Yeast Ppz1 protein phosphatase toxicity involves the alteration of multiple cellular targets

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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 ...

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 ...

Sophisticated genetic engineering tasks such as protein domain grafting and multi-gene fusions are hampered by the lack of suitable vector backbones. In particular, many restriction sites are in the backbone outside the polylinker region (multiple cloning ...

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 ...

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 ...

Atmospheric pressure low power plasma jets operating in noble gases are a widespread tool in plasma medicine studies. We present experimental results obtained in one such device, which combine physical, chemical and biological measurements to assess the ef ...

Although cardinal cortical interneuron identity is established upon cell-cycle exit, it remains unclear whether specific interneuron subtypes are pre-established, and if so, how their identity is maintained prior to circuit integration. We conditionally re ...

DNA mechanics plays a crucial role in many biological processes, including nucleosome positioning and protein-DNA interactions. It is believed that nature employs epigenetic modifications in DNA to further regulate gene expression. Moreover, double-strande ...

The ratio of nuclear content to cytoplasmic volume (N/C ratio) is a key regulator driving the maternal-to -zy-gotic transition in most animal embryos. Altering this ratio often impacts zygotic genome activation and de-regulates the timing and outcome of em ...

Tissues are organized in cellular niches, the composition and interactions of which can be investigated using spatial omics technologies. However, systematic analyses of tissue composition are challenged by the scale and diversity of the data. Here we pres ...

NOTCH1 is a well-established lineage specifier for T cells and among the most frequently mutated genes throughout all subclasses of T cell acute lymphoblastic leukemia (T-ALL). How oncogenic NOTCH1 signaling launches a leukemia-prone chromatin landscape du ...

All metazoan guts are subject to opposing pressures wherein the immune system must eliminate pathogens while tolerating the presence of symbiotic microbiota. The Imd pathway is an essential defense against invading pathogens in insect guts, but tolerance m ...

The transcription factor network required for primordial germ cell (PGC) specification is known to diverge in mammals. Here the authors show that hominidae-specific transposable element (TE) LTR5Hs becomes transcriptionally active during PGC specification, ...

The role and coexistence of oxidative stress (OS) and inflammation in type C hepatic encephalopathy (C HE) is a subject of intense debate. Under normal conditions the physiological levels of intracellular reactive oxygen species are controlled by the count ...

The vertebrate axis is segmented into repetitive structures, the vertebrae. In fish, these segmented structures are thought to form from the paraxial mesoderm and the adjacent notochord. Recent work revealed an autonomous patterning mechanism in the zebraf ...

Aggregated alpha-synuclein (alpha-synuclein) is the main component of Lewy bodies (LBs), Lewy neurites (LNs), and glial cytoplasmic inclusions (GCIs), which are pathological hallmarks of idiopathic Parkinson's disease (IPD) and multiple system atrophy (MSA ...

Compared to estrogen receptor-negative (ER-) breast cancer (BC), ER+ BC often manifests with a latent disease that recurs decades after initial diagnosis. The mechanisms governing dormancy and distant recurrence of ER+ tumors remain elusive due to the lack ...

Background RNA splicing is a key post-transcriptional mechanism that generates protein diversity and contributes to the fine-tuning of gene expression, which may facilitate adaptation to environmental challenges. Here, we employ a systems approach to study ...

We designed and engineered a dye production cassette encoding a heterologous pathway, including human tyrosine hydroxylase and Amanita muscaria 4,5-DOPA dioxygenase, for the biosynthesis of the betaxanthin family of plant and fungal pigments in mammalian c ...

Developmental genes are often controlled by large regulatory landscapes matching topologically associating domains (TADs). In various contexts, the associated chromatin backbone is modified by specific enhancer-enhancer and enhancer-promoter interactions. ...

Yeast Ppz1 protein phosphatase toxicity involves the alteration of multiple cellular targets

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

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

Minimal shuttle vectors for Saccharomyces cerevisiae

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

Context transcription factors establish cooperative environments and mediate enhancer communication

Combined Characterization of a Plasma Jet: FTIR, Chemical Surveys and Antibacterial Effect

Transcriptional maintenance of cortical somatostatin interneuron subtype identity during migration

cgNA+: A sequence-dependent coarse-grain model of double-stranded nucleic acids

The nuclear-to-cytoplasmic ratio drives cellularization in the close animal relative Sphaeroforma arctica

CellCharter reveals spatial cell niches associated with tissue remodeling and cell plasticity

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

Compartmentalized PGRP expression along the dipteran Bactrocera dorsalis gut forms a zone of protection for symbiotic bacteria

Human reproduction is regulated by retrotransposons derived from ancient Hominidae-specific viral infections

Central nervous system and systemic oxidative stress interplay with inflammation in a bile duct ligation rat model of type C hepatic encephalopathy

Reaction wavefront theory of notochord segment patterning

Pathological Relevance of Post-Translationally Modified Alpha-Synuclein (pSer87, pSer129, nTyr39) in Idiopathic Parkinson's Disease and Multiple System Atrophy

Intraductal xenografts model estrogen receptor-positive (ER+) breast cancer dormancy and reveal a critical role for epithelial-mesenchymal transition (EMT) in its establishment

Enteric infection induces Lark-mediated intron retention at the 5 ' end of Drosophila genes

Genetically encoded betaxanthin-based small-molecular fluorescent reporter for mammalian cells

A complex regulatory landscape involved in the development of mammalian external genitals