keyword
https://read.qxmd.com/read/38519987/depletion-of-lamins-b1-and-b2-promotes-chromatin-mobility-and-induces-differential-gene-expression-by-a-mesoscale-motion-dependent-mechanism
#1
JOURNAL ARTICLE
Emily M Pujadas Liwag, Xiaolong Wei, Nicolas Acosta, Lucas M Carter, Jiekun Yang, Luay M Almassalha, Surbhi Jain, Ali Daneshkhah, Suhas S P Rao, Fidan Seker-Polat, Kyle L MacQuarrie, Joe Ibarra, Vasundhara Agrawal, Erez Lieberman Aiden, Masato T Kanemaki, Vadim Backman, Mazhar Adli
BACKGROUND: B-type lamins are critical nuclear envelope proteins that interact with the three-dimensional genomic architecture. However, identifying the direct roles of B-lamins on dynamic genome organization has been challenging as their joint depletion severely impacts cell viability. To overcome this, we engineered mammalian cells to rapidly and completely degrade endogenous B-type lamins using Auxin-inducible degron technology. RESULTS: Using live-cell Dual Partial Wave Spectroscopic (Dual-PWS) microscopy, Stochastic Optical Reconstruction Microscopy (STORM), in situ Hi-C, CRISPR-Sirius, and fluorescence in situ hybridization (FISH), we demonstrate that lamin B1 and lamin B2 are critical structural components of the nuclear periphery that create a repressive compartment for peripheral-associated genes...
March 22, 2024: Genome Biology
https://read.qxmd.com/read/38517894/evolutionary-analysis-of-gene-ages-across-tads-associates-chromatin-topology-with-whole-genome-duplications
#2
JOURNAL ARTICLE
Caelinn James, Marco Trevisan-Herraz, David Juan, Daniel Rico
Topologically associated domains (TADs) are interaction subnetworks of chromosomal regions in 3D genomes. TAD boundaries frequently coincide with genome breaks while boundary deletion is under negative selection, suggesting that TADs may facilitate genome rearrangements and evolution. We show that genes co-localize by evolutionary age in humans and mice, resulting in TADs having different proportions of younger and older genes. We observe a major transition in the age co-localization patterns between the genes born during vertebrate whole-genome duplications (WGDs) or before and those born afterward...
March 21, 2024: Cell Reports
https://read.qxmd.com/read/38502563/structural-basis-for-the-preservation-of-a-subset-of-topologically-associating-domains-in-interphase-chromosomes-upon-cohesin-depletion
#3
JOURNAL ARTICLE
Davin Jeong, Guang Shi, Xin Li, D Thirumalai
Compartment formation in interphase chromosomes is a result of spatial segregation between euchromatin and heterochromatin on a few megabase pairs (Mbp) scale. On the sub-Mbp scales, topologically associating domains (TADs) appear as interacting domains along the diagonal in the ensemble averaged Hi-C contact map. Hi-C experiments showed that most of the TADs vanish upon deleting cohesin, while the compartment structure is maintained, and perhaps even enhanced. However, closer inspection of the data reveals that a non-negligible fraction of TADs is preserved (P-TADs) after cohesin loss...
March 19, 2024: ELife
https://read.qxmd.com/read/38501074/personalized-patch-based-normality-assessment-of-brain-atrophy-in-alzheimer-s-disease
#4
JOURNAL ARTICLE
Jianwei Zhang, Yonggang Shi
Cortical thickness is an important biomarker associated with gray matter atrophy in neurodegenerative diseases. In order to conduct meaningful comparisons of cortical thickness between different subjects, it is imperative to establish correspondence among surface meshes. Conventional methods achieve this by projecting surface onto canonical domains such as the unit sphere or averaging feature values in anatomical regions of interest (ROIs). However, due to the natural variability in cortical topography, perfect anatomically meaningful one-to-one mapping can be hardly achieved and the practice of averaging leads to the loss of detailed information...
October 2023: Medical Image Computing and Computer-assisted Intervention: MICCAI ..
https://read.qxmd.com/read/38499570/direct-space-time-manipulation-mechanism-for-spatio-temporal-coupling-of-ultrafast-light-field
#5
JOURNAL ARTICLE
Qinggang Lin, Fu Feng, Yi Cai, Xiaowei Lu, Xuanke Zeng, Congying Wang, Shixiang Xu, Jingzhen Li, Xiaocong Yuan
Traditionally, manipulation of spatiotemporal coupling (STC) of the ultrafast light fields can be actualized in the space-spectrum domain with some 4-f pulse shapers, which suffers usually from some limitations, such as spectral/pixel resolution and information crosstalk associated with the 4-f pulse shapers. This work introduces a novel mechanism for direct space-time manipulation of ultrafast light fields to overcome the limitations. This mechanism combines a space-dependent time delay with some spatial geometrical transformations, which has been experimentally proved by generating a high-quality STC light field, called light spring (LS)...
March 18, 2024: Nature Communications
https://read.qxmd.com/read/38497675/a-ph-responsive-topological-switch-based-on-a-dna-quadruplex-duplex-hybrid
#6
JOURNAL ARTICLE
Yoanes Maria Vianney, Jagannath Jana, Klaus Weisz
A guanine-rich oligonucleotide based on a human telomeric sequence but with the first three-nucleotide intervening stretch replaced by a putative 15-nucleotide hairpin-forming sequence shows a pH-dependent folding into different quadruplex-duplex hybrids in a potassium containing buffer. At slightly acidic pH, the quadruplex domain adopts a chair-type conformation. Upon increasing the pH, a transition with a midpoint close to neutral pH to a major and minor (3+1) hybrid topology with either a coaxially stacked or orthogonally oriented duplex stem-loop occurs...
March 18, 2024: Chemistry: a European Journal
https://read.qxmd.com/read/38495565/machine-and-deep-learning-methods-for-predicting-3d-genome-organization
#7
Brydon P G Wall, My Nguyen, J Chuck Harrell, Mikhail G Dozmorov
Three-Dimensional (3D) chromatin interactions, such as enhancer-promoter interactions (EPIs), loops, Topologically Associating Domains (TADs), and A/B compartments play critical roles in a wide range of cellular processes by regulating gene expression. Recent development of chromatin conformation capture technologies has enabled genome-wide profiling of various 3D structures, even with single cells. However, current catalogs of 3D structures remain incomplete and unreliable due to differences in technology, tools, and low data resolution...
March 4, 2024: ArXiv
https://read.qxmd.com/read/38494248/bioinformatics-approach-for-prediction-and-analysis-of-the-non-structural-protein-4b-nsp4b-of-the-zika-virus
#8
JOURNAL ARTICLE
Mohamed E Hasan, Aya Samir, Magdy M Khalil, Medhat W Shafaa
BACKGROUND: The Nonstructural Protein (NSP) 4B of Zika virus of 251 amino acids from (ZIKV/Human/POLG_ZIKVF) with accession number (A0A024B7W1), Induces the production of Endoplasmic Reticulum ER-derived membrane vesicles, which are the sites of viral replication. To understand the physical basis of how proteins fold in nature and to solve the challenge of protein structure prediction, Ab-initio and comparative modeling are crucial tools. RESULTS: The systematic in silico technique, ThreaDom, had only predicted one domain (4 - 190) of NSP4B...
March 2024: Journal, Genetic Engineering & Biotechnology
https://read.qxmd.com/read/38490101/enhancer-infestation-drives-tumorigenic-activation-of-inactive-b-compartment-in-epstein-barr-virus-positive-nasopharyngeal-carcinoma
#9
JOURNAL ARTICLE
Harue Mizokami, Atsushi Okabe, Ruchi Choudhary, Masato Mima, Kenta Saeda, Masaki Fukuyo, Bahityar Rahmutulla, Motoaki Seki, Boon-Cher Goh, Satoru Kondo, Hirotomo Dochi, Makiko Moriyama-Kita, Kiyoshi Misawa, Toyoyuki Hanazawa, Patrick Tan, Tomokazu Yoshizaki, Melissa Jane Fullwood, Atsushi Kaneda
BACKGROUND: Nasopharyngeal carcinoma (NPC) is an Epstein-Barr virus (EBV)-associated malignant epithelial tumor endemic to Southern China and Southeast Asia. While previous studies have revealed a low frequency of gene mutations in NPC, its epigenomic aberrations are not fully elucidated apart from DNA hypermethylation. Epigenomic rewiring and enhancer dysregulation, such as enhancer hijacking due to genomic structural changes or extrachromosomal DNA, drive cancer progression. METHODS: We conducted Hi-C, 4C-seq, ChIP-seq, and RNA-seq analyses to comprehensively elucidate the epigenome and interactome of NPC using C666-1 EBV(+)-NPC cell lines, NP69T immortalized nasopharyngeal epithelial cells, clinical NPC biopsy samples, and in vitro EBV infection in HK1 and NPC-TW01 EBV(-) cell lines...
March 14, 2024: EBioMedicine
https://read.qxmd.com/read/38484732/the-sirtuin-associated-human-senescence-program-converges-on-the-activation-of-placenta-specific-gene-pappa
#10
JOURNAL ARTICLE
Shijia Bi, Xiaoyu Jiang, Qianzhao Ji, Zehua Wang, Jie Ren, Si Wang, Yang Yu, Ruoqi Wang, Zunpeng Liu, Junhang Liu, Jianli Hu, Guoqiang Sun, Zeming Wu, Zhiqing Diao, Jingyi Li, Liang Sun, Juan Carlos Izpisua Belmonte, Weiqi Zhang, Guang-Hui Liu, Jing Qu
Sirtuins are pro-longevity genes with chromatin modulation potential, but how these properties are connected is not well understood. Here, we generated a panel of isogeneic human stem cell lines with SIRT1-SIRT7 knockouts and found that any sirtuin deficiency leads to accelerated cellular senescence. Through large-scale epigenomic analyses, we show how sirtuin deficiency alters genome organization and that genomic regions sensitive to sirtuin deficiency are preferentially enriched in active enhancers, thereby promoting interactions within topologically associated domains and the formation of de novo enhancer-promoter loops...
March 11, 2024: Developmental Cell
https://read.qxmd.com/read/38481440/case-report-management-of-pediatric-gigantism-caused-by-the-tadopathy-x-linked-acrogigantism
#11
Manuela Caruso, Diego Mazzatenta, Sofia Asioli, Giuseppe Costanza, Giampaolo Trivellin, Martin Franke, Dayana Abboud, Julien Hanson, Véronique Raverot, Patrick Pétrossians, Albert Beckers, Marco Cappa, Adrian F Daly
X-linked acrogigantism (X-LAG) is a rare form of pituitary gigantism that is associated with growth hormone (GH) and prolactin-secreting pituitary adenomas/pituitary neuroendocrine tumors (PitNETs) that develop in infancy. It is caused by a duplication on chromosome Xq26.3 that leads to the misexpression of the gene GPR101 , a constitutively active stimulator of pituitary GH and prolactin secretion. GPR101 normally exists within its own topologically associating domain (TAD) and is insulated from surrounding regulatory elements...
2024: Frontiers in Endocrinology
https://read.qxmd.com/read/38478617/proximity-effect-of-emergent-field-from-spin-ice-in-an-oxide-heterostructure
#12
JOURNAL ARTICLE
Mizuki Ohno, Takahiro C Fujita, Masashi Kawasaki
Geometrical frustration endows magnets with degenerate ground states, resulting in exotic spin structures and quantum phenomena. Such magnets, called quantum magnets, can display non-coplanar spin textures and be a viable platform for the topological Hall effect driven by "emergent field." However, most quantum magnets are insulators, making it challenging to electrically detect associated fluctuations and excitations. Here, we probe magnetic transitions in the spin ice insulator Dy2 Ti2 O7 , a prototypical quantum magnet, as emergent magnetotransport phenomena at the heterointerface with the nonmagnetic metal Bi2 Rh2 O7 ...
March 15, 2024: Science Advances
https://read.qxmd.com/read/38473917/structural-variant-disrupting-the-expression-of-the-remote-foxc1-gene-in-a-patient-with-syndromic-complex-microphthalmia
#13
Julie Plaisancié, Bertrand Chesneau, Lucas Fares-Taie, Jean-Michel Rozet, Jacmine Pechmeja, Julien Noero, Véronique Gaston, Isabelle Bailleul-Forestier, Patrick Calvas, Nicolas Chassaing
Ocular malformations (OMs) arise from early defects during embryonic eye development. Despite the identification of over 100 genes linked to this heterogeneous group of disorders, the genetic cause remains unknown for half of the individuals following Whole-Exome Sequencing. Diagnosis procedures are further hampered by the difficulty of studying samples from clinically relevant tissue, which is one of the main obstacles in OMs. Whole-Genome Sequencing (WGS) to screen for non-coding regions and structural variants may unveil new diagnoses for OM individuals...
February 25, 2024: International Journal of Molecular Sciences
https://read.qxmd.com/read/38473815/integrating-dynamic-3d-chromatin-architecture-and-gene-expression-alterations-reveal-heterosis-in-brassica-rapa
#14
JOURNAL ARTICLE
Liu E, Shanwu Lyu, Yaolong Wang, Dong Xiao, Tongkun Liu, Xilin Hou, Ying Li, Changwei Zhang
Heterosis plays a significant role in enhancing variety, boosting yield, and raising economic value in crops, but the molecular mechanism is still unclear. We analyzed the transcriptomes and 3D genomes of a hybrid (F1 ) and its parents (w30 and 082). The analysis of the expression revealed a total of 485 specially expressed genes (SEGs), 173 differentially expressed genes (DEGs) above the parental expression level, more actively expressed genes, and up-regulated DEGs in the F1 . Further study revealed that the DEGs detected in the F1 and its parents were mainly involved in the response to auxin, plant hormone signal transduction, DNA metabolic process, purine metabolism, starch, and sucrose metabolism, which suggested that these biological processes may play a crucial role in the heterosis of Brassica rapa ...
February 22, 2024: International Journal of Molecular Sciences
https://read.qxmd.com/read/38462450/topology-of-ubiquitin-chains-in-the-chromatosomal-environment-of-the-e3-ubiquitin-ligase-rnf168
#15
JOURNAL ARTICLE
Anna A Kudriaeva, Lyudmila A Yakubova, George A Saratov, Vasiliy I Vladimirov, Valeriy M Lipkin, Alexey A Belogurov
Genome stability is critical for normal functioning of cells, it depends on accuracy of DNA replication, chromosome segregation, and DNA repair. Cellular defense mechanisms against DNA damage are important for preventing cancer development and aging. The E3 ubiquitin ligase RNF168 of the RING superfamily is an essential component of the complex responsible for ubiquitination of the H2A/H2A.X histones near DNA double-strand breaks, which is a key step in attracting repair factors to the damage site. In this study, we unequivocally showed that RNF168 does not have the ability to directly distinguish architecture of polyubiquitin chains, except for the tropism of its two ubiquitin-binding domains UDM1/2 to K63 ubiquitin chains...
December 2023: Biochemistry. Biokhimii︠a︡
https://read.qxmd.com/read/38454063/a-self-regulatory-cell-wall-sensing-module-at-cell-edges-controls-plant-growth
#16
JOURNAL ARTICLE
Liam Elliott, Monika Kalde, Ann-Kathrin Schürholz, Xinyu Zhang, Sebastian Wolf, Ian Moore, Charlotte Kirchhelle
Morphogenesis of multicellular organs requires coordination of cellular growth. In plants, cell growth is determined by turgor pressure and the mechanical properties of the cell wall, which also glues cells together. Because plants have to integrate tissue-scale mechanical stresses arising through growth in a fixed tissue topology, they need to monitor cell wall mechanical status and adapt growth accordingly. Molecular factors have been identified, but whether cell geometry contributes to wall sensing is unknown...
March 7, 2024: Nature Plants
https://read.qxmd.com/read/38452764/dissection-of-a-ctcf-topological-boundary-uncovers-principles-of-enhancer-oncogene-regulation
#17
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
#18
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
#19
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
#20
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
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