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https://www.readbyqxmd.com/read/29774079/long-non-coding-rnas-ac026904-1-and-uca1-a-one-two-punch-for-tgf-%C3%AE-induced-snai2-activation-and-epithelial-mesenchymal-transition-in-breast-cancer
#1
Guo-Yin Li, Wei Wang, Jian-Yong Sun, Bo Xin, Xiang Zhang, Ting Wang, Qian-Feng Zhang, Li-Bo Yao, Hua Han, Dai-Ming Fan, An-Gang Yang, Lin-Tao Jia, Lei Wang
Transforming growth factor-β (TGF-β) has received much attention as a major inducer of epithelial-mesenchymal transition (EMT) during cancer progression, mainly by activating a set of pleiotropic transcription factors including SNAI2/Slug. However, the involvement of long non-coding RNAs (lncRNAs) in TGF-β-induced Slug activation and EMT remains largely unknown. Methods: In this study, we used microarray analysis to compare lncRNA expression profiles between TGF-β treated and untreated breast cancer cells...
2018: Theranostics
https://www.readbyqxmd.com/read/29772403/theoretical-study-of-the-intermolecular-recognition-mechanism-between-survivin-and-substrate-based-on-conserved-binding-mode-analysis
#2
Chao Wu, Liguang Mao, Xie Huang, Weitao Fu, Xiong Cai, Yuepiao Cai, Liqun Shen, Xiaoxia Ye
Survivin is the smallest member of IAP (inhibitor of apoptosis protein) family, which plays important roles in both mitosis and apoptosis. It has become an attractive drug target due to its overexpression in many human cancers. Survivin has been proven to bind to Smac/DIABLO protein that indirectly inhibits apoptosis. Meanwhile, it is the key subunit of chromosome passenger complex (CPC) which bind to the N-terminal tail of phosphorylated histone H3T3ph during mitosis. Up to now, Survivin directly targeting inhibitor has yet to merge since the difficulty of disrupting the protein-protein interactions (PPIs) between Survivin and its substrate proteins...
May 8, 2018: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/29772275/5c-id-increased-resolution-chromosome-conformation-capture-carbon-copy-with-in-situ-3c-and-double-alternating-primer-design
#3
Ji Hun Kim, Katelyn R Titus, Wanfeng Gong, Jonathan A Beagan, Zhendong Cao, Jennifer E Phillips-Cremins
Mammalian genomes are folded in a hierarchy of compartments, topologically associating domains (TADs), subTADs, and looping interactions. Currently, there is a great need to evaluate the link between chromatin topology and genome function across many biological conditions and genetic perturbations. Hi-C can generate genome-wide maps of looping interactions but is intractable for high-throughput comparison of loops across multiple conditions due to the enormous number of reads (>6 Billion) required per library...
May 14, 2018: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/29767704/gene-regulation-in-the-3d-genome
#4
Yun Li, Ming Hu, Yin Shen
The spatial organization of the genome is essential for the precise control of gene expression. Recent advances in sequencing and imaging technologies allow us to explore the 3D genome and its relationship to gene regulation at an unprecedented scale. In this review, we provide an overview of lessons learned from studying the chromatin structure and their implications in communications between gene promoters and distal cis-regulatory elements, such as enhancers. We first review the current knowledge of general genome organization, followed by the importance of chromatin folding in gene regulation...
May 14, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29763375/chromosomal-architecture-and-placental-expression-of-the-human-growth-hormone-gene-family-are-targeted-by-pre-pregnancy-maternal-obesity
#5
Yan Jin, Hana Vakili, SongYan Liu, Savas Menticoglou, Margaret E Bock, Peter A Cattini
The human (h) placental lactogenic hormone chorionic somatomammotropin (CS) is highly produced during pregnancy and acts as a metabolic adaptor in response to maternal insulin resistance. Maternal obesity can exacerbate this "resistance" and a >75% decrease in CS RNA levels was observed in term placentas from obese versus lean women. The genes coding for hCS (hCS-A and hCS-B) and placental growth hormone (hGH-V) as well as the hCS-L pseudogene and pituitary growth hormone (GH) gene (hGH-N) are located at a single locus on chromosome 17...
May 15, 2018: American Journal of Physiology. Endocrinology and Metabolism
https://www.readbyqxmd.com/read/29748383/fshd2-and-bams-associated-mutations-confer-opposing-effects-on-smchd1-function
#6
Alexandra D Gurzau, Kelan Chen, Shifeng Xue, Weiwen Dai, Isabelle S Lucet, Thanh Thao Nguyen Ly, Bruno Reversade, Marnie E Blewitt, James M Murphy
Structural maintenance of chromosomes flexible hinge domain-containing 1 (Smchd1) plays important roles in epigenetic silencing and normal mammalian development. Recently, heterozygous mutations in SMCHD1 have been reported in two disparate disorders: facioscapulohumeral muscular dystrophy type 2 (FSHD2) and Bosma arhinia microphthalmia syndrome (BAMS). FSHD2-associated mutations lead to loss of function, however whether BAMS is associated with loss or gain of function mutations in SMCHD1 is unclear. Here, we have assessed the effect of SMCHD1 missense mutations from FSHD2 and BAMS patients on ATP hydrolysis activity, protein conformation and the effect of BAMS mutations on craniofacial development in a Xenopus model...
May 10, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29745835/graphteams-a-method-for-discovering-spatial-gene-clusters-in-hi-c-sequencing-data
#7
Tizian Schulz, Jens Stoye, Daniel Doerr
BACKGROUND: Hi-C sequencing offers novel, cost-effective means to study the spatial conformation of chromosomes. We use data obtained from Hi-C experiments to provide new evidence for the existence of spatial gene clusters. These are sets of genes with associated functionality that exhibit close proximity to each other in the spatial conformation of chromosomes across several related species. RESULTS: We present the first gene cluster model capable of handling spatial data...
May 8, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29733521/hmga2-promotes-glioma-invasion-and-poor-prognosis-via-a-long-range-chromatin-interaction
#8
Shanshan Zhang, Huibian Zhang, Lin Yu
To identify the function and underlying mechanisms of HMGA2 on the prognosis and invasion of gliomas, HMGA2 was detected by immunohistochemistry. The Kaplan-Meier and Cox's regression analysis results showed that higher HMGA2 level predicted the poorer outcomes of glioma patients. ChIP-qPCR, DNA electrophoretic mobility shift assay, chromosome conformation capture, and co-immunoprecipitation were applied to identify HMGA2-activated target sites, which were further verified by mRNA and protein expression detection...
May 7, 2018: Cancer Medicine
https://www.readbyqxmd.com/read/29733418/genome-wide-association-study-and-functional-analysis-of-feet-and-leg-conformation-traits-in-nellore-cattle
#9
Giovana Vargas, Haroldo H R Neves, Gregório Miguel F Camargo, Vânia Cardoso, Danísio P Munari, Roberto Carvalheiro
Feet and leg conformation is evaluated as a subset of conformational structure traits in dairy and beef cattle and is related to the feet and leg quality that can compromise the animals' productive performance and longevity. The aim of this study was to perform a genome-wide association study (GWAS) of two traits related to feet and leg conformation in Nellore cattle to identify chromosomal regions related to the expression of these traits. Phenotypic and pedigree data from 104,725 animals and genotypes from 1,435 animals and 407,730 SNPs were used...
May 4, 2018: Journal of Animal Science
https://www.readbyqxmd.com/read/29723572/iteratively-improving-hi-c-experiments-one-step-at-a-time
#10
Rosela Golloshi, Jacob Sanders, Rachel Patton McCord
The 3D organization of eukaryotic chromosomes affects key processes such as gene expression, DNA replication, cell division, and response to DNA damage. The genome-wide chromosome conformation capture (Hi-C) approach can characterize the landscape of 3D genome organization by measuring interaction frequencies between all genomic regions. Hi-C protocol improvements and rapid advances in DNA sequencing power have made Hi-C useful to study diverse biological systems, not only to elucidate the role of 3D genome structure in proper cellular function, but also to characterize genomic rearrangements, assemble new genomes, and consider chromatin interactions as potential biomarkers for diseases...
April 30, 2018: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/29712907/theoretical-principles-of-transcription-factor-traffic-on-folded-chromatin
#11
Ruggero Cortini, Guillaume J Filion
All organisms regulate transcription of their genes. To understand this process, a complete understanding of how transcription factors find their targets in cellular nuclei is essential. The DNA sequence and other variables are known to influence this binding, but the distribution of transcription factor binding patterns remains mostly unexplained in metazoan genomes. Here, we investigate the role of chromosome conformation in the trajectories of transcription factors. Using molecular dynamics simulations, we uncover the principles of their diffusion on chromatin...
April 30, 2018: Nature Communications
https://www.readbyqxmd.com/read/29712868/-insulin-promoter-in-human-pancreatic-%C3%AE-cells-contacts-diabetes-susceptibility-loci-and-regulates-genes-affecting-insulin-metabolism
#12
Xing Jian, Gary Felsenfeld
Both type 1 and type 2 diabetes involve a complex interplay between genetic, epigenetic, and environmental factors. Our laboratory has been interested in the physical interactions, in nuclei of human pancreatic β cells, between the insulin ( INS) gene and other genes that are involved in insulin metabolism. We have identified, using Circularized Chromosome Conformation Capture (4C), many physical contacts in a human pancreatic β cell line between the INS promoter on chromosome 11 and sites on most other chromosomes...
April 30, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29703667/entering-the-next-dimension-plant-genomes-in-3d
#13
REVIEW
Mariana Sotelo-Silveira, Ricardo A Chávez Montes, Jose R Sotelo-Silveira, Nayelli Marsch-Martínez, Stefan de Folter
After linear sequences of genomes and epigenomic landscape data, the 3D organization of chromatin in the nucleus is the next level to be explored. Different organisms present a general hierarchical organization, with chromosome territories at the top. Chromatin interaction maps, obtained by chromosome conformation capture (3C)-based methodologies, for eight plant species reveal commonalities, but also differences, among them and with animals. The smallest structures, found in high-resolution maps of the Arabidopsis genome, are single genes...
April 24, 2018: Trends in Plant Science
https://www.readbyqxmd.com/read/29700467/digestion-ligation-only-hi-c-is-an-efficient-and-cost-effective-method-for-chromosome-conformation-capture
#14
Da Lin, Ping Hong, Siheng Zhang, Weize Xu, Muhammad Jamal, Keji Yan, Yingying Lei, Liang Li, Yijun Ruan, Zhen F Fu, Guoliang Li, Gang Cao
Chromosome conformation capture (3C) technologies can be used to investigate 3D genomic structures. However, high background noise, high costs, and a lack of straightforward noise evaluation in current methods impede the advancement of 3D genomic research. Here we developed a simple digestion-ligation-only Hi-C (DLO Hi-C) technology to explore the 3D landscape of the genome. This method requires only two rounds of digestion and ligation, without the need for biotin labeling and pulldown. Non-ligated DNA was efficiently removed in a cost-effective step by purifying specific linker-ligated DNA fragments...
April 26, 2018: Nature Genetics
https://www.readbyqxmd.com/read/29699482/structural-disorder-of-plasmid-encoded-proteins-in-bacteria-and-archaea
#15
Nenad S Mitić, Saša N Malkov, Jovana J Kovačević, Gordana M Pavlović-Lažetić, Miloš V Beljanski
BACKGROUND: In the last decade and a half it has been firmly established that a large number of proteins do not adopt a well-defined (ordered) structure under physiological conditions. Such intrinsically disordered proteins (IDPs) and intrinsically disordered (protein) regions (IDRs) are involved in essential cell processes through two basic mechanisms: the entropic chain mechanism which is responsible for rapid fluctuations among many alternative conformations, and molecular recognition via short recognition elements that bind to other molecules...
April 25, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29699389/a-synopsis-on-current-practice-in-the-diagnosis-and-management-of-patients-with-turner-syndrome-in-turkey-a-survey-of-18-pediatric-endocrinology-centers
#16
Ahmet Uçar, Ayhan Abacı, Özgür Pirgon, Bumin Dündar, Filiz Tütüncüler, Gönül Çatlı, Ahmet Anık, Aylin Kılınç Uğurlu, Atilla Büyükgebiz
Objective: A comprehensive survey was conducted courtesy of the Turkish Turner study group to evaluate the shortcomings of clinical care in patients with Turner syndrome (TS) in Turkey. Methods: A structured questionnaire prepared by the Turner study group in Turkey, which covers relevant aspects of the care of patients with TS, was sent to all pediatric endocrinology centers. Results: Eighteen centers (41%) returned the questionnaire. In the majority of the centers, diagnostic genetic testing, screening for Y chromosomal material, protocols regarding the timing and posology of growth hormone (GH) and estrogen, thrombophilia screening, fertility information, and screening for glucose intolerance, thyroid, and coeliac diseases in patients with TS were in line with the current consensus...
April 27, 2018: Journal of Clinical Research in Pediatric Endocrinology
https://www.readbyqxmd.com/read/29686321/chromatin-conformation-regulates-the-coordination-between-dna-replication-and-transcription
#17
Ricardo Almeida, José Miguel Fernández-Justel, Cristina Santa-María, Jean-Charles Cadoret, Laura Cano-Aroca, Rodrigo Lombraña, Gonzalo Herranz, Alessandra Agresti, María Gómez
Chromatin is the template for the basic processes of replication and transcription, making the maintenance of chromosomal integrity critical for cell viability. To elucidate how dividing cells respond to alterations in chromatin structure, here we analyse the replication programme of primary cells with altered chromatin configuration caused by the genetic ablation of the HMGB1 gene, or three histone H1 genes. We find that loss of chromatin compaction in H1-depleted cells triggers the accumulation of stalled forks and DNA damage as a consequence of transcription-replication conflicts...
April 23, 2018: Nature Communications
https://www.readbyqxmd.com/read/29685368/principles-of-chromosome-architecture-revealed-by-hi-c
#18
REVIEW
Kyle P Eagen
Chromosomes are folded and compacted in interphase nuclei, but the molecular basis of this folding is poorly understood. Chromosome conformation capture methods, such as Hi-C, combine chemical crosslinking of chromatin with fragmentation, DNA ligation, and high-throughput DNA sequencing to detect neighboring loci genome-wide. Hi-C has revealed the segregation of chromatin into active and inactive compartments and the folding of DNA into self-associating domains and loops. Depletion of CTCF, cohesin, or cohesin-associated proteins was recently shown to affect the majority of domains and loops in a manner that is consistent with a model of DNA folding through extrusion of chromatin loops...
April 20, 2018: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/29681056/a-cytological-approach-to-study-meiotic-recombination-and-chromosome-dynamics-of-arabidopsis-thaliana-male-meiocytes-in-three-dimensions
#19
Aurélie Hurel, Dylan Phillips, Nathalie Vrielynck, Christine Mézard, Mathilde Grelon, Nicolas Christophorou
During meiotic prophase I chromosomes undergo dramatic conformational changes that accompany chromosome condensation, pairing and recombination between homologs. These changes include the anchoring of telomeres to the nuclear envelope and their clustering to form a bouquet. In plants, these events have been studied and illustrated in intact meiocytes of large genome species. Arabidopsis thaliana is an excellent genetic model where major molecular pathways that control synapsis and recombination between homologs have been uncovered...
April 22, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29678955/studying-x-chromosome-inactivation-in-the-single-cell-genomic-era
#20
REVIEW
Andrew Keniry, Marnie E Blewitt
Single-cell genomics is set to revolutionise our understanding of how epigenetic silencing works; by studying specific epigenetic marks or chromatin conformations in single cells, it is possible to ask whether they cause transcriptional silencing or are instead a consequence of the silent state. Here, we review what single-cell genomics has revealed about X chromosome inactivation, perhaps the best characterised mammalian epigenetic process, highlighting the novel findings and important differences between mouse and human X inactivation uncovered through these studies...
April 20, 2018: Biochemical Society Transactions
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