Gene Regulatory Networks for Key Nutrient Responses Revealed

Scientists Develop Methods to Validate Gene Regulation Networks

A team of biologists and computer scientists has mapped out a network of interactions for how plant genes coordinate their response to nitrogen, a crucial nutrient and the main component of fertilizer.

Findings Reveal How Plants Respond to Key Nutrient in Fertilizer

A team of biologists and computer scientists has mapped out a network of interactions for how plant genes coordinate their response to nitrogen, a crucial nutrient and the main component of fertilizer. The work, published in the journal Nature Communications, offers a potential framework and more efficient methods that can be used to investigate a wide-range of vital pathways in any organism.

“The sequencing of whole genomes has transformed life sciences, leading to breakthroughs in medicine, agriculture, and basic research,” explains Matthew Brooks, an NIH-postdoctoral fellow in New York University’s Department of Biology and the paper’s lead author. “The challenge now is to determine how the genes that are encoded by an organism are regulated and work together in networks that allow plants and animals to respond to their environment.”

The scientists, working in NYU’s Center for Genomics and Systems Biology, focused on gene regulatory networks, which consist of transcription factors and the target genes that they regulate. These gene regulatory networks enable organisms to adapt to fluctuating surroundings.

Snake venom genomics provides important insights

New insights into chromosome evolution, venom regulation in snakes

How do snake genomes direct the production of deadly venom toxins and other key extreme features of snakes?

Snake genomes encode the secrets to their unique and often extreme adaptations, but genome resources for snakes and other reptiles have lagged behind their mammal and bird counterparts.

In a new paper, a team of biologists led by Todd Castoe, associate professor of biology at The University of Texas at Arlington, addressed these questions by generating and analyzing the first most complete chromosome-level genome for a snake – the prairie rattlesnake (Crotalus viridis). Their work, “The origins and evolution of chromosomes, dosage compensation, and mechanisms underlying venom regulation in snakes,” is published in the April issue of Genome Research, the scientific journal published by Cold Spring Harbor Laboratory.

How transcription shapes the genome

The role of transcription in shaping the spatial organization of the genome

Bas van Steensel & Eileen E. M. Furlong

Nature Reviews Molecular Cell Biology (Review Article)

Abstract—The spatial organization of the genome into compartments and topologically associated domains can have an important role in the regulation of gene expression. But could gene expression conversely regulate genome organization? Here, we review recent studies that assessed the requirement of transcription and/or the transcription machinery for the establishment or maintenance of genome topology. The results reveal different requirements at different genomic scales. Transcription is generally not required for higher-level genome compartmentalization, has only moderate effects on domain organization and is not sufficient to create new domain boundaries. However, on a finer scale, transcripts or transcription does seem to have a role in the formation of subcompartments and subdomains and in stabilizing enhancer–promoter interactions. Recent evidence suggests a dynamic, reciprocal interplay between fine-scale genome organization and transcription, in which each is able to modulate or reinforce the activity of the other.

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