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https://www.readbyqxmd.com/read/29626921/banding-pattern-of-polytene-chromosomes-as-a-representation-of-universal-principles-of-chromatin-organization-into-topological-domains
#1
REVIEW
T D Kolesnikova
Drosophila polytene chromosomes are widely used as a model of eukaryotic interphase chromosomes. The most noticeable feature of polytene chromosome is transverse banding associated with alternation of dense stripes (dark or black bands) and light diffuse areas that encompass alternating less compact gray bands and interbands visible with an electron microscope. In recent years, several approaches have been developed to predict location of morphological structures of polytene chromosomes based on the distribution of proteins on the molecular map of Drosophila genome...
April 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29626919/the-4d-nucleome-genome-compartmentalization-in-an-evolutionary-context
#2
REVIEW
T Cremer, M Cremer, C Cremer
4D nucleome research aims to understand the impact of nuclear organization in space and time on nuclear functions, such as gene expression patterns, chromatin replication, and the maintenance of genome integrity. In this review we describe evidence that the origin of 4D genome compartmentalization can be traced back to the prokaryotic world. In cell nuclei of animals and plants chromosomes occupy distinct territories, built up from ~1 Mb chromatin domains, which in turn are composed of smaller chromatin subdomains and also form larger chromatin domain clusters...
April 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29625054/a-pan-cancer-analysis-of-enhancer-expression-in-nearly-9000-patient-samples
#3
Han Chen, Chunyan Li, Xinxin Peng, Zhicheng Zhou, John N Weinstein, Han Liang
The role of enhancers, a key class of non-coding regulatory DNA elements, in cancer development has increasingly been appreciated. Here, we present the detection and characterization of a large number of expressed enhancers in a genome-wide analysis of 8928 tumor samples across 33 cancer types using TCGA RNA-seq data. Compared with matched normal tissues, global enhancer activation was observed in most cancers. Across cancer types, global enhancer activity was positively associated with aneuploidy, but not mutation load, suggesting a hypothesis centered on "chromatin-state" to explain their interplay...
April 5, 2018: Cell
https://www.readbyqxmd.com/read/29625035/inter-chromosomal-contact-properties-in-live-cell-imaging-and-in-hi-c
#4
Philipp G Maass, A Rasim Barutcu, Catherine L Weiner, John L Rinn
No abstract text is available yet for this article.
April 5, 2018: Molecular Cell
https://www.readbyqxmd.com/read/29622804/producing-genome-structure-populations-with-the-dynamic-and-automated-pgs-software
#5
Nan Hua, Harianto Tjong, Hanjun Shin, Ke Gong, Xianghong Jasmine Zhou, Frank Alber
Chromosome conformation capture technologies such as Hi-C are widely used to investigate the spatial organization of genomes. Because genome structures can vary considerably between individual cells of a population, interpreting ensemble-averaged Hi-C data can be challenging, in particular for long-range and interchromosomal interactions. We pioneered a probabilistic approach for the generation of a population of distinct diploid 3D genome structures consistent with all the chromatin-chromatin interaction probabilities from Hi-C experiments...
May 2018: Nature Protocols
https://www.readbyqxmd.com/read/29615554/flying-the-rna-nest-drosophila-reveals-novel-insights-into-the-transcriptome-dynamics-of-early-development
#6
REVIEW
Fabio Alexis Lefebvre, Éric Lécuyer
Early development is punctuated by a series of pervasive and fast paced transitions. These events reshape a differentiated oocyte into a totipotent embryo and allow it to gradually mount a genetic program of its own, thereby framing a new organism. Specifically, developmental transitions that ensure the maternal to embryonic control of developmental events entail a deep remodeling of transcriptional and transcriptomic landscapes. Drosophila provides an elegant and genetically tractable system to investigate these conserved changes at a dazzling developmental pace...
March 7, 2018: Journal of Developmental Biology
https://www.readbyqxmd.com/read/29614055/cell-specific-pear1-methylation-studies-reveal-a-locus-that-coordinates-expression-of-multiple-genes
#7
Benedetta Izzi, Fabrizia Noro, Katrien Cludts, Kathleen Freson, Marc F Hoylaerts
Chromosomal interactions connect distant enhancers and promoters on the same chromosome, activating or repressing gene expression. PEAR1 encodes the Platelet-Endothelial Aggregation Receptor 1, a contact receptor involved in platelet function and megakaryocyte and endothelial cell proliferation. PEAR1 expression during megakaryocyte differentiation is controlled by DNA methylation at its first CpG island. We identified a PEAR1 cell-specific methylation sensitive region in endothelial cells and megakaryocytes that showed strong chromosomal interactions with ISGL20L2 , RRNAD1 , MRLP24 , HDGF and PRCC , using available promoter capture Hi-C datasets...
April 3, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29605857/analysis-of-chromatin-interactions-mediated-by-specific-architectural-proteins-in-drosophila-cells
#8
Masami Ando-Kuri, I Sarahi M Rivera, M Jordan Rowley, Victor G Corces
Chromosome conformation capture assays have been established, modified, and enhanced for over a decade with the purpose of studying nuclear organization. A recently published method uses in situ Hi-C followed by chromatin immunoprecipitation (HiChIP) to enrich the overall yield of significant genome-wide interactions mediated by a specific protein. Here we applied a modified version of the HiChIP protocol to retrieve the significant contacts mediated by architectural protein CP190 in D. melanogaster cells.
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29570716/the-long-range-interaction-map-of-ribosomal-dna-arrays
#9
Shoukai Yu, Bernardo Lemos
The repeated rDNA array gives rise to the nucleolus, an organelle that is central to cellular processes as varied as stress response, cell cycle regulation, RNA modification, cell metabolism, and genome stability. The rDNA array is also responsible for the production of more than 70% of all cellular RNAs (the ribosomal RNAs). The rRNAs are produced from two sets of loci: the 5S rDNA array resides exclusively on human chromosome 1 while the 45S rDNA arrays reside on the short arm of five human acrocentric chromosomes...
March 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29554289/genomedisco-a-concordance-score-for-chromosome-conformation-capture-experiments-using-random-walks-on-contact-map-graphs
#10
Oana Ursu, Nathan Boley, Maryna Taranova, Y X Rachel Wang, Galip Gurkan Yardimci, William Stafford Noble, Anshul Kundaje
Motivation: The three-dimensional organization of chromatin plays a critical role in gene regulation and disease. High-throughput chromosome conformation capture experiments such as Hi-C are used to obtain genome-wide maps of 3D chromatin contacts. However, robust estimation of data quality and systematic comparison of these contact maps is challenging due to the multi-scale, hierarchical structure of chromatin contacts and the resulting properties of experimental noise in the data. Measuring concordance of contact maps is important for assessing reproducibility of replicate experiments and for modeling variation between different cellular contexts...
March 15, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29541161/3c-and-3c-based-techniques-the-powerful-tools-for-spatial-genome-organization-deciphering
#11
REVIEW
Jinlei Han, Zhiliang Zhang, Kai Wang
It is well known that the chromosomes are organized in the nucleus and this spatial arrangement of genome play a crucial role in gene regulation and genome stability. Different techniques have been developed and applied to uncover the intrinsic mechanism of genome architecture, especially the chromosome conformation capture (3C) and 3C-derived methods. 3C and 3C-derived techniques provide us approaches to perform high-throughput chromatin architecture assays at the genome scale. However, the advantage and disadvantage of current methodologies of C-technologies have not been discussed extensively...
2018: Molecular Cytogenetics
https://www.readbyqxmd.com/read/29531791/evidence-for-a-second-ankylosing-spondylitis-associated-runx3-regulatory-polymorphism
#12
Matteo Vecellio, Adrian Cortes, Amity R Roberts, Jonathan Ellis, Carla Jayne Cohen, Julian C Knight, Matthew A Brown, Paul Bowness, Bryan Paul Wordsworth
Objectives: To explore the functions of RUNX3 single nucleotide polymorphisms (SNPs) associated with ankylosing spondylitis (AS). Methods: Individual SNP associations were evaluated in 4230 UK cases. Their effects on transcription factor (TF) binding, transcription regulation, chromatin modifications, gene expression and gene interactions were tested by database interrogation, luciferase reporter assays, electrophoretic mobility gel shifts, chromatin immunoprecipitation and real-time PCR...
2018: RMD Open
https://www.readbyqxmd.com/read/29531215/capture-hi-c-identifies-putative-target-genes-at-33-breast-cancer-risk-loci
#13
Joseph S Baxter, Olivia C Leavy, Nicola H Dryden, Sarah Maguire, Nichola Johnson, Vita Fedele, Nikiana Simigdala, Lesley-Ann Martin, Simon Andrews, Steven W Wingett, Ioannis Assiotis, Kerry Fenwick, Ritika Chauhan, Alistair G Rust, Nick Orr, Frank Dudbridge, Syed Haider, Olivia Fletcher
Genome-wide association studies (GWAS) have identified approximately 100 breast cancer risk loci. Translating these findings into a greater understanding of the mechanisms that influence disease risk requires identification of the genes or non-coding RNAs that mediate these associations. Here, we use Capture Hi-C (CHi-C) to annotate 63 loci; we identify 110 putative target genes at 33 loci. To assess the support for these target genes in other data sources we test for associations between levels of expression and SNP genotype (eQTLs), disease-specific survival (DSS), and compare them with somatically mutated cancer genes...
March 12, 2018: Nature Communications
https://www.readbyqxmd.com/read/29528523/multiple-functional-variants-at-13q14-risk-locus-for-osteoporosis-regulate-rankl-expression-through-long-range-super-enhancer
#14
Dong-Li Zhu, Xiao-Feng Chen, Wei-Xin Hu, Shan-Shan Dong, Bing-Jie Lu, Yu Rong, Yi-Xiao Chen, Hao Chen, Hlaing Nwe Thynn, Nai-Ning Wang, Yan Guo, Tie-Lin Yang
RANKL is a key regulator involved in bone metabolism, and a drug target for osteoporosis. The clinical diagnosis and assessment of osteoporosis are mainly based on bone mineral density (BMD). Previous powerful genome-wide association studies (GWASs) have identified multiple intergenic single nucleotide polymorphisms (SNPs) located over 100 kb upstream of RANKL and 65 kb downstream of AKAP11 at 13q14.11 for osteoporosis. Whether these SNPs exert their roles on osteoporosis through RANKL is unknown. In this study, we conducted integrative analyses combining expression quantitative trait locus (eQTL), genomic chromatin interaction (Hi-C), epigenetic annotation and a series of functional assays...
March 12, 2018: Journal of Bone and Mineral Research: the Official Journal of the American Society for Bone and Mineral Research
https://www.readbyqxmd.com/read/29526697/inter-chromosomal-contact-properties-in-live-cell-imaging-and-in-hi-c
#15
Philipp G Maass, A Rasim Barutcu, Catherine L Weiner, John L Rinn
Imaging (fluorescence in situ hybridization [FISH]) and genome-wide chromosome conformation capture (Hi-C) are two major approaches to the study of higher-order genome organization in the nucleus. Intra-chromosomal and inter-chromosomal interactions (referred to as non-homologous chromosomal contacts [NHCCs]) have been observed by several FISH-based studies, but locus-specific NHCCs have not been detected by Hi-C. Due to crosslinking, neither of these approaches assesses spatiotemporal properties. Toward resolving the discrepancies between imaging and Hi-C, we sought to understand the spatiotemporal properties of NHCCs in living cells by CRISPR/Cas9 live-cell imaging (CLING)...
February 27, 2018: Molecular Cell
https://www.readbyqxmd.com/read/29522804/molecular-dynamics-simulations-of-the-strings-and-binders-switch-model-of-chromatin
#16
REVIEW
Carlo Annunziatella, Andrea M Chiariello, Andrea Esposito, Simona Bianco, Luca Fiorillo, Mario Nicodemi
In recent years interest has grown on the applications of polymer physics to model chromatin folding in order to try to make sense of the complexity of experimental data emerging from new technologies such as Hi-C or GAM, in a principled way. Here we review the methods employed to efficiently implement Molecular Dynamics computer simulations of polymer models, focusing in particular on the String&Binders Switch (SBS) model. The constant improvement of such methods and computer power is returning increasingly more accurate insights on the structure and molecular mechanisms underlying the spatial organization of chromosomes in the cell nucleus...
March 6, 2018: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/29522512/4cin-a-computational-pipeline-for-3d-genome-modeling-and-virtual-hi-c-analyses-from-4c-data
#17
Ibai Irastorza-Azcarate, Rafael D Acemel, Juan J Tena, Ignacio Maeso, José Luis Gómez-Skarmeta, Damien P Devos
The use of 3C-based methods has revealed the importance of the 3D organization of the chromatin for key aspects of genome biology. However, the different caveats of the variants of 3C techniques have limited their scope and the range of scientific fields that could benefit from these approaches. To address these limitations, we present 4Cin, a method to generate 3D models and derive virtual Hi-C (vHi-C) heat maps of genomic loci based on 4C-seq or any kind of 4C-seq-like data, such as those derived from NG Capture-C...
March 9, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29514091/long-range-enhancer-interactions-are-prevalent-in-mouse-embryonic-stem-cells-and-are-reorganized-upon-pluripotent-state-transition
#18
Clara Lopes Novo, Biola-Maria Javierre, Jonathan Cairns, Anne Segonds-Pichon, Steven W Wingett, Paula Freire-Pritchett, Mayra Furlan-Magaril, Stefan Schoenfelder, Peter Fraser, Peter J Rugg-Gunn
Transcriptional enhancers, including super-enhancers (SEs), form physical interactions with promoters to regulate cell-type-specific gene expression. SEs are characterized by high transcription factor occupancy and large domains of active chromatin, and they are commonly assigned to target promoters using computational predictions. How promoter-SE interactions change upon cell state transitions, and whether transcription factors maintain SE interactions, have not been reported. Here, we used promoter-capture Hi-C to identify promoters that interact with SEs in mouse embryonic stem cells (ESCs)...
March 6, 2018: Cell Reports
https://www.readbyqxmd.com/read/29507293/dissecting-super-enhancer-hierarchy-based-on-chromatin-interactions
#19
Jialiang Huang, Kailong Li, Wenqing Cai, Xin Liu, Yuannyu Zhang, Stuart H Orkin, Jian Xu, Guo-Cheng Yuan
Recent studies have highlighted super-enhancers (SEs) as important regulatory elements for gene expression, but their intrinsic properties remain incompletely characterized. Through an integrative analysis of Hi-C and ChIP-seq data, here we find that a significant fraction of SEs are hierarchically organized, containing both hub and non-hub enhancers. Hub enhancers share similar histone marks with non-hub enhancers, but are distinctly associated with cohesin and CTCF binding sites and disease-associated genetic variants...
March 5, 2018: Nature Communications
https://www.readbyqxmd.com/read/29503869/tads-are-3d-structural-units-of-higher-order-chromosome-organization-in-drosophila
#20
Quentin Szabo, Daniel Jost, Jia-Ming Chang, Diego I Cattoni, Giorgio L Papadopoulos, Boyan Bonev, Tom Sexton, Julian Gurgo, Caroline Jacquier, Marcelo Nollmann, Frédéric Bantignies, Giacomo Cavalli
Deciphering the rules of genome folding in the cell nucleus is essential to understand its functions. Recent chromosome conformation capture (Hi-C) studies have revealed that the genome is partitioned into topologically associating domains (TADs), which demarcate functional epigenetic domains defined by combinations of specific chromatin marks. However, whether TADs are true physical units in each cell nucleus or whether they reflect statistical frequencies of measured interactions within cell populations is unclear...
February 2018: Science Advances
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