(Press-News.org)
Chinese researchers have developed a groundbreaking technology that sheds light on how the three-dimensional (3D) organization of plant genomes influences gene expression—especially in photosynthesis.
The research, which was led by Prof. XIAO Jun at the Institute of Genetics and Developmental Biology of the Chinese Academy of Sciences, in collaboration with BGI Research, was published in Science Advances on May 30.
The innovative method not only provides a more precise tool for understanding the intricate 3D interactions between genes, but also highlights the critical role of long-range chromatin interactions in gene regulation.
Within plant nuclei, chromatin is not arranged randomly. Instead, chromatin—a combination of DNA and proteins—forms a carefully organized 3D structure that plays a vital role in regulating biological processes.
Although scientists have identified many long-range regulatory elements involved in key agronomic traits, current tools such as Hi-C, ChIA-PET, HiChIP, and OCEAN-C struggle to capture active chromatin interactions at high resolution in a cost-effective and unbiased manner. Moreover, the mechanisms by which these structures form and are maintained—and how they influence gene expression—have largely been unclear.
To overcome these limitations, the researchers integrated ATAC-seq, which detects open (active) chromatin regions, with Hi-C, which maps genome-wide chromatin interactions. The resulting technique, called Transposase-Accessible Chromosome Conformation Capture (TAC-C), enables targeted capture of interactions in accessible chromatin regions while offering improved resolution and efficiency at lower sequencing depths compared to traditional methods.
The researchers used TAC-C to successfully build high-quality 3D chromatin interaction maps for four major crop species, demonstrating the robustness of the tool. Their analysis revealed that genomic regions acting as interaction hubs are associated with higher gene expression and reduced sequence variation, suggesting their importance as regulatory elements. These chromatin “anchor” regions are also significantly enriched with quantitative trait loci (QTLs) and expression QTLs (eQTLs), providing strong spatial evidence that 3D chromatin interactions connect distant regulatory elements to their target genes, thereby contributing to phenotypic variation.
In hexaploid wheat, the researchers observed asymmetrical chromatin interactions among the A, B, and D subgenomes, driven by transposable element insertions and sequence variations in anchor regions. This asymmetry led to biased expression of homoeologous genes across subgenomes.
In animals, chromatin loop formation is regulated by the CTCF/cohesin complex. In contrast, the mechanisms governing chromatin architecture in plants have not been well understood. In this study, though, the researchers found a concentration of binding sites for the SBP, MYB, Dof, ERF, and GATA transcription factor (TF) families at chromatin interaction anchors. Among these, chromatin loops enriched with SBP-binding motifs showed stronger interactions and were located in functionally active regions.
Further analysis of mutants lacking the SBP TFs TaSPL7 and TaSPL15 revealed loss of chromatin loops associated with several photosynthesis-related genes, including TaCKX11-B, TaSGR-5D, TaNRR-A1, and TaTK-2D. This led to altered gene expression and impacted leaf development and photosynthetic efficiency.
SBP TFs are plant-specific and play essential roles in the development of leaves, flowers, roots, and fruits, as well as the transition between vegetative and reproductive growth. This study suggests that SPL-mediated changes in 3D chromatin architecture may be involved in the regulation of plant development.
In summary, this study offers a clear example of how plant TFs regulate photosynthesis-related genes through 3D organization of the genome. It also shows how the new TAC-C technology opens the door to deeper understanding of long-range genetic regulation in plants and may guide future crop improvement efforts.
END
The calcitic layers of the eggshells of archosaurs (including crocodilians and birds) and turtles are composed of distinctive crystalline structures known as eggshell units. Those growing from the shell membrane are called primary eggshell units (PEUs), while those forming within the calcitic layer are called secondary eggshell units (SEUs). Although rare in modern bird eggs, SEUs are common in dinosaur eggs. Due to the lack of in-depth research on this structure, however, scientists are uncertain whether they are biogenic or abiogenic in origin.
To tackle this issue, an international ...
The University of Pittsburgh’s Natasa Miskov-Zivanov, assistant professor of electrical and computer engineering, has received a prestigious Faculty Early Career Development (CAREER) Award of $581,503 from the National Science Foundation (NSF) for her project titled “Artificial Intelligence-Driven Framework for Efficient and Explainable Immunotherapy Design.” Through her novel approach and the development of an automated system that leverages AI and knowledge graphs to design more effective lymphocytes, she hopes to transform the ...
More than two decades ago, Denise Hines began investigating a topic most researchers wouldn’t touch: men as victims of intimate partner violence (IPV). She and collaborator Emily Douglas were the first in the U.S. to earn federal funding for this line of research, publishing studies that challenged entrenched gender assumptions and provoked debate in the field.
Their new book, The Routledge Handbook of Men’s Victimization in Intimate Relationships, offers the most thorough international synthesis ...
UNIVERSITY OF WISCONSIN-OSHKOSH – A new study led by University of Wisconsin-Oshkosh geologist Timothy Paulsen and University of Colorado Boulder thermochronologist Jeff Benowitz advances the understanding of the geologic history of Transantarctic Mountains bedrock, with implications for understanding the evolution of landscapes lying beneath the ice sheets covering Antarctica.
The team of researchers analyzed the chemistry of mineral grains commonly found in igneous rocks, like granite, from the Transantarctic Mountains. The research team includes other scientists from the University of Arizona, St. Louis University, The Ohio State University, and the University of Alaska ...
In the world of black holes, there are generally three size categories: stellar-mass black holes (about five to 50 times the mass of the sun), supermassive black holes (millions to billions of times the mass of the sun), and intermediate-mass black holes with masses somewhere in between.
While we know that intermediate-mass black holes should exist, little is known about their origins or characteristics—they are considered the rare “missing links” in black hole evolution.
However, four new studies have ...
Below ocean wind farms, oil rigs and other offshore installations are mammoth networks of underwater structures, including pipelines, anchors, risers and cables, that are essential to harness the energy source. But much like terrestrial structures, these subsea constructions are also vulnerable to natural events, like submarine landslides, that can hamper the productivity of installations below the sea.
Researchers at Texas A&M may now be able to accurately predict the occurrence of marine landslides using underwater site characterization data.
“One ...
America’s primary care doctors are burning out, cutting back their hours, and leaving their practices early, driven in part by the demands of handling the flood of digital messages from their patients.
But a trio of new University of Michigan studies offer hope for easing this crisis, and improving both the care that patients get and the work lives of those who provide it. The studies could help primary care clinics nationwide take steps to keep the bedrock of American health care from crumbling further.
All three papers, published in the Journal of ...
What if some of the smallest ocean currents turned out to be some of the most powerful forces shaping our planet’s climate?
This question is at the center of new research co-led by Texas A&M University Department of Oceanography Associate Professor Jinbo Wang, whose work is featured on the cover of the April 17 issue of Nature. It’s a big moment for Wang and his colleagues and the global science community — marking a milestone in a billion-dollar, international water mission two decades in the making, and reflecting Texas A&M University’s long-term strategy ...
The job of a catalyst is to ultimately speed up reactions, which could reduce an hour-long process into several minutes. It has recently been shown that using external magnetic fields to modulate spin states of single-atom catalysts (SACs) is highly effective - enhancing oxygen evolution reaction magnetocurrent by a staggering 2,880%.
With this in mind, researchers at Tohoku University proposed a completely novel strategy to apply an external magnetic field to modulate spin states, and thereby improve electrocatalytic performance. This study provides valuable insights regarding the development of efficient and sustainable electrochemical technologies ...
Researchers have proposed an metasurface-integrated quantum analog computing system. This system ingeniously combines multi-channel metasurfaces with quantum entanglement sources, enabling quantitative phase reconstruction with high signal-to-noise ratio at low signal photon levels. Traditional phase reconstruction often involves complex operation steps, while this technology effectively simplifies the complexity of traditional phase reconstruction. It shows application potential in multiple important fields. For example, in the field of optical chips, it helps improve the performance ...
