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chromosome conformation

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https://www.readbyqxmd.com/read/28439858/circular-chromosome-conformation-capture-in-plants
#1
Stefan Grob
The study of nuclear architecture promises novel insights into genome function and regulation. Hereby, quantitative methods based on chromosome conformation capture (3C) revolutionized the field, as they allow accurate and unbiased characterization of 3D genome organization of genomic regions of interest. The choice of the appropriate 3C derivate is crucial to acquire results suited for a specific research question. Circular 3C (4C) is the method of choice to study the genome-wide 3D architecture of a specific genomic region of interest...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28435001/hi-c-2-0-an-optimized-hi-c-procedure-for-high-resolution-genome-wide-mapping-of-chromosome-conformation
#2
Houda Belaghzal, Job Dekker, Johan H Gibcus
Chromosome conformation capture-based methods such as Hi-C have become mainstream techniques for the study of the 3D organization of genomes. These methods convert chromatin interactions reflecting topological chromatin structures into digital information (counts of pair-wise interactions). Here, we describe an updated protocol for Hi-C (Hi-C 2.0) that integrates recent improvements into a single protocol for efficient and high-resolution capture of chromatin interactions. This protocol combines chromatin digestion and frequently cutting enzymes to obtain kilobase (Kb) resolution...
April 18, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28426986/schr%C3%A3-dinger-s-code-script-not-a-genetic-cipher-but-a-code-of-development
#3
A E Walsby, M J S Hodge
In his book What is Life? Erwin Schrödinger coined the term 'code-script', thought by some to be the first published suggestion of a hereditary code and perhaps a forerunner of the genetic code. The etymology of 'code' suggests three meanings relevant to 'code-script which we distinguish as 'cipher-code', 'word-code' and 'rule-code'. Cipher-codes and word-codes entail translation of one set of characters into another. The genetic code comprises not one but two cipher-codes: the first is the DNA 'base-pairing cipher'; the second is the 'nucleotide-amino-acid cipher', which involves the translation of DNA base sequences into amino-acid sequences...
April 17, 2017: Studies in History and Philosophy of Biological and Biomedical Sciences
https://www.readbyqxmd.com/read/28426272/temperature-dependent-regulation-of-rdna-condensation-in-saccharomyces-cerevisiae
#4
Donglai Shen, Robert V Skibbens
Chromatin condensation during mitosis produces detangled and discrete DNA entities required for high fidelity sister chromatid segregation during mitosis and positions DNA away from the cleavage furrow during cytokinesis. Regional condensation during G1 also establishes a nuclear architecture through which gene transcription is regulated but remains plastic so that cells can respond to changes in nutrient levels, temperature and signaling molecules. To date, however, the potential impact of this plasticity on mitotic chromosome condensation remains unknown...
April 20, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28424341/alterations-in-three-dimensional-organization-of-the-cancer-genome-and-epigenome
#5
Joanna Achinger-Kawecka, Phillippa C Taberlay, Susan J Clark
The structural and functional basis of the genome is provided by the three-dimensional (3D) chromatin state. To enable accurate gene regulation, enhancer elements and promoter regions are brought into close spatial proximity to ensure proper, cell type-specific gene expression. In cancer, genetic and epigenetic processes can deregulate the transcriptional program. To investigate whether the 3D chromatin state is also disrupted in cancer we performed Hi-C chromosome conformation sequencing in normal and prostate cancer cells and compared the chromatin interaction maps with changes to the genome and epigenome...
April 19, 2017: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/28411415/chromosome-conformation-capture-based-studies-reveal-novel-features-of-plant-nuclear-architecture
#6
REVIEW
Stefan Grob, Ueli Grossniklaus
Nuclear genome organization has recently received increasing attention due to its manifold functions in basic nuclear processes, such as replication, transcription, and the maintenance of genome integrity. Using technologies based on chromosome conformation capture, such as Hi-C, we now have the possibility to study the three-dimensional organization of the genome at unprecedented resolution, shedding light onto a previously unexplored level of nuclear architecture. In plants, research in this field is still in its infancy but a number of publications provided first insights into basic principles of nuclear genome organization and the factors that influence it...
April 12, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28407191/genome-wide-association-analysis-of-body-conformation-traits-in-mexican-holstein-cattle-using-a-mix-of-sampled-and-imputed-snp-genotypes
#7
M E González, V M González, M F Montaño, G E Medina, P Mahadevan, C Villa, R Villa
In arid and semi-arid zones, animal health and production are closely correlated with body conformation traits. These selected traits, in turn, allow livestock to adapt unfavorable soil and environmental conditions. The primary objective of this study was to perform a genome-wide association analysis for a set of sampled and imputed SNPs with 16 conformation traits in a population of Holstein cows from a desert area of Northwestern Mexico. Imputation from 6K to 50K SNPs was performed as a low-cost optimization strategy...
April 13, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28407103/a-network-of-cis-and-trans-interactions-is-required-for-parb-spreading
#8
Dan Song, Kristen Rodrigues, Thomas G W Graham, Joseph J Loparo
Most bacteria utilize the highly conserved parABS partitioning system in plasmid and chromosome segregation. This system depends on a DNA-binding protein ParB, which binds specifically to the centromere DNA sequence parS and to adjacent non-specific DNA over multiple kilobases in a phenomenon called spreading. Previous single-molecule experiments in combination with genetic, biochemical and computational studies have argued that ParB spreading requires cooperative interactions between ParB dimers including DNA bridging and possible nearest-neighbor interactions...
April 12, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28399820/multi-scale-structural-community-organisation-of-the-human-genome
#9
Rasha E Boulos, Nicolas Tremblay, Alain Arneodo, Pierre Borgnat, Benjamin Audit
BACKGROUND: Structural interaction frequency matrices between all genome loci are now experimentally achievable thanks to high-throughput chromosome conformation capture technologies. This ensues a new methodological challenge for computational biology which consists in objectively extracting from these data the structural motifs characteristic of genome organisation. RESULTS: We deployed the fast multi-scale community mining algorithm based on spectral graph wavelets to characterise the networks of intra-chromosomal interactions in human cell lines...
April 11, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28393832/structural-insights-into-pot1-tpp1-interaction-and-pot1-c-terminal-mutations-in-human-cancer
#10
Cong Chen, Peili Gu, Jian Wu, Xianyun Chen, Shuangshuang Niu, Hong Sun, Lijie Wu, Na Li, Junhui Peng, Shaohua Shi, Cuiying Fan, Min Huang, Catherine C L Wong, Qingguo Gong, Chandan Kumar-Sinha, Rongguang Zhang, Lajos Pusztai, Rekha Rai, Sandy Chang, Ming Lei
Mammalian shelterin proteins POT1 and TPP1 form a stable heterodimer that protects chromosome ends and regulates telomerase-mediated telomere extension. However, how POT1 interacts with TPP1 remains unknown. Here we present the crystal structure of the C-terminal portion of human POT1 (POT1C) complexed with the POT1-binding motif of TPP1. The structure shows that POT1C contains two domains, a third OB fold and a Holliday junction resolvase-like domain. Both domains are essential for binding to TPP1. Notably, unlike the heart-shaped structure of ciliated protozoan Oxytricha nova TEBPα-β complex, POT1-TPP1 adopts an elongated V-shaped conformation...
April 10, 2017: Nature Communications
https://www.readbyqxmd.com/read/28377929/expression-mutation-and-amplification-status-of-egfr-and-its-correlation-with-five-mirnas-in-salivary-gland-tumours
#11
Emanuela Boštjančič, Nina Hauptman, Aleš Grošelj, Damjan Glavač, Metka Volavšek
Malignant salivary gland tumours are rare histologically and clinically heterogeneous group of tumours, missing prognostic factors and therapeutic targets. MicroRNAs (miRNAs), small noncoding RNAs, and posttranscriptional regulators of mRNA are poorly described in different subtypes of salivary gland tumours. Epidermal growth factor receptor (EGFR), an important therapeutic target and target of certain miRNAs (i.e., miR-133b), shows variable degrees of expression in salivary gland tumours. Our study included 70 parotid gland tumours of different histological subtypes...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28377493/roles-of-leu28-side-chain-intercalation-in-the-interaction-between-cren7-and-dna
#12
Zhenfeng Zhang, Mohan Zhao, Li Wang, Yuanyuan Chen, Yuhui Dong, Yong Gong, Li Huang
Crenarchaeal chromatin protein Cren7 binds double-stranded DNA in the minor groove, introducing a sharp single-step DNA kink. The side chain of Leu28, a residue conserved among all Cren7 homologues, intercalates into the kink DNA step. In this study, we replaced Leu28 with a residue containing a hydrophobic side chain of different sizes (i.e., L28A, L28V, L28I, L28M and L28F). Both the stability of the Cren7-DNA complex and the ability of Cren7 to constrain DNA supercoils correlated well with the size of the intercalated side chain...
April 4, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28373564/cmg-pol-epsilon-dynamics-suggests-a-mechanism-for-the-establishment-of-leading-strand-synthesis-in-the-eukaryotic-replisome
#13
Jin Chuan Zhou, Agnieszka Janska, Panchali Goswami, Ludovic Renault, Ferdos Abid Ali, Abhay Kotecha, John F X Diffley, Alessandro Costa
The replisome unwinds and synthesizes DNA for genome duplication. In eukaryotes, the Cdc45-MCM-GINS (CMG) helicase and the leading-strand polymerase, Pol epsilon, form a stable assembly. The mechanism for coupling DNA unwinding with synthesis is starting to be elucidated, however the architecture and dynamics of the replication fork remain only partially understood, preventing a molecular understanding of chromosome replication. To address this issue, we conducted a systematic single-particle EM study on multiple permutations of the reconstituted CMG-Pol epsilon assembly...
April 3, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28373206/structures-of-partition-protein-para-with-nonspecific-dna-and-parb-effector-reveal-molecular-insights-into-principles-governing-walker-box-dna-segregation
#14
Hengshan Zhang, Maria A Schumacher
Walker-box partition systems are ubiquitous in nature and mediate the segregation of bacterial and archaeal DNA. Well-studied plasmid Walker-box partition modules require ParA, centromere-DNA, and a centromere-binding protein, ParB. In these systems, ParA-ATP binds nucleoid DNA and uses it as a substratum to deliver ParB-attached cargo DNA, and ParB drives ParA dynamics, allowing ParA progression along the nucleoid. How ParA-ATP binds nonspecific DNA and is regulated by ParB is unclear. Also under debate is whether ParA polymerizes on DNA to mediate segregation...
April 3, 2017: Genes & Development
https://www.readbyqxmd.com/read/28369584/clustered-abasic-lesions-profoundly-change-the-structure-and-stability-of-human-telomeric-g-quadruplexes
#15
Iva Kejnovská, Klára Bednárová, Daniel Renciuk, Zuzana Dvoráková, Petra Školáková, Lukáš Trantírek, Radovan Fiala, Michaela Vorlícková, Janos Sagi
Ionizing radiation produces clustered damage to DNA which is difficult to repair and thus more harmful than single lesions. Clustered lesions have only been investigated in dsDNA models. Introducing the term 'clustered damage to G-quadruplexes' we report here on the structural effects of multiple tetrahydrofuranyl abasic sites replacing loop adenines (A/AP) and tetrad guanines (G/AP) in quadruplexes formed by the human telomere d[AG3(TTAG3)3] (htel-22) and d[TAG3(TTAG3)3TT] (htel-25) in K+ solutions. Single to triple A/APs increased the population of parallel strands in their structures by stabilizing propeller type loops, shifting the antiparallel htel-22 into hybrid or parallel quadruplexes...
March 22, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28358394/long-read-chia-pet-for-base-pair-resolution-mapping-of-haplotype-specific-chromatin-interactions
#16
Xingwang Li, Oscar Junhong Luo, Ping Wang, Meizhen Zheng, Danjuan Wang, Emaly Piecuch, Jacqueline Jufen Zhu, Simon Zhongyuan Tian, Zhonghui Tang, Guoliang Li, Yijun Ruan
Chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) is a robust method for capturing genome-wide chromatin interactions. Unlike other 3C-based methods, it includes a chromatin immunoprecipitation (ChIP) step that enriches for interactions mediated by specific target proteins. This unique feature allows ChIA-PET to provide the functional specificity and higher resolution needed to detect chromatin interactions, which chromosome conformation capture (3C)/Hi-C approaches have not achieved. The original ChIA-PET protocol generates short paired-end tags (2 × 20 base pairs (bp)) to detect two genomic loci that are far apart on linear chromosomes but are in spatial proximity in the folded genome...
May 2017: Nature Protocols
https://www.readbyqxmd.com/read/28356074/a-deletion-in-the-intergenic-region-upstream-of-ednrb-causes-head-spot-in-the-rat-strain-kfrs4-kyo
#17
Minako Yoshihara, Tetsuya Sato, Daisuke Saito, Osamu Ohara, Takashi Kuramoto, Mikita Suyama
BACKGROUND: Head spot is one of the phenotypes identified in the KFRS4/Kyo rat strain. Although previous linkage analysis suggested that Ednrb, which is frequently involved in coat color variations in various animals, could be the gene responsible for this phenotype, no mutations have been identified in its coding region. RESULTS: To identify mutations causative of this phenotype in KFRS4/Kyo, we analyzed target capture sequencing data that we recently generated...
March 29, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28355183/single-nucleus-hi-c-reveals-unique-chromatin-reorganization-at-oocyte-to-zygote-transition
#18
Ilya M Flyamer, Johanna Gassler, Maxim Imakaev, Hugo B Brandão, Sergey V Ulianov, Nezar Abdennur, Sergey V Razin, Leonid A Mirny, Kikuë Tachibana-Konwalski
Chromatin is reprogrammed after fertilization to produce a totipotent zygote with the potential to generate a new organism. The maternal genome inherited from the oocyte and the paternal genome provided by sperm coexist as separate haploid nuclei in the zygote. How these two epigenetically distinct genomes are spatially organized is poorly understood. Existing chromosome conformation capture-based methods are not applicable to oocytes and zygotes owing to a paucity of material. To study three-dimensional chromatin organization in rare cell types, we developed a single-nucleus Hi-C (high-resolution chromosome conformation capture) protocol that provides greater than tenfold more contacts per cell than the previous method...
April 6, 2017: Nature
https://www.readbyqxmd.com/read/28352471/genetic-mapping-of-principal-components-of-canine-pelvic-morphology
#19
Mark J Fealey, Joy Li, Rebel J E Todhunter, Ursula Krotscheck, Kei Hayashi, Marina J McConkey, Adam R Boyko, Jessica J Hayward, Rory J Todhunter
BACKGROUND: Concentrated breeding effort to produce various body structures and behaviors of dogs to suit human demand has inadvertently produced unwanted traits and diseases that accompany the morphological and behavioral phenotypes. We explored the relationship between pelvic conformation and canine hip dysplasia (HD) because purebred dogs which are predisposed, or not, to HD share common morphologic features, respectively. Thirteen unique bilateral anatomical features of the pelvis were measured on 392 dogs of 51 breeds and 95 mixed breed dogs...
2017: Canine Genetics and Epidemiology
https://www.readbyqxmd.com/read/28348222/form-and-function-of-topologically-associating-genomic-domains-in-budding-yeast
#20
Umut Eser, Devon Chandler-Brown, Ferhat Ay, Aaron F Straight, Zhijun Duan, William Stafford Noble, Jan M Skotheim
The genome of metazoan cells is organized into topologically associating domains (TADs) that have similar histone modifications, transcription level, and DNA replication timing. Although similar structures appear to be conserved in fission yeast, computational modeling and analysis of high-throughput chromosome conformation capture (Hi-C) data have been used to argue that the small, highly constrained budding yeast chromosomes could not have these structures. In contrast, herein we analyze Hi-C data for budding yeast and identify 200-kb scale TADs, whose boundaries are enriched for transcriptional activity...
April 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
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