Regulator EspR of Mycobacterium tuberculosis Is a Nucleoid-Associated Protein

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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 ...

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 ...

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 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 ...

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 ...

Bacteria are ubiquitous single cellular organisms. Compared to eukaryotic cells, bacteria have two unique characteristics: the membrane-less nucleoid and the cell wall built of peptidoglycan (PG). In most bacteria, a single circular chromosome is compacted ...

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 ...

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 ...

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 ...

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 ...

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 ( ...

Cyclic GMP-AMP synthase (cGAS) senses aberrant DNA during infection, cancer and inflammatory disease, and initiates potent innate immune responses through the synthesis of 2 ' 3 '-cyclic GMP-AMP (cGAMP)1-7. The indiscriminate activity of cGAS towards DNA d ...

Cells are the smallest operational units of living systems. Through synthesis of various biomolecules and exchange of signals with the environment, cells tightly regulate their composition to realize a specific functional state. The transformation of a cel ...

Mycobacterium Tuberculosis is a highly effective pathogen infecting nearly a third of the world's population. An M. tuberculosis infection starts when droplets containing bacteria enter an individual's lungs. The first host cells to contact the bacteria ar ...

Steroid hormone receptors (HRs) are ligand-activated transcription factors that play a pivotal role in breast development and carcinogenesis. It is well established that estrogen receptor (ER) signaling is a major proliferative driver in estrogen receptor ...

Genes implicated in translation control have been associated with autism spectrum disorders (ASDs). However, some important genetic causes of autism, including the 16p11.2 microdeletion, bear no obvious connection to translation. Here, we use proteomics, g ...

The early branching eukaryote Naegleria gruberi can transform transiently from an amoeboid life form lacking centrioles and flagella to a flagellate life form where these elements are present, followed by reversion to the amoeboid state. The mechanisms imp ...

High throughput wide-field second harmonic imaging enables the label-free imaging of interfacial (< 3 nm thick) water, with a spatial resolution of similar to 370 nm using similar to 100 ms acquisition times per image. The obtained interfacial orientationa ...

Virulence Regulator EspR of Mycobacterium tuberculosis Is a Nucleoid-Associated Protein

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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

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

Ancestral genome reconstruction enhances transposable element annotation by identifying degenerate integrants

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

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

Resolving bacterial cell biology: from replisome dynamics to cell wall synthesis

Context transcription factors establish cooperative environments and mediate enhancer communication

Decoding Chromatin Ubiquitylation: A Chemical Biology Perspective

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

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

The dynamic genetic determinants of increased transcriptional divergence in spermatids

Inheritance of H3K9 methylation regulates genome architecture in Drosophila early embryos

The CRL5-SPSB3 ubiquitin ligase targets nuclear cGAS for degradation

Deciphering the nature of cell state transitions in single cells using quantitative modeling of temporal dynamics

Single-cell analysis of the interactions between Mycobacterium tuberculosis and macrophages

Androgen Receptor Signaling in in vivo models of Estrogen Receptor-positive Breast Cancer and Normal Breast Epithelium

The autism susceptibility kinase, TAOK2, phosphorylates eEF2 and modulates translation

Mechanisms of axoneme and centriole elimination in Naegleria gruberi

Quantified interface chemistry and biophysics via water imaging