Topological Domains, Metagenes, and the Emergence of Pleiotropic Regulations at Hox Loci

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In this study, Amandio et al. sought to understand the functions of the highly conserved CTCF sites distributed over the Hox gene clusters. The authors produced an allelic series of cumulative in cis mutations in these sites, up to the abrogation of CTCF b ...

Biogenesis of eukaryotic box C/D small nucleolar ribonucleoproteins initiates co-transcriptionally and requires the action of the assembly machinery including the Hsp90/R2TP complex, the Rsa1p:Hit1p heterodimer and the Bcd1 protein. We present genetic inte ...

Vertebrate genomes are partitioned into contact domains defined by enhanced internal contact frequency and formed by two principal mechanisms: compartmentalization of transcriptionally active and inactive domains, and stalling of chromosomal loop-extruding ...

Single-molecule measurements provide detailed mechanistic insights into molecular processes, for example in genome regulation where DNA access is controlled by nucleosomes and the chromatin machinery. However, real-time single-molecule observations of nucl ...

Our genome is a long sequence of DNA that contains all the information to be able to constitute a living organism like us, similarly to what the letters in a book do to create a story. This sequence, which is a stretch of molecules called nucleotides, is a ...

In cancer cells, enhancer hijacking mediated by chromosomal alterations and/or increased deposition of acetylated histone H3 lysine 27 (H3K27ac) can support oncogene expression. However, how the chromatin conformation of enhancer-promoter interactions is a ...

The circadian clock drives extensive temporal gene expression programs controlling daily changes in behavior and physiology. In mouse liver, transcription factors dynamics, chromatin modifications, and RNA Polymerase II (PolII) activity oscillate throughou ...

Regulation of gene expression is essential for the functioning of all eukaryotic organisms. Understanding gene expression regulation requires determining which proteins interact with regulatory elements in chromatin. MS-based analysis of chromatin has emer ...

Author summary Transcription of genes by the RNA polymerase II enzyme initiates at a genomic region termed the core promoter. The core promoter is a regulatory region that may contain diverse short DNA sequence motifs/elements that confer specific properti ...

Advances in single-cell genomics now enable large-scale comparisons of cell states across two or more experimental conditions. Numerous statistical tools are available to identify individual genes, proteins or chromatin regions that differ between conditio ...

Topological Domains, Metagenes, and the Emergence of Pleiotropic Regulations at Hox Loci

Chattez avec Graph Search

Sequential in cis mutagenesis in vivo reveals various functions for CTCF sites at the mouse HoxD cluster

The box C/D snoRNP assembly factor Bcd1 interacts with the histone chaperone Rtt106 and controls its transcription dependent activity

CTCF loss has limited effects on global genome architecture in Drosophila despite critical regulatory functions

Multiplexed Single-Molecule Experiments Reveal Nucleosome Invasion Dynamics of the Cas9 Genome Editor

Toward a mechanistic understanding of variable chromatin modules

Histone acetylation dynamics modulates chromatin conformation and allele-specific interactions at oncogenic loci

Oscillating and stable genome topologies underlie hepatic physiological rhythms during the circadian cycle

Chromatin Proteomics to Study Epigenetics - Challenges and Opportunities

Computational identification and experimental characterization of preferred downstream positions in human core promoters

Prioritization of cell types responsive to biological perturbations in single-cell data with Augur