Nav: Home

Biologists capture fleeting interactions between regulatory proteins and their genome-wide targets

March 02, 2020

New York University biologists captured highly transient interactions between transcription factors--proteins that control gene expression--and target genes in the genome and showed that these typically missed interactions have important practical implications. In a new study published in Nature Communications, the researchers developed a method to capture transient interactions of NLP7, a master transcription factor involved in nitrogen use in plants, revealing that the majority of a plant's response to nitrogen is controlled by these short-lived regulatory interactions.

"Our approaches to capturing transient transcription factor-target interactions genome-wide can be applied to validate dynamic interactions of transcription factors for any pathway of interest in agriculture or medicine," said Gloria Coruzzi, Carroll & Milton Petrie Professor in NYU's Department of Biology and Center for Genomics and Systems Biology and the paper's senior author.

Dynamic interactions between regulatory proteins and DNA are important for triggering controlled expression of genes into RNA in response to a changing cellular or external environment. However, the underlying transient interactions between transcription factors and their genome-wide targets have been largely missed, as current biochemical methods require stable--not fleeting--interactions between a transcription factor and its DNA target.

In the Nature Communications study, the researchers witnessed these elusive transient interactions between NLP7, a master transcription factor in plants that regulates genes involved in nitrogen uptake for plant growth, and its target genes. Nitrogen is a key nutrient for plant development and is found in soil and fertilizer.

The researchers captured highly transient interactions of NLP7 with genome-wide targets that even defied capture by biochemical detection methods performed within minutes of NLP7 nuclear import. They did this by fusing NLP7 to a DNA methylation enzyme from bacteria, which they then induced to enter the nucleus of a plant cell. At any time NLP7 touched a gene--even briefly--it would leave a permanent methylation mark on the DNA. They also showed that this highly transient interaction between NLP7 and its target genes in the genome led to new and continued transcription of the gene into RNA.

"We found that more than 50 percent of the genes regulated by NLP7 in whole plants involve highly transient transcription factor-DNA interactions that occur within five minutes of controlled NLP7 nuclear import captured in isolated plant cells. Moreover, the transient NLP7 binding activates a transcriptional cascade that regulates more than 50 percent of the nitrogen responsive genes in whole plant roots," explained Coruzzi.

Given that more than half of gene responses to nitrogen in plants are controlled by transient interactions with NLP7, the researchers note that the discovery of these elusive genome-wide targets of NLP7 have implications for improving nitrogen use efficiency, which can benefit agriculture and sustainability.
In addition to Coruzzi, study authors include José Miguel Alvarez of NYU's Center for Genomics and Systems Biology and Universidad Mayor in Chile; Anna-Lena Schinke, Matthew Brooks, Angelo Pasquino, and Lauriebeth Leonelli of NYU's Center for Genomics and Systems Biology; Kranthi Varala of Purdue University; Alaeddine Safi, Gabriel Krouk of CNRS in Montpellier, France and Anne Krapp of INRA Versailles, France. The research was supported by the National Institutes of Health's National Institute of General Medical Sciences (GM032877; F32GM116347) and National Science Foundation's Plant Genome Research Program (IOS-1339362), and in part by the Laboratoire International Associé (LIA-CoopNet) funded by the Centre National de Recherche Scientifique (CNRS), and LabEx Saclay Plant Sciences-SPS (ANR-10-LABX-0040-SPS).

New York University

Related Dna Articles:

Zigzag DNA
How the cell organizes DNA into tightly packed chromosomes. Nature publication by Delft University of Technology and EMBL Heidelberg.
Scientists now know what DNA's chaperone looks like
Researchers have discovered the structure of the FACT protein -- a mysterious protein central to the functioning of DNA.
DNA is like everything else: it's not what you have, but how you use it
A new paradigm for reading out genetic information in DNA is described by Dr.
A new spin on DNA
For decades, researchers have chased ways to study biological machines.
From face to DNA: New method aims to improve match between DNA sample and face database
Predicting what someone's face looks like based on a DNA sample remains a hard nut to crack for science.
Self-healing DNA nanostructures
DNA assembled into nanostructures such as tubes and origami-inspired shapes could someday find applications ranging from DNA computers to nanomedicine.
DNA design that anyone can do
Researchers at MIT and Arizona State University have designed a computer program that allows users to translate any free-form drawing into a two-dimensional, nanoscale structure made of DNA.
DNA find
A Queensland University of Technology-led collaboration with University of Adelaide reveals that Australia's pint-sized banded hare-wallaby is the closest living relative of the giant short-faced kangaroos which roamed the continent for millions of years, but died out about 40,000 years ago.
DNA structure impacts rate and accuracy of DNA synthesis
DNA sequences with the potential to form unusual conformations, which are frequently associated with cancer and neurological diseases, can in fact slow down or speed up the DNA synthesis process and cause more or fewer sequencing errors.
Changes in mitochondrial DNA control how nuclear DNA mutations are expressed in cardiomyopathy
Differences in the DNA within the mitochondria, the energy-producing structures within cells, can determine the severity and progression of heart disease caused by a nuclear DNA mutation.
More DNA News and DNA Current Events

Trending Science News

Current Coronavirus (COVID-19) News

Top Science Podcasts

We have hand picked the top science podcasts of 2020.
Now Playing: TED Radio Hour

Listen Again: Reinvention
Change is hard, but it's also an opportunity to discover and reimagine what you thought you knew. From our economy, to music, to even ourselves–this hour TED speakers explore the power of reinvention. Guests include OK Go lead singer Damian Kulash Jr., former college gymnastics coach Valorie Kondos Field, Stockton Mayor Michael Tubbs, and entrepreneur Nick Hanauer.
Now Playing: Science for the People

#562 Superbug to Bedside
By now we're all good and scared about antibiotic resistance, one of the many things coming to get us all. But there's good news, sort of. News antibiotics are coming out! How do they get tested? What does that kind of a trial look like and how does it happen? Host Bethany Brookeshire talks with Matt McCarthy, author of "Superbugs: The Race to Stop an Epidemic", about the ins and outs of testing a new antibiotic in the hospital.
Now Playing: Radiolab

Dispatch 6: Strange Times
Covid has disrupted the most basic routines of our days and nights. But in the middle of a conversation about how to fight the virus, we find a place impervious to the stalled plans and frenetic demands of the outside world. It's a very different kind of front line, where urgent work means moving slow, and time is marked out in tiny pre-planned steps. Then, on a walk through the woods, we consider how the tempo of our lives affects our minds and discover how the beats of biology shape our bodies. This episode was produced with help from Molly Webster and Tracie Hunte. Support Radiolab today at