keyword
https://read.qxmd.com/read/38452764/dissection-of-a-ctcf-topological-boundary-uncovers-principles-of-enhancer-oncogene-regulation
#21
JOURNAL ARTICLE
Kyung Lock Kim, Gilbert J Rahme, Viraat Y Goel, Chadi A El Farran, Anders S Hansen, Bradley E Bernstein
Enhancer-gene communication is dependent on topologically associating domains (TADs) and boundaries enforced by the CCCTC-binding factor (CTCF) insulator, but the underlying structures and mechanisms remain controversial. Here, we investigate a boundary that typically insulates fibroblast growth factor (FGF) oncogenes but is disrupted by DNA hypermethylation in gastrointestinal stromal tumors (GISTs). The boundary contains an array of CTCF sites that enforce adjacent TADs, one containing FGF genes and the other containing ANO1 and its putative enhancers, which are specifically active in GIST and its likely cell of origin...
February 28, 2024: Molecular Cell
https://read.qxmd.com/read/38452213/dna-fragility-at-topologically-associated-domain-boundaries-is-promoted-by-alternative-dna-secondary-structure-and-topoisomerase-ii-activity
#22
JOURNAL ARTICLE
Heather M Raimer Young, Pei-Chi Hou, Anna R Bartosik, Naomi D Atkin, Lixin Wang, Zhenjia Wang, Aakrosh Ratan, Chongzhi Zang, Yuh-Hwa Wang
CCCTC-binding factor (CTCF) binding sites are hotspots of genome instability. Although many factors have been associated with CTCF binding site fragility, no study has integrated all fragility-related factors to understand the mechanism(s) of how they work together. Using an unbiased, genome-wide approach, we found that DNA double-strand breaks (DSBs) are enriched at strong, but not weak, CTCF binding sites in five human cell types. Energetically favorable alternative DNA secondary structures underlie strong CTCF binding sites...
March 7, 2024: Nucleic Acids Research
https://read.qxmd.com/read/38449288/identifying-tad-like-domains-on-single-cell-hi-c-data-by-graph-embedding-and-changepoint-detection
#23
JOURNAL ARTICLE
Erhu Liu, Hongqiang Lyu, Yuan Liu, Laiyi Fu, Xiaoliang Cheng, Xiaoran Yin
MOTIVATION: Topologically associating domains (TADs) are fundamental building blocks of three-dimensional genome. TAD-like domains in single cells are regarded as the underlying genesis of TADs discovered in bulk cells. Understanding the organization of TAD-like domains helps to get deeper insights into their regulatory functions. Unfortunately, it remains a challenge to identify TAD-like domains on single-cell Hi-C data due to its ultra-sparsity. RESULTS: We propose scKTLD, an in silico tool for the identification of TAD-like domains on single-cell Hi-C data...
March 6, 2024: Bioinformatics
https://read.qxmd.com/read/38448979/reorganization-of-3d-genome-architecture-provides-insights-into-pathogenesis-of-early-fatty-liver-disease-in-laying-hens
#24
JOURNAL ARTICLE
Yanli Liu, Zhuqing Zheng, Chaohui Wang, Yumeng Wang, Xi Sun, Zhouzheng Ren, Xin Yang, Xiaojun Yang
BACKGROUND: Fatty liver disease causes huge economic losses in the poultry industry due to its high occurrence and lethality rate. Three-dimensional (3D) chromatin architecture takes part in disease processing by regulating transcriptional reprogramming. The study is carried out to investigate the alterations of hepatic 3D genome and H3K27ac profiling in early fatty liver (FLS) and reveal their effect on hepatic transcriptional reprogramming in laying hens. RESULTS: Results show that FLS model is constructed with obvious phenotypes including hepatic visible lipid deposition as well as higher total triglyceride and cholesterol in serum...
March 7, 2024: Journal of Animal Science and Biotechnology
https://read.qxmd.com/read/38440211/understanding-genomic-medicine-for-thoracic-aortic-disease-through-the-lens-of-induced-pluripotent-stem-cells
#25
REVIEW
Aminder A Singh, Deeti K Shetty, Aishwarya G Jacob, Semih Bayraktar, Sanjay Sinha
Thoracic aortic disease (TAD) is often silent until a life-threatening complication occurs. However, genetic information can inform both identification and treatment at an early stage. Indeed, a diagnosis is important for personalised surveillance and intervention plans, as well as cascade screening of family members. Currently, only 20% of heritable TAD patients have a causative mutation identified and, consequently, further advances in genetic coverage are required to define the remaining molecular landscape...
2024: Frontiers in Cardiovascular Medicine
https://read.qxmd.com/read/38440005/retinoids-for-the-treatment-of-refractory-grover-s-disease-a-case-series-and-review-of-the-literature
#26
David Moodie, Charles Dunn, Chloe Fernandez, Rajiv Nathoo
Grover's disease, also known as transient acantholytic dermatosis (TAD), currently has no published randomized control trials regarding the treatment of the disease; thus, evidence for treatment is largely derived from case studies and case reports. In this case series, we summarize the current treatment options for Grover's disease and discuss two cases of refractory Grover's disease treated with low-dose oral isotretinoin in patients who previously failed to reach clearance with multiple treatment options...
February 2024: Curēus
https://read.qxmd.com/read/38439523/genetic-insights-into-tietz-albinism-deafness-syndrome-a-new-dominant-negative-mutation-in-mitf
#27
JOURNAL ARTICLE
Kohei Yamamoto, Ken Okamura, Kazumasa Wakamatsu, Shosuke Ito, Kozue Akabane, Yosuke Arai, Junnosuke Kawaguchi, Yutaka Hozumi, Tamio Suzuki
Tietz albinism-deafness syndrome (TADS) is a rare and severe manifestation of Waardenburg syndrome that is primarily linked to mutations in MITF. In this report, we present a case of TADS resulting from a novel c.637G>C mutation in MITF (p.Glu213Gln; GenBank Accession number: NM_000248). A 3-year-old girl presented with congenital generalized hypopigmentation of the hair, skin, and irides along with complete sensorineural hearing loss. Histopathological and electron microscopy investigations indicated that this variant did not alter the number of melanocytes in the skin but significantly impaired melanosome maturation within melanocytes...
March 4, 2024: Pigment Cell & Melanoma Research
https://read.qxmd.com/read/38438377/structural-variants-in-the-epb41l4a-locus-tad-disruption-and-nrep-gene-misregulation-as-hypothetical-drivers-of-neurodevelopmental-outcomes
#28
JOURNAL ARTICLE
Paul Salnikov, Alexey Korablev, Irina Serova, Polina Belokopytova, Aleksandra Yan, Yana Stepanchuk, Savelii Tikhomirov, Veniamin Fishman
Structural variations are a pervasive feature of human genomes, and there is growing recognition of their role in disease development through their impact on spatial chromatin architecture. This understanding has led us to investigate the clinical significance of CNVs in noncoding regions that influence TAD structures. In this study, we focused on the Epb41l4a locus, which contains a highly conserved TAD boundary present in both human chromosome 5 and mouse chromosome 18, and its association with neurodevelopmental phenotypes...
March 4, 2024: Scientific Reports
https://read.qxmd.com/read/38436147/assessment-of-machine-learning-predictions-for-the-mediator-complex-subunit-med25-acid-domain-interactions-with-transactivation-domains
#29
JOURNAL ARTICLE
Didier Monté, Zoé Lens, Frédérique Dewitte, Vincent Villeret, Alexis Verger
The human Mediator complex subunit MED25 binds transactivation domains (TADs) present in various cellular and viral proteins using two binding interfaces, named H1 and H2, which are found on opposite sides of its ACID domain. Here, we use and compare deep learning methods to characterize human MED25-TAD interfaces and assess the predicted models to published experimental data. For the H1 interface, AlphaFold produces predictions with high-reliability scores that agree well with experimental data, while the H2 interface predictions appear inconsistent, preventing reliable binding modes...
March 4, 2024: FEBS Letters
https://read.qxmd.com/read/38427160/clipping-a-positive-lymph-node-improves-accuracy-of-nodal-staging-after-neoadjuvant-chemotherapy-for-breast-cancer-patients-but-does-it-drive-management-changes
#30
JOURNAL ARTICLE
Leopoldo Costarelli, Francesca Arienzo, Laura Broglia, Massimo La Pinta, Paola Scavina, Emanuele Zarba Meli, Maria Helena Colavito, Alessandra Ascarelli, Domenico Campagna, Tiziana Mastropietro, Elena Manna, Michela Amato, Angela Damiana Andrulli, Alfonso Schiavone, Mauro Minelli, Lucio Fortunato
BACKGROUND: Sentinel lymph node (SLN) biopsy for cN+ breast cancer patients after neoadjuvant chemotherapy (NAC) is controversial because the false-negative rate (FNR) is high. Identification of three or more SLNs with a dual tracer improves these results, and inclusion of a clipped lymph node (CLN) (targeted axillary dissection [TAD]) may be even more effective. METHODS: A retrospective, single-institution analysis of consecutive cN+ patients undergoing NAC from 2019 to 2021 was performed...
March 1, 2024: Annals of Surgical Oncology
https://read.qxmd.com/read/38423140/identification-of-two-mef2s-and-their-role-in-inhibiting-the-transcription-of-the-mstn2a-gene-in-the-yellowfin-seabream-acanthopagrus-latus-hottuyn-1782
#31
JOURNAL ARTICLE
Kecheng Zhu, Hongxi He, Huayang Guo, Baosuo Liu, Xin He, Nan Zhang, Lin Xian, Dianchang Zhang
Myocyte-specific enhancer binding factor 2 (MEF2), which belongs to the MADS superfamily, is a pivotal and conserved transcription factor that combines with the E-box motif to control the expression of muscle genes. Myostatin (mstn), a muscle growth inhibitor, is a vital member of the TGF-β superfamily. Currently, an understanding of the mechanisms of A. latus mstn (Almstn) transcriptional regulation mediated by MEF2 in fish muscle development is lacking. In the present study, two AlMEF2s (AlMEF2A and AlMEF2B) and Almstn2a were characterized from Acanthopagrus latus...
February 27, 2024: Gene
https://read.qxmd.com/read/38420822/immune-response-associated-gene-signatures-in-aortic-dissection-compared-to-aortic-aneurysm
#32
JOURNAL ARTICLE
Christian Doppler, Marlene Rezk, Barbara Arbeithuber, David Bernhard
BACKGROUND: Thoracic aortic dissections (TAD) are life-threatening events mostly requiring immediate surgical treatment. Although dissections mainly occur independently of thoracic aortic aneurysms (TAA), both share a high comorbidity. There are several indications for an involvement of the immune system in the development of TAD, just as in TAA. Nevertheless, specific disease-relevant genes, biomolecular processes, and immune-specific phenotypes remain unknown. METHODS: RNA from isolated aortic smooth muscle cells from TAD (n = 4), TAA (n = 3), and control patients were analyzed using microarray-based technologies...
February 6, 2024: Frontiers in Bioscience (Landmark Edition)
https://read.qxmd.com/read/38415767/correlation-between-cephalic-screw-positioning-of-standard-gamma-3-nail-for-intertrochanteric-fractures-and-cut-out-incidence
#33
JOURNAL ARTICLE
Alessandro Ortolani, Debora Lana, Antonio Martucci, Francesco Pesce, Stefano Stallone, Lorenzo Milani, Roberto Urso, Giuseppe Melucci, Domenico Tigani
INTRODUCTION: Lateral fractures of proximal femur are the most frequent fractures in elderly people. Internal fixation using medullary nails is the gold standard of treatment (Gamma 3 nail is the most implanted device) due to reduced incidence of complications than other devices. We report our experience in treating this kind of fractures with Gamma 3 nail, between January 2015 and December 2021. METHODS: We performed a retrospective cohort study of patients treated in our orthopaedic department; level of clinical care is III: 559 patients (431 females and 128 males, with an average age of 85...
2024: SICOT-J
https://read.qxmd.com/read/38413326/disease-investigations-initial-response-considerations-from-policy-to-farm
#34
REVIEW
Kelli Kirtley Werling, Kyle Shipman, Nick Lyons
Transboundary animal disease (TAD) investigations are conducted routinely across the United States to rule out diseases of significant economic, trade, and/or food security importance. Established protocols exist for TAD investigations and disease response based on national and international policy; however, now more than ever, private practitioners may be called upon to assist in these investigations and response activities and may play an important role in communications, sample collection, and disease surveillance...
February 26, 2024: Veterinary Clinics of North America. Food Animal Practice
https://read.qxmd.com/read/38410476/kras-silencing-impacts-chromatin-organization-and-transcriptional-activity-in-colorectal-cancer-cells
#35
Flávia Martins, Ana Luísa Machado, Andreia Ribeiro, Susana Mendonça Oliveira, Joana Carvalho, Rune Matthiesen, Vadim Backman, Sérgia Velho
Preclinical and clinical data have highlighted the challenges in targeting KRAS mutant tumors, revealing that cancer cells initially sensitive to treatment circumvent KRAS dependence and become tolerant. However, the exact mechanisms governing the transition from a drug-sensitive to a drug-tolerant state remain unclear. Herein, we used 3D culture models of mutant KRAS colorectal cancer cells with distinct KRAS dependencies to show that sensitive and resistant cells undergo distinct chromatin and transcriptional adaptations upon acute KRAS loss...
February 14, 2024: Research Square
https://read.qxmd.com/read/38405937/the-interaction-of-nf-%C3%AE%C2%BAb-transcription-factor-with-centromeric-chromatin
#36
Shaun Filliaux, Chloe Bertelsen, Hannah Baughman, Elizabeth Komives, Yuri L Lyubchenko
Centromeric chromatin is a subset of chromatin structure and governs chromosome segregation. The centromere is composed of both CENP-A nucleosomes (CENP-A nuc ) and H3 nucleosomes (H3 nuc ) and is enriched with alpha-satellite (α-sat) DNA repeats. These CENP-A nuc have a different structure than H3 nuc , decreasing the base pairs (bp) of wrapped DNA from 147 bp for H3 nuc to 121 bp for CENP-A nuc . All these factors can contribute to centromere function. We investigated the interaction of H3 nuc and CENP-A nuc with NF-κB, a crucial transcription factor in regulating immune response and inflammation...
February 16, 2024: bioRxiv
https://read.qxmd.com/read/38402218/implications-of-the-three-dimensional-chromatin-organization-for-genome-evolution-in-a-fungal-plant-pathogen
#37
JOURNAL ARTICLE
David E Torres, H Martin Kramer, Vittorio Tracanna, Gabriel L Fiorin, David E Cook, Michael F Seidl, Bart P H J Thomma
The spatial organization of eukaryotic genomes is linked to their biological functions, although it is not clear how this impacts the overall evolution of a genome. Here, we uncover the three-dimensional (3D) genome organization of the phytopathogen Verticillium dahliae, known to possess distinct genomic regions, designated adaptive genomic regions (AGRs), enriched in transposable elements and genes that mediate host infection. Short-range DNA interactions form clear topologically associating domains (TADs) with gene-rich boundaries that show reduced levels of gene expression and reduced genomic variation...
February 24, 2024: Nature Communications
https://read.qxmd.com/read/38399136/realization-of-large-low-stress-elastocaloric-effect-in-tizrnbal-alloy
#38
JOURNAL ARTICLE
Bang-He Lv, Hua-You Xiang, Shang Gao, Yan-Xin Guo, Jin-Han Yang, Nai-Fu Zou, Xiaoli Zhao, Zongbin Li, Bo Yang, Nan Jia, Hai-Le Yan, Liang Zuo
Seeking novel high-performance elastocaloric materials with low critical stress plays a crucial role in advancing the development of elastocaloric refrigeration technology. Here, as a first attempt, the elastocaloric effect of TiZrNbAl shape memory alloy at both room temperature and finite temperatures ranging from 245 K to 405 K, is studied systematically. Composition optimization shows that Ti-19Zr-14Nb-1Al (at.%), possessing excellent room-temperature superelasticity with a critical stress of around 100 MPa and a small stress hysteresis of around 70 MPa and outstanding fracture resistance with a compressive strain of 20% and stress of 1...
February 14, 2024: Materials
https://read.qxmd.com/read/38383502/giant-pandas-in-captivity-undergo-short-term-adaptation-in-nerve-related-pathways
#39
JOURNAL ARTICLE
Yan Li, Wei Xu, Juan Wang, Hong Liu, Jiawen Liu, Liang Zhang, Rong Hou, Fujun Shen, Yuliang Liu, Kailai Cai
BACKGROUND: Behaviors in captive animals, including changes in appetite, activity level, and social interaction, are often seen as adaptive responses. However, these behaviors may become progressively maladaptive, leading to stress, anxiety, depression, and other negative reactions in animals. RESULTS: In this study, we investigated the whole-genome sequencing data of 39 giant panda individuals, including 11 in captivity and 28 in the wild. To eliminate the mountain range effect and focus on the factor of captivity only, we first performed a principal component analysis...
February 21, 2024: BMC Zoology
https://read.qxmd.com/read/38364683/comparison-of-patient-positions-without-traction-table-for-proximal-femoral-nailing-supine-semilithotomy-and-lateral-decubitus-positions
#40
JOURNAL ARTICLE
Melih Unal, Yusuf Alper Kati, Muhammed Ergun, Cemil Aktan, Omer Faruk Celik, Ferhat Guler
BACKGROUND: Femur intertrochanteric fractures are performed commonly in a supine position with a traction table. There is a challenge in obtaining traction tables, especially in low- and middle-income countries. However, there is still a debate on which position should be preferred if the traction table cannot be obtained. METHODS: A total of 123 patients who were treated for femur intertrochanteric fracture (AO/OTA A1 or A2) using cephalomedullary nail (CN) were retrospectively analyzed...
February 1, 2024: Injury
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