keyword
https://read.qxmd.com/read/38536538/competing-endogenous-rnas-crosstalk-in-hippocampus-a-potential-mechanism-for-neuronal-developing-defects-in-down-syndrome
#1
JOURNAL ARTICLE
Huiru Zhao, Guiyu Lou, Yupu Shao, Tao Wang, Hongdan Wang, Qiannan Guo, Wenke Yang, Hongyan Liu, Shixiu Liao
Down syndrome (DS) is the most example of aneuploidy, resulting from an additional copy of all or part of chromosome 21. Competing endogenous RNAs (ceRNAs) play important roles in neuronal development and neurological defects. This study aimed to identify hub genes and synergistic crosstalk among ceRNAs in the DS fetal hippocampus as potential targets for the treatment of DS-related neurodegenerative diseases. We profiled differentially expressed long non-coding RNAs (DElncRNAs), differentially expressed circular RNAs (DEcircRNAs), differentially expressed microRNAs (DEmiRNAs), and differentially expressed messenger RNAs (DEmRNAs) in hippocampal samples from patients with or without DS...
March 27, 2024: Journal of Molecular Neuroscience: MN
https://read.qxmd.com/read/38516975/footprints-of-loop-extrusion-in-statistics-of-intra-chromosomal-distances-an-analytically-solvable-model
#2
JOURNAL ARTICLE
Sergey Belan, Vladimir Parfenyev
Active loop extrusion-the process of formation of dynamically growing chromatin loops due to the motor activity of DNA-binding protein complexes-is a firmly established mechanism responsible for chromatin spatial organization at different stages of a cell cycle in eukaryotes and bacteria. The theoretical insight into the effect of loop extrusion on the experimentally measured statistics of chromatin conformation can be gained with an appropriately chosen polymer model. Here, we consider the simplest analytically solvable model of an interphase chromosome, which is treated as an ideal chain with disorder of sufficiently sparse random loops whose conformations are sampled from the equilibrium ensemble...
March 28, 2024: Journal of Chemical Physics
https://read.qxmd.com/read/38508544/a-comprehensive-review-on-role-of-aurora-kinase-inhibitors-akis-in-cancer-therapeutics
#3
REVIEW
Deepali Gupta, Mukesh Kumar, Sana Saifi, Shivani Rawat, A S Ethayathulla, Punit Kaur
Aurora kinases (AURKs) are a family of serine /threonine protein kinases that have a crucial role in cell cycle process mainly in the event of chromosomal segregation, centrosome maturation and cytokinesis. The family consists of three members including Aurora kinase A (AURK-A), Aurora kinase B (AURK-B) and Aurora kinase C (AURK-C). All AURKs contain a conserved kinase domain for their activity but differ in their cellular localization and functions. AURK-A and AURK-B is expressed mainly in somatic cells while the expression of AURK-C is limited to germ cells...
March 18, 2024: International Journal of Biological Macromolecules
https://read.qxmd.com/read/38496446/regulation-of-immune-signal-integration-and-memory-by-inflammation-induced-chromosome-conformation
#4
Bence Daniel, Andy Y Chen, Katalin Sandor, Wenxi Zhang, Zhuang Miao, Caleb A Lareau, Kathryn E Yost, Howard Y Chang, Ansuman T Satpathy
3-dimensional (3D) genome conformation is central to gene expression regulation, yet our understanding of its contribution to rapid transcriptional responses, signal integration, and memory in immune cells is limited. Here, we study the molecular regulation of the inflammatory response in primary macrophages using integrated transcriptomic, epigenomic, and chromosome conformation data, including base pair-resolution Micro-Capture C. We demonstrate that interleukin-4 (IL-4) primes the inflammatory response in macrophages by stably rewiring 3D genome conformation, juxtaposing endotoxin-, interferon-gamma-, and dexamethasone-responsive enhancers in close proximity to their cognate gene promoters...
March 4, 2024: bioRxiv
https://read.qxmd.com/read/38496214/an-improved-chromosome-level-genome-assembly-of-perennial-ryegrass-lolium-perenne-l
#5
JOURNAL ARTICLE
Yutang Chen, Roland Kölliker, Martin Mascher, Dario Copetti, Axel Himmelbach, Nils Stein, Bruno Studer
This work is an update and extension of the previously published article "Ultralong Oxford Nanopore Reads Enable the Development of a Reference-Grade Perennial Ryegrass Genome Assembly" by Frei et al.  The published genome assembly of the doubled haploid perennial ryegrass ( Lolium perenne L.) genotype Kyuss (Kyuss v1.0) marked a milestone for forage grass research and breeding. However, order and orientation errors may exist in the pseudo-chromosomes of Kyuss, since barley ( Hordeum vulgare L.), which diverged 30 million years ago from perennial ryegrass, was used as the reference to scaffold Kyuss...
2024: GigaByte
https://read.qxmd.com/read/38496077/a-case-of-hypofractionated-radiation-therapy-for-early-stage-breast-cancer-in-a-patient-with-fabry-disease
#6
Motoki Honda, Yojiro Ishikawa, Kengo Ito, Satoshi Teramura, Seki Yasuhiro, Takayuki Yamada
Fabry disease is a metabolic disorder caused by a deficiency in lysosomal enzymes and is inherited as an X-chromosomal disorder. Patients with Fabry disease have a low incidence of cancer, and reports of malignant tumors, especially in the thoracic region, are rare. In this case report, we describe our experience with radiation therapy following breast-conserving surgery in a patient with left breast cancer and Fabry disease, and we review the existing literature. The patient, a woman in her 40s, required postoperative irradiation for left breast cancer (pT1N0M0)...
February 2024: Curēus
https://read.qxmd.com/read/38493342/scencore-leveraging-single-cell-epigenetic-data-to-predict-chromatin-conformation-using-graph-embedding
#7
JOURNAL ARTICLE
Ziheng Duan, Siwei Xu, Shushrruth Sai Srinivasan, Ahyeon Hwang, Che Yu Lee, Feng Yue, Mark Gerstein, Yu Luan, Matthew Girgenti, Jing Zhang
Dynamic compartmentalization of eukaryotic DNA into active and repressed states enables diverse transcriptional programs to arise from a single genetic blueprint, whereas its dysregulation can be strongly linked to a broad spectrum of diseases. While single-cell Hi-C experiments allow for chromosome conformation profiling across many cells, they are still expensive and not widely available for most labs. Here, we propose an alternate approach, scENCORE, to computationally reconstruct chromatin compartments from the more affordable and widely accessible single-cell epigenetic data...
January 22, 2024: Briefings in Bioinformatics
https://read.qxmd.com/read/38491617/chromatin-structure-from-high-resolution-microscopy-scaling-laws-and-microphase-separation
#8
JOURNAL ARTICLE
Loucif Remini, Midas Segers, John Palmeri, Jean-Charles Walter, Andrea Parmeggiani, Enrico Carlon
Recent advances in experimental fluorescence microscopy allow high accuracy determination (resolution of 50 nm) of the three-dimensional physical location of multiple (up to ∼10^{2}) tagged regions of the chromosome. We investigate publicly available microscopy data for two loci of the human Chr21 obtained from multiplexed fluorescence in situ hybridization (FISH) methods for different cell lines and treatments. Inspired by polymer physics models, our analysis centers around distance distributions between different tags with the aim being to unravel the chromatin conformational arrangements...
February 2024: Physical Review. E
https://read.qxmd.com/read/38490540/signatures-of-positive-selection-after-the-introduction-of-genomic-selection-in-the-finnish-ayrshire-population
#9
JOURNAL ARTICLE
Katri Sarviaho, Pekka Uimari, Katja Martikainen
The Finnish Ayrshire (FAY) belongs to the Nordic Red breeds and is characterized by high milk yield, high milk components, good fertility, and functional conformation. The FAY breeding program is based on genomic selection. Despite the benefits of selection on breeding values, autozygosity in the genome may increase due to selection, and increased autozygosity may cause inbreeding depression in selected traits. However, there is lack of studies concerning selection signatures in the FAY after genomic selection introduction...
March 13, 2024: Journal of Dairy Science
https://read.qxmd.com/read/38479837/haplotype-resolved-3d-chromatin-architecture-of-the-hybrid-pig
#10
JOURNAL ARTICLE
Yu Lin, Jing Li, Yiren Gu, Long Jin, Jingyi Bai, Jiaman Zhang, Yujie Wang, Pengliang Liu, Keren Long, Mengnan He, Diyan Li, Can Liu, Ziyin Han, Yu Zhang, Xiaokai Li, Bo Zeng, Lu Lu, Fanli Kong, Ying Sun, Yongliang Fan, Xun Wang, Tao Wang, An'an Jiang, Jideng Ma, Linyuan Shen, Li Zhu, Yanzhi Jiang, Guoqing Tang, Xiaolan Fan, Qingyou Liu, Hua Li, Jinyong Wang, Li Chen, Liangpeng Ge, Xuewei Li, Qianzi Tang, Mingzhou Li
In diploid mammals, allele-specific three-dimensional (3D) genome architecture may lead to imbalanced gene expression. Through ultradeep in situ Hi-C sequencing of three representative somatic tissues (liver, skeletal muscle, and brain) from hybrid pigs generated by reciprocal crosses of phenotypically and physiologically divergent Berkshire and Tibetan pigs, we uncover extensive chromatin reorganization between homologous chromosomes across multiple scales. Haplotype-based interrogation of multi-omic data revealed the tissue dependence of 3D chromatin conformation, suggesting that parent-of-origin-specific conformation may drive gene imprinting...
March 13, 2024: Genome Research
https://read.qxmd.com/read/38479789/primary-osteoarthritis-chondrocyte-map-of-chromatin-conformation-reveals-novel-candidate-effector-genes
#11
JOURNAL ARTICLE
Norbert Bittner, Chenfu Shi, Danyun Zhao, James Ding, Lorraine Southam, Diane Swift, Peter Kreitmaier, Mauro Tutino, Odysseas Stergiou, Jackson T S Cheung, Georgia Katsoula, Jenny Hankinson, Jeremy Mark Wilkinson, Gisela Orozco, Eleftheria Zeggini
OBJECTIVES: Osteoarthritis is a complex disease with a huge public health burden. Genome-wide association studies (GWAS) have identified hundreds of osteoarthritis-associated sequence variants, but the effector genes underpinning these signals remain largely elusive. Understanding chromosome organisation in three-dimensional (3D) space is essential for identifying long-range contacts between distant genomic features (e.g., between genes and regulatory elements), in a tissue-specific manner...
March 13, 2024: Annals of the Rheumatic Diseases
https://read.qxmd.com/read/38471646/three-dimensional-chromatin-analysis-reveals-sp1-as-a-mediator-to-program-and-reprogram-hpv-host-epigenetic-architecture-in-cervical-cancer
#12
JOURNAL ARTICLE
Canhui Cao, Qian Xu, Zhixian Zhu, Miaochun Xu, Ye Wei, Shitong Lin, Sheng Cheng, Wenhua Zhi, Ping Hong, Xingyu Huang, Da Lin, Gang Cao, Yifan Meng, Ping Wu, Ting Peng, Juncheng Wei, Wencheng Ding, Xiaoyuan Huang, WingKin Sung, Gang Chen, Ding Ma, Guoliang Li, Peng Wu
Human papillomavirus (HPV) is predominantly associated with HPV-related cancers, however, the precise mechanisms underlying the HPV-host epigenetic architectures in HPV carcinogenesis remain elusive. Here, we employed high-throughput chromosome conformation capture (Hi-C) to comprehensively map HPV16/18-host chromatin interactions. Our study identified the transcription factor Sp1 as a pivotal mediator in programming HPV-host interactions. By targeting Sp1, the active histone modifications (H3K27ac, H3K4me1, and H3K4me3) and the HPV-host chromatin interactions are reprogrammed, which leads to the downregulation of oncogenes located near the integration sites in both HPV (E6/E7) and the host genome (KLF5/MYC)...
March 10, 2024: Cancer Letters
https://read.qxmd.com/read/38462715/a-chromosome-level-genome-of-mango-exclusively-from-long-read-sequence-data
#13
JOURNAL ARTICLE
Upendra Kumari Wijesundara, Ardashir Kharabian Masouleh, Agnelo Furtado, Natalie L Dillon, Robert J Henry
Improvements in long-read sequencing techniques have greatly accelerated plant genome sequencing. Current de novo assemblies are routinely achieved by assembling long-read sequence data into contigs that are assembled to chromosome level by chromatin conformation capture. We report here a chromosome-level mango genome using only PacBio high-fidelity (HiFi) long reads. HiFi reads at high coverage (204x) resulted in the assembly of 17 chromosomes, each as a single contig with telomeres at both ends. The remaining three chromosomes were represented each by two contigs, with telomeres at one end and ribosomal repeats at the other end...
March 10, 2024: Plant Genome
https://read.qxmd.com/read/38448979/reorganization-of-3d-genome-architecture-provides-insights-into-pathogenesis-of-early-fatty-liver-disease-in-laying-hens
#14
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/38447270/cytogenetics-in-the-management-of-hematological-malignancies-an-overview-of-alternative-technologies-for-cytogenetic-characterization
#15
JOURNAL ARTICLE
Valentin Lestringant, Hélène Guermouche-Flament, Mélanie Jimenez-Pocquet, Jean-Baptiste Gaillard, Dominique Penther
Genomic characterization is an essential part of the clinical management of hematological malignancies for diagnostic, prognostic and therapeutic purposes. Although CBA and FISH are still the gold standard in hematology for the detection of CNA and SV, some alternative technologies are intended to complement their deficiencies or even replace them in the more or less near future. In this article, we provide a technological overview of these alternatives. CMA is the historical and well established technique for the high-resolution detection of CNA...
January 12, 2024: Current Research in Translational Medicine
https://read.qxmd.com/read/38447062/chromosome-scale-genome-assembly-for-clubrush-bolboschoenus-planiculmis-indicates-a-karyotype-with-high-chromosome-number-and-heterogeneous-centromere-distribution
#16
JOURNAL ARTICLE
Yu Ning, Yang Li, Hai Yan Lin, En Ze Kang, Yu Xin Zhao, Shu Bin Dong, Yong Li, Xiao Fei Xia, Yi Fei Wang, Chun Yi Li
Bolboschoenus planiculmis (F.Schmidt) T.V.Egorova is a typical wetland plant in the species-rich Cyperaceae family. This species contributes prominently to carbon dynamics and trophic integration in wetland ecosystems.Previous studies have reported that the chromosomes of B. planiculmis are holocentric, i.e. they have kinetic activity along their entire length and carry multiple centromeres. This feature was suggested to lead to a rapid genome evolution through chromosomal fissions and fusions, and participate to the diversification and ecological success of the Bolboschoenus genus...
March 6, 2024: Genome Biology and Evolution
https://read.qxmd.com/read/38432395/ncapd3-promotes-diffuse-large-b-cell-lymphoma-progression-through-modulating-sirt1-expression-in-an-h3k9-monomethylation-dependent-manner
#17
JOURNAL ARTICLE
Tiange Lu, Juan Yang, Yiqing Cai, Mengfei Ding, Zhuoya Yu, Xiaosheng Fang, Xiangxiang Zhou, Xin Wang
INTRODUCTION: Condensin, a family of structural maintenance of chromosome complexes, has been shown to regulate chromosome compaction and segregation during mitosis. NCAPD3, a HEAT-repeat subunit of condensin II, plays a dominant role in condensin-mediated chromosome dynamics but remains unexplored in lymphoma. OBJECTIVES: The study aims to unravel the molecular function and mechanism of NCAPD3 in diffuse large B-cell lymphoma (DLBCL). METHODS: The expression and clinical significance of NCAPD3 were assessed in public database and clinical specimens...
March 2, 2024: Journal of Advanced Research
https://read.qxmd.com/read/38430521/hi-c-techniques-from-genome-assemblies-to-transcription-regulation
#18
JOURNAL ARTICLE
Hana Šimková, Amanda Souza Câmara, Martin Mascher
The invention of chromosome-conformation capture (3C) techniques, in particular the key method Hi-C providing genome-wide information about chromatin contacts, revolutionized the way we study the three-dimensional (3D) organization of the nuclear genome and how it impacts transcription, replication and DNA repair. Since the frequency of chromatin contacts between pairs of genomic segments predictably relates to the distance in the linear genome, the Hi-C information has also proved useful for scaffolding genomic sequences...
March 2, 2024: Journal of Experimental Botany
https://read.qxmd.com/read/38427693/the-impact-of-htlv-1-expression-on-the-3d-structure-and-expression-of-host-chromatin
#19
JOURNAL ARTICLE
Hiroko Yaguchi, Anat Melamed, Saumya Ramanayake, Helen Kiik, Aviva Witkover, Charles R M Bangham
A typical HTLV-1-infected individual carries >104 different HTLV-1-infected T cell clones, each with a single-copy provirus integrated in a unique genomic site. We previously showed that the HTLV-1 provirus causes aberrant transcription in the flanking host genome and, by binding the chromatin architectural protein CTCF, forms abnormal chromatin loops with the host genome. However, it remained unknown whether these effects were exerted simply by the presence of the provirus or were induced by its transcription...
March 1, 2024: PLoS Pathogens
https://read.qxmd.com/read/38417378/identification-of-a-distal-enhancer-regulating-hedgehog-interacting-protein-gene-in-human-lung-epithelial-cells
#20
JOURNAL ARTICLE
Feng Guo, Li Zhang, Yuzhen Yu, Lu Gong, Shiyue Tao, Rhiannon B Werder, Shreya Mishra, Yihan Zhou, Wardatul Jannat Anamika, Taotao Lao, Hiroyuki Inuzuka, Yihan Zhang, Betty Pham, Tao Liu, Tiffany S Tufenkjian, Bradley W Richmond, Wenyi Wei, Hongmei Mou, Andrew A Wilson, Ming Hu, Wei Chen, Xiaobo Zhou
BACKGROUND: An intergenic region at chromosome 4q31 is one of the most significant regions associated with COPD susceptibility and lung function in GWAS. In this region, the implicated causal gene HHIP has a unique epithelial expression pattern in adult human lungs, in contrast to dominant expression in fibroblasts in murine lungs. However, the mechanism underlying the species-dependent cell type-specific regulation of HHIP remains largely unknown. METHODS: We employed snATAC-seq analysis to identify open chromatin regions within the COPD GWAS region in various human lung cell types...
February 27, 2024: EBioMedicine
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