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Category: computing

CPSF73 activation and 3′ RNA polymerase II pausing are lost during readthrough transcription after heat shock

Here, we identified key signatures of transcriptional termination mechanisms that are altered by heat shock, enabling global readthrough of the 3′ends of mRNA genes. The Pol II 3′ pause is lost, CTD phosphorylation at Ser2 and Tyr1 changes, and endonucleolytic cleavage of the transcript is impaired, which is relieved by expression of RBBP6, a cleavage activator. Our data support a multifaceted mechanism of readthrough during stress, whereby changes to both Pol II and the termination machinery trigger transcription to bypass normal termination sites.

The stress-induced readthrough we observed was pervasive, with 85% of the analyzable genes showing downstream transcription after heat shock. There was no correlation with the level of transcription or activation/repression and no indication of any gene class specificity. Prior work has shown that genes with readthrough are largely overlapping between types of cellular stress.19 Moreover, only loose correlations have been found between sequence markers for termination, such as the strength of the PAS and/or flanking GA-rich regions, and readthrough transcription.26 Distinguishing characteristics of readthrough susceptibility for any given stress remain to be elucidated.

Our Pol II ChIP-seq data show that heat shock induces global loss of 3′ Pol II pausing. This occurred at genes with and without readthrough, indicating that lack of Pol II pausing is not sufficient to cause readthrough. This raises interesting questions about the relationship between Pol II deceleration and transcription termination mechanisms. Current models suggest the slowing of Pol II helps the 5′-to-3′ exonuclease XRN2 to degrade the nascent RNA, catch up to transcribing Pol II, and trigger the dissociation of the polymerase from the DNA.9,10,34 This model requires that nascent RNA cleavage occurs to generate the 5′ end for XRN2 to bind. For readthrough genes that retain RNA cleavage during heat shock, the failure of Pol II to decelerate could prevent XRN2 from “catching up,” thereby enabling downstream transcription. For readthrough genes that lose cleavage, Pol II deceleration likely enhances readthrough by having a fast-moving polymerase.

Dual-rail superconducting qubits generate high-fidelity logical entanglement, study finds

Quantum computers, systems that process information leveraging quantum mechanical effects, could outperform classical computers on some advanced tasks. These systems rely on qubits, the fundamental units of quantum information, that become linked via an effect known as quantum entanglement and share a unified quantum state.

Qubits are known to be highly sensitive to slight changes or disturbances in their surrounding environment, also referred to as noise. Noise can prompt them to lose quantum information via a process called decoherence, which in turn leads to errors.

In recent years, quantum scientists and engineers have introduced various approaches aimed at mitigating or correcting quantum errors, with the goal of realizing fault-tolerant quantum computing. Some of these approaches rely on so-called erasure qubits, qubits whose errors are easier to detect and locate in real time.

Tiny LED design could power next-generation technology

From 3D movie screens to augmented-reality devices, many modern technologies rely on our ability to manipulate light. Doing so in a cost-effective and efficient way, however, is often a formidable task. In an article published in Optics Letters, researchers from the University of Osaka announced a new light-emitting diode (LED) design that may help shrink complex optical systems into much smaller devices. The LED produces circularly polarized light using a built-in nanostructured surface, eliminating the need for bulky external optical components.

Circularly polarized light, whose electric field rotates like a corkscrew as it travels, is essential for technologies such as 3D displays, advanced imaging systems, and quantum communication tools. Traditionally, generating this kind of light requires optical components such as polarizers and special plates that modify the light’s phase. However, these components make devices larger, more complex, and harder to integrate.

“Our goal is to simplify the way circularly polarized light is produced,” says corresponding author Shuhei Ichikawa. “By integrating polarization control directly into the LED with a specially designed metasurface, we remove the need for additional optical components.”

Quantum computer accurately simulates real magnetic materials, reproducing national laboratory data

Studying and designing novel materials is a central application of quantum mechanics. Chemists, materials scientists, and physicists focus on subtle interactions in quantum materials and to uncover them they rely on sophisticated computational and experimental techniques. Computer simulations that connect microscopic quantum interactions to measurable material properties complement experimental data to connect structure to function—but classical computers can struggle to simulate those properties. Fortunately, scientists today have a new tool in their toolbox: quantum computers.

In new preprint, a team of researchers from Oak Ridge National Lab’s (ORNL’s) Quantum Science Center (QSC), Purdue University, Los Alamos Laboratory, the University of Illinois at Urbana-Champaign, the University of Tennessee, and IBM used quantum simulation to compute the energy-momentum spectrum of a well-studied magnetic material, KCuF3, showing strong agreement with the spectra measured via neutron scattering. The research is published on the arXiv preprint server.

The quantum simulations employed the IBM Quantum Heron processor, while the experimental data was acquired from neutron sources at the Spallation Neutron Source (SNS) at ORNL and at the Rutherford Appleton Laboratory in the United Kingdom. This work serves as another realization of Richard Feynman’s vision: the use of a well-controlled, programmable quantum system to simulate the properties of a quantum system of interest.

Small RNAs offer new clues to schizophrenia and bipolar disorder

For decades, scientists studying brain disorders have focused almost exclusively on proteins and the genes encoding them. Now, research from Thomas Jefferson University’s Computational Medicine Center suggests that several classes of small regulatory molecules, fittingly known as small RNAs, may play a much larger role in schizophrenia and bipolar disorder, and in a healthy brain, than previously thought.

In a study recently published in Translational Psychiatry, a team led by Isidore Rigoutsos, Ph.D. took a comprehensive look at small RNAs in brain samples from people with schizophrenia, bipolar disorder and individuals without psychiatric illness. Their goal was to find out what kind of small RNAs are active in the brain, and whether their levels change in disease.

“Little attention had been paid to small RNAs in these disorders,” says Dr. Rigoutsos, “even though small RNAs help control numerous processes by modulating the abundance of genes.”

Brain computer interface enables rapid communication for two people with paralysis

Researchers from Brown University and Mass General Brigham have developed an implantable brain-computer interface that allowed two people with paralysis — one with ALS and one with a spinal cord injury — to communicate through rapid, accurate typing. The system uses microelectrode sensors in the motor cortex, maps letters to attempted finger movements on a QWERTY keyboard, and decodes those neural signals into text.

In the study, one participant reached a top speed of 110 characters per minute (about 22 words per minute) with a 1.6% word error rate, and both participants were able to use the system from home after calibration with as few as 30 sentences. The results were published in Nature Neuroscience.

This is the kind of neurotechnology that starts to close the gap between thought and communication.

Implantable device research from the BrainGate clinical trial enables communication through rapid typing for a patient with ALS and a patient with a spinal cord injury.

DNA origami precisely positions single-photon emitters for quantum technologies

An international research team led by scientists from Skoltech has developed a method to position molecules on the surface of ultrathin materials with unprecedented precision using molecular DNA self-assembly, enabling the creation of quantum light sources. The results, published in the journal Light: Science & Applications, pave the way for the production of compact and efficient components for future quantum computers and secure communication networks.

Two-dimensional materials such as molybdenum disulfide are promising candidates for quantum light sources due to their ability to emit photons under laser excitation. However, until now, scientists have been unable to precisely control the location of emission centers—they emerged randomly upon ion beam irradiation or mechanical deformation of the material.

The authors of the study proposed a different approach. The research is based on the DNA origami method, which allows the construction of nanoscale objects of a specified shape from DNA molecules. Triangular structures measuring 127 nanometers were assembled, each carrying 18 thiol molecules. These structures were placed onto a silicon chip with a lithographic pattern. The positioning yield of each DNA origami structure at its designated location exceeded 90%, significantly surpassing the statistical limit of traditional single molecule deposition methods.

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