Inherent asymmetry of Rpd3S coordinates its nucleosome engagement and association with elongating RNA polymerase II.

The Rpd3S histone deacetylase complex has a crucial role in genomic integrity by deacetylating transcribed nucleosomes following RNA polymerase (Pol) II passage. Cryo-EM studies highlight the importance of asymmetrical Rco1-Eaf3 dimers in nucleosome binding, yet the interaction dynamics with nucleosomal substrates alongside elongating Pol II are poorly understood. Here we demonstrate the essential function of the Rco1 N-terminal intrinsically disordered region (IDR) in modulating Pol II association, in which K/R mutations within the Rco1 IDR impair interaction of Rpd3S with the C-terminal domain (CTD) of Rpb1, without affecting nucleosome recognition or complex integrity.

Diverse modes of H3K36me3-guided nucleosomal deacetylation by Rpd3S.

Context-dependent dynamic histone modifications constitute a key epigenetic mechanism in gene regulation. The Rpd3 small (Rpd3S) complex recognizes histone H3 trimethylation on lysine 36 (H3K36me3) and deacetylates histones H3 and H4 at multiple sites across transcribed regions. Here we solved the cryo-electron microscopy structures of Saccharomyces cerevisiae Rpd3S in its free and H3K36me3 nucleosome-bound states.

scRNA-seq profiling of neonatal and adult thymus-derived CD4+ T cells by a T cell origin-time tracing model.

It is well documented that the neonatal thymus-derived (neonatal-TD) regulatory T cells (Treg) are essential to prevent lethal autoimmune diseases and allergies, and neonatal and adult thymus possesses distinct output potentials for naïve T cells, including Treg. However, the molecular features and detailed functional differences between neonatal-TD and adult thymus-derived (adult-TD) T cells in terms of their ability to maintain immune homeostasis during long-term environmental influences are still largely unknown, partially due to the lack of appropriate animal models to precisely trace these cells at specific time points. In this study, neonatal-TD and adult-TD CD4+ T cells from the spleen and Peyer's patches were traced for 9 weeks by a T cell origin-time tracing mouse model and analysed by single-cell RNA sequencing.

Sin1-mediated mTOR signaling in cell growth, metabolism and immune response.

The mammalian target of rapamycin (mTOR) is an evolutionarily conserved Ser/Thr protein kinase with essential cellular function via processing various extracellular and intracellular inputs. Two distinct multi-protein mTOR complexes (mTORC), mTORC1 and mTORC2, have been identified and well characterized in eukaryotic cells from yeast to human. Sin1, which stands for ty1/Spc1-teracting rotein1, also known as mitogen-activated protein kinase () ssociated rotein (MAPKAP)1, is an evolutionarily conserved adaptor protein.

Data of CT bow tie filter profiles from three modern CT scanners.

As one of the key hardware components in Computed Tomography (CT) scanners, a bowtie filter reduces unnecessary radiation dose to the peripheries of a patient and equalizes radiation signal to the detector. Knowledge of the exact profiles from different bowtie filters are critical to model the imaging process of CT scanners and to estimate patient dose. However, bowtie filter profiles remain proprietary to most CT vendors.

Time-cumulated blood pressure exposure and incident impairment of glucose tolerance and diabetes mellitus.

Background: With the marked increase in the prevalence of diabetes mellitus, it was the purpose of our study to assess a potential association of time-cumulated exposure to systolic (CumSBP) and of diastolic blood pressure (CumDBP) with onset of impaired glucose tolerance and diabetes mellitus.

Methods: The prospective investigation included participants of the longitudinal Kailuan Study with three baseline examinations in 2006-2007, 2008-2009 and 2010-2011, re-examination in 2012-2013, and no diabetes mellitus at baseline. Cumulative blood pressure (BP) was calculated as cumBP = [(BP + BP)/2 × time] + [(BP + BP)/2 × time].

Ideal cardiovascular health and incident hypertension: The longitudinal community-based Kailuan study.

Ideal cardiovascular health (CVH) has been defined by the American Heart Association as the absence of disease and presence of 7 key health factors. Since it is unknown whether cumulative exposure to CVH reduces the risk of developing arterial hypertension, we prospectively examined the potential association between cumulative CVH (cumCVH) score (except for blood pressure metrics) and incident hypertension.Of the 101,510 participants with an age range of 18 to 98 years in this longitudinal community-based Kailuan study, our cohort included those 15,014 participants without hypertension at baseline and who had follow-up examinations 2, 4, and 6 years later.

Combinatorial Histone Readout by the Dual Plant Homeodomain (PHD) Fingers of Rco1 Mediates Rpd3S Chromatin Recruitment and the Maintenance of Transcriptional Fidelity.

The plant homeodomain (PHD) finger is found in many chromatin-associated proteins and functions to recruit effector proteins to chromatin through its ability to bind both methylated and unmethylated histone residues. Here, we show that the dual PHD fingers of Rco1, a member of the Rpd3S histone deacetylase complex recruited to transcribing genes, operate in a combinatorial manner in targeting the Rpd3S complex to histone H3 in chromatin. Although mutations in either the first or second PHD finger allow for Rpd3S complex formation, the assembled complexes from these mutants cannot recognize nucleosomes or function to maintain chromatin structure and prevent cryptic transcriptional initiation from within transcribed regions.

Homodimeric PHD Domain-containing Rco1 Subunit Constitutes a Critical Interaction Hub within the Rpd3S Histone Deacetylase Complex.

Recognition of histone post-translational modifications is pivotal for directing chromatin-modifying enzymes to specific genomic regions and regulating their activities. Emerging evidence suggests that other structural features of nucleosomes also contribute to precise targeting of downstream chromatin complexes, such as linker DNA, the histone globular domain, and nucleosome spacing. However, how chromatin complexes coordinate individual interactions to achieve high affinity and specificity remains unclear.

Multimodality Imaging in Pediatric Osteosarcoma in the Era of Image Gently and Image Wisely Campaign With a Close Look at the CT Scan Radiation Dose.

The increasing use of serial multimodality imaging in the management of pediatric osteosarcoma raises concern of over exposure to ionizing radiation in children, especially from repeated computed tomographic (CT) scans. This study reviews the utilization of multimodality imaging in patients with osteosarcoma at our institution and analyzes any potential radiation-related complications. Twenty-eight patients were identified.

Nucleosome contact triggers conformational changes of Rpd3S driving high-affinity H3K36me nucleosome engagement.

The Rpd3S histone deacetylase complex utilizes two subunits, Eaf3 and Rco1, to recognize nucleosomes methylated at H3K36 (H3K36me) with high affinity and strong specificity. However, the chromobarrel domain of Eaf3 (CHD) that is responsible for H3K36me recognition only binds weakly and with little specificity to histone peptides. Here, using deuterium exchange mass spectrometry (DXMS), we detected conformational changes of Rpd3S upon its contact with chromatin.

Evaluation of different techniques for CT radiation profile width measurement.

This work has been conducted to demonstrate a procedure for using a Konica Minolta computed radiography (CR) system for the measurement of computed tomography (CT) radiation profile width, and to compare this method with conventional and GAFCHROMIC XR-QA2 film measurements. The exposure and processing conditions of a Konica Minolta CR reader system were characterized to establish the relationship between exposure at the imaging plate (IP) and pixel value. A 6 cc ionization chamber was exposed at the isocenter of a CT scanner using 80 kVp, 0.

Reconstitution of modified chromatin templates for in vitro functional assays.

To study the functions of histone modifications in the context of chromatin, it is necessary to be able to prepare nucleosomal templates that carry specific posttranslational modifications in a defined biochemical system. Here, we describe two sets of protocols for reconstituting designer nucleosomes that contain specifically modified histones. The resulting nucleosomes are suitable for electromobility shift assays, chromatin remodeling assays, and other functional and structural studies.

Determination of multislice computed tomography dose index (CTDI) using optically stimulated luminescence technology.

Purpose: The extensive use of multislice computed tomography (MSCT) and the associated increase in patient dose calls for an accurate dose evaluation technique. Optically stimulated luminescence (OSL) dosimetry provides a potential solution to the arising concerns over patient dose. This study was intended to evaluate the feasibility and accuracy of OSL dosimeter systems in the diagnostic CT x-ray beam energy range.

Phosphorylated Pol II CTD recruits multiple HDACs, including Rpd3C(S), for methylation-dependent deacetylation of ORF nucleosomes.

Methylation of histone H3 by Set1 and Set2 is required for deacetylation of nucleosomes in coding regions by histone deacetylase complexes (HDACs) Set3C and Rpd3C(S), respectively. We report that Set3C and Rpd3C(S) are cotranscriptionally recruited in the absence of Set1 and Set2, but in a manner stimulated by Pol II CTD kinase Cdk7/Kin28. Consistently, Rpd3C(S) and Set3C interact with Ser5-phosphorylated Pol II and histones in extracts, but only the histone interactions require H3 methylation.

Contrast-enhanced first-pass myocardial perfusion magnetic resonance imaging with parallel acquisition at 3.0 Tesla.

Objective: Magnetic resonance imaging (MRI) at 3 T is significantly different than 1.5 T and needs to be optimized due to increased signal-to-noise ratio (SNR) and specific absorption ratio (SAR). This study tests the hypothesis that first-pass myocardial perfusion MRI using saturation recovery (SR)-TrueFISP with parallel imaging is superior to SR-TurboFLASH and a more achievable technique for clinical application at 3 T.

First-pass contrast-enhanced myocardial perfusion MRI using a maximum up-slope parametric map.

Magnetic resonance first-pass perfusion imaging offers a noninvasive method for the rapid, accurate, and reproducible assessment of cardiac function without ionizing radiation. Quantitative or semiquantitative analysis of changes in signal intensity (SI) over the whole image sequence yields a more efficient analysis than direct visual inspection. In this paper, a method to generate maximum up-slope myocardial perfusion maps is presented.

The DNA repair protein yKu80 regulates the function of recombination enhancer during yeast mating type switching.

Recombination enhancer (RE) is essential for regulating donor preference during yeast mating type switching. In this study, by using minichromosome affinity purification (MAP) and mass spectrometry, we found that yeast Ku80p is associated with RE in MATa cells. Chromatin immunoprecipitation assays confirmed its occupancy in vivo.

Histones: should I stay or should I go?

A report on the American Society for Biochemistry and Molecular Biology symposium 'Transcriptional Regulation by Chromatin and RNA polymerase II', Lake Tahoe, USA, 29 October-1 November 2004.