A regulatory cascade of three transcription factors in a single specific...
Homeobox proteins are critical regulators of developmental gene transcription and cell specification. Many insights into transcriptional regulation have been gained from studies in the nematode...
View ArticleEnhanced Y1H assays for Arabidopsis
We present an Arabidopsis thaliana full-length transcription factor resource of 92% of root stele-expressed transcription factors and 74.5% of root-expressed transcription factors. We demonstrate its...
View ArticleAn encyclopedia of mouse DNA elements (Mouse ENCODE)
To complement the human Encyclopedia of DNA Elements (ENCODE) project and to enable a broad range of mouse genomics efforts, the Mouse ENCODE Consortium is applying the same experimental pipelines...
View ArticleYeast one-hybrid assays: A historical and technical perspective
Since its development about two decades ago, the yeast one-hybrid (Y1H) assay has become an important technique for detecting physical interactions between sequence-specific regulatory transcription...
View ArticleHiTC : Exploration of High-Throughput 'C' experiments
The R/Bioconductor package HiTC facilitates the exploration of high-throughtput 3C-based data. It allows users to import and export 'C' data, to transform, normalize, annotate and visualize...
View ArticleIterative correction of Hi-C data reveals hallmarks of chromosome organization
Extracting biologically meaningful information from chromosomal interactions obtained with genome-wide chromosome conformation capture (3C) analyses requires the elimination of systematic biases. We...
View Article3C-based technologies to study the shape of the genome
Guest editors' introduction to November 2012 issue of Methods, which provides detailed and up-to-date lab protocols of the many 3C (chromosome conformation capture) methodologies, provided by expert...
View ArticleCorrelated alterations in genome organization, histone methylation, and...
Hutchinson-Gilford progeria syndrome (HGPS) is a premature aging disease that is frequently caused by a de novo point mutation at position 1824 in LMNA. This mutation activates a cryptic splice donor...
View ArticleFrom cells to chromatin: Capturing snapshots of genome organization with 5C...
In eukaryotes, genome organization can be observed on many levels and at different scales. This organization is important not only to reduce chromosome length but also for the proper execution of...
View ArticleAnalysis of long-range chromatin interactions using Chromosome Conformation...
Chromosome Conformation Capture, or 3C, is a pioneering method for investigating the three-dimensional structure of chromatin. 3C is used to analyze long-range looping interactions between any pair of...
View ArticleAn integrated encyclopedia of DNA elements in the human genome
The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically...
View ArticleThe Hierarchy of the 3D Genome
Mammalian genomes encode genetic information in their linear sequence, but appropriate expression of their genes requires chromosomes to fold into complex three-dimensional structures. Transcriptional...
View ArticleIntegration of Metabolic and Gene Regulatory Networks Modulates the C....
Expression profiles are tailored according to dietary input. However, the networks that control dietary responses remain largely uncharacterized. Here, we combine forward and reverse genetic screens...
View ArticleComplex expression dynamics and robustness in C. elegans insulin networks
Gene families expand by gene duplication and resulting paralogs diverge through mutation. Functional diversification can include neo-functionalization as well as sub-functionalization of ancestral...
View ArticleA compendium of Caenorhabditis elegans RNA binding proteins predicts...
Gene expression is regulated at multiple levels, including transcription and translation, as well as mRNA and protein stability. Although systems-level functions of transcription factors and microRNAs...
View ArticleDiet-Induced Developmental Acceleration Independent of TOR and Insulin in C....
Dietary composition has major effects on physiology. Here, we show that developmental rate, reproduction, and lifespan are altered in C. elegans fed Comamonas DA1877 relative to those fed a standard...
View ArticleExploring the three-dimensional organization of genomes: interpreting...
How DNA is organized in three dimensions inside the cell nucleus and how this affects the ways in which cells access, read and interpret genetic information are among the longest standing questions in...
View ArticleArchitectural Protein Subclasses Shape 3D Organization of Genomes during...
Understanding the topological configurations of chromatin may reveal valuable insights into how the genome and epigenome act in concert to control cell fate during development. Here, we generate...
View ArticleHandbook of Systems Biology: Concepts and Insights
Publisher's description: This book provides an entry point into Systems Biology for researchers in genetics, molecular biology, cell biology, microbiology and biomedical science to understand the key...
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