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https://www.readbyqxmd.com/read/28426659/three-distinct-mechanisms-of-long-distance-modulation-of-gene-expression-in-yeast
#1
Manyu Du, Qian Zhang, Lu Bai
Recent Hi-C measurements have revealed numerous intra- and inter-chromosomal interactions in various eukaryotic cells. To what extent these interactions regulate gene expression is not clear. This question is particularly intriguing in budding yeast because it has extensive long-distance chromosomal interactions but few cases of gene regulation over-a-distance. Here, we developed a medium-throughput assay to screen for functional long-distance interactions that affect the average expression level of a reporter gene as well as its cell-to-cell variability (noise)...
April 20, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28424341/alterations-in-three-dimensional-organization-of-the-cancer-genome-and-epigenome
#2
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/28420341/genetic-sequence-based-prediction-of-long-range-chromatin-interactions-suggests-a-potential-role-of-short-tandem-repeat-sequences-in-genome-organization
#3
Sarvesh Nikumbh, Nico Pfeifer
BACKGROUND: Knowing the three-dimensional (3D) structure of the chromatin is important for obtaining a complete picture of the regulatory landscape. Changes in the 3D structure have been implicated in diseases. While there exist approaches that attempt to predict the long-range chromatin interactions, they focus only on interactions between specific genomic regions - the promoters and enhancers, neglecting other possibilities, for instance, the so-called structural interactions involving intervening chromatin...
April 18, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28411415/chromosome-conformation-capture-based-studies-reveal-novel-features-of-plant-nuclear-architecture
#4
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/28388874/pgltools-a-genomic-arithmetic-tool-suite-for-manipulation-of-hi-c-peak-and-other-chromatin-interaction-data
#5
William W Greenwald, He Li, Erin N Smith, Paola Benaglio, Naoki Nariai, Kelly A Frazer
BACKGROUND: Genomic interaction studies use next-generation sequencing (NGS) to examine the interactions between two loci on the genome, with subsequent bioinformatics analyses typically including annotation, intersection, and merging of data from multiple experiments. While many file types and analysis tools exist for storing and manipulating single locus NGS data, there is currently no file standard or analysis tool suite for manipulating and storing paired-genomic-loci: the data type resulting from "genomic interaction" studies...
April 7, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28388850/auditory-and-visual-executive-functions-in-children-and-response-to-methylphenidate-a-randomized-controlled-trial
#6
Yaffa Hadar, Shraga Hocherman, Oren Lamm, Emanuel Tirosh
OBJECTIVES: The aim of the study was to assess auditory and visually based executive functions (EFs) and the effect of methylphenidate (MPH) in children with ADHD. METHODS: Thirty-six boys between the ages of 8.3 and 9.7 years with ADHD and 36 matched controls were included. The study group was randomized into MPH and placebo for 7 days each in a crossover design. A Cued Choice Reaction Time (CCRT) test that included incongruent cuing was administered at baseline and following 1 and 2 weeks...
April 1, 2017: Journal of Attention Disorders
https://www.readbyqxmd.com/read/28387224/multi-scale-chromatin-state-annotation-using-a-hierarchical-hidden-markov-model
#7
Eugenio Marco, Wouter Meuleman, Jialiang Huang, Kimberly Glass, Luca Pinello, Jianrong Wang, Manolis Kellis, Guo-Cheng Yuan
Chromatin-state analysis is widely applied in the studies of development and diseases. However, existing methods operate at a single length scale, and therefore cannot distinguish large domains from isolated elements of the same type. To overcome this limitation, we present a hierarchical hidden Markov model, diHMM, to systematically annotate chromatin states at multiple length scales. We apply diHMM to analyse a public ChIP-seq data set. diHMM not only accurately captures nucleosome-level information, but identifies domain-level states that vary in nucleosome-level state composition, spatial distribution and functionality...
April 7, 2017: Nature Communications
https://www.readbyqxmd.com/read/28385993/hi-c-for-mosquito-genomes
#8
EDITORIAL
Laura M Zahn
No abstract text is available yet for this article.
April 7, 2017: Science
https://www.readbyqxmd.com/read/28385710/non-random-domain-organization-of-the-arabidopsis-genome-at-the-nuclear-periphery
#9
Xiuli Bi, Yingjuan Cheng, Bo Hu, Xiaoli Ma, Rui Wu, Jiawei Wang, Chang Liu
The nuclear space is not a homogeneous biochemical environment. Many studies have demonstrated that the transcriptional activity of a gene is linked to its positioning within the nuclear space. Following the discovery of lamin-associated domains (LADs), which are transcriptionally repressed chromatin regions, the non-random positioning of chromatin at the nuclear periphery and its biological relevance have been studied extensively in animals. However, it remains unknown whether comparable chromatin organizations exist in plants...
April 6, 2017: Genome Research
https://www.readbyqxmd.com/read/28381300/linkages-between-changes-in-the-3d-organization-of-the-genome-and-transcription-during-myotube-differentiation-in-vitro
#10
Malina D Doynova, James F Markworth, David Cameron-Smith, Mark H Vickers, Justin M O'Sullivan
BACKGROUND: The spatial organization of eukaryotic genomes facilitates and reflects the underlying nuclear processes that are occurring in the cell. As such, the spatial organization of a genome represents a window on the genome biology that enables analysis of the nuclear regulatory processes that contribute to mammalian development. METHODS: In this study, Hi-C and RNA-seq were used to capture the genome organization and transcriptome in mouse muscle progenitor cells (C2C12 myoblasts) before and after differentiation to myotubes, in the presence or absence of the cytidine analogue AraC...
April 5, 2017: Skeletal Muscle
https://www.readbyqxmd.com/read/28379994/gothic-a-probabilistic-model-to-resolve-complex-biases-and-to-identify-real-interactions-in-hi-c-data
#11
Borbala Mifsud, Inigo Martincorena, Elodie Darbo, Robert Sugar, Stefan Schoenfelder, Peter Fraser, Nicholas M Luscombe
Hi-C is one of the main methods for investigating spatial co-localisation of DNA in the nucleus. However, the raw sequencing data obtained from Hi-C experiments suffer from large biases and spurious contacts, making it difficult to identify true interactions. Existing methods use complex models to account for biases and do not provide a significance threshold for detecting interactions. Here we introduce a simple binomial probabilistic model that resolves complex biases and distinguishes between true and false interactions...
2017: PloS One
https://www.readbyqxmd.com/read/28369658/tracking-the-evolution-of-3d-gene-organization-demonstrates-its-connection-to-phenotypic-divergence
#12
Alon Diament, Tamir Tuller
It has recently been shown that the organization of genes in eukaryotic genomes, and specifically in 3D, is strongly related to gene expression and function and partially conserved between organisms. However, previous studies of 3D genomic organization analyzed each organism independently from others. Here, we propose an approach for unified inter-organismal analysis of gene organization based on a network representation of Hi-C data. We define and detect four classes of spatially co-evolving orthologous modules (SCOMs), i...
March 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28369554/the-haploinsufficient-tumor-suppressor-cux1-acts-as-an-analog-transcriptional-regulator-that-controls-target-genes-through-distal-enhancers-that-loop-to-target-promoters
#13
Robert K Arthur, Ningfei An, Saira Khan, Megan E McNerney
One third of tumor suppressors are haploinsufficient transcriptional regulators, yet it remains unknown how a 50% reduction of a transcription factor is translated at the cis-regulatory level into a malignant transcriptional program. We studied CUX1, a haploinsufficient transcription factor that is recurrently mutated in hematopoietic and solid tumors. We determined CUX1 DNA-binding and target gene regulation in the wildtype and haploinsufficient states. CUX1 binds with transcriptional activators and cohesin at distal enhancers across three different human cell types...
March 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28369339/hic-spector-a-matrix-library-for-spectral-and-reproducibility-analysis-of-hi-c-contact-maps
#14
Koon-Kiu Yan, Galip Gürkan Yardimci, Chengfei Yan, William S Noble, Mark Gerstein
Summary: Genome-wide proximity ligation based assays like Hi-C have opened a window to the 3D organization of the genome. In so doing, they present data structures that are different from conventional 1D signal tracks. To exploit the 2D nature of Hi-C contact maps, matrix techniques like spectral analysis are particularly useful. Here, we present HiC-spector, a collection of matrix-related functions for analyzing Hi-C contact maps. In particular, we introduce a novel reproducibility metric for quantifying the similarity between contact maps based on spectral decomposition...
March 22, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28358394/long-read-chia-pet-for-base-pair-resolution-mapping-of-haplotype-specific-chromatin-interactions
#15
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
#16
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
#17
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/28348222/form-and-function-of-topologically-associating-genomic-domains-in-budding-yeast
#18
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
https://www.readbyqxmd.com/read/28336562/de-novo-assembly-of-the-aedes-aegypti-genome-using-hi-c-yields-chromosome-length-scaffolds
#19
Olga Dudchenko, Sanjit S Batra, Arina D Omer, Sarah K Nyquist, Marie Hoeger, Neva C Durand, Muhammad S Shamim, Ido Machol, Eric S Lander, Aviva Presser Aiden, Erez Lieberman Aiden
The Zika outbreak, spread by the Aedes aegypti mosquito, highlights the need to create high-quality assemblies of large genomes in a rapid and cost-effective fashion. Here, we combine Hi-C data with existing draft assemblies to generate chromosome-length scaffolds. We validate this method by assembling a human genome, de novo, from short reads alone (67X coverage). We then combine our method with draft sequences to create genome assemblies of the mosquito disease vectors Aedes aegypti and Culex quinquefasciatus, each consisting of three scaffolds corresponding to the three chromosomes in each species...
March 23, 2017: Science
https://www.readbyqxmd.com/read/28334818/chromosomal-dynamics-predicted-by-an-elastic-network-model-explains-genome-wide-accessibility-and-long-range-couplings
#20
Natalie Sauerwald, She Zhang, Carl Kingsford, Ivet Bahar
Understanding the three-dimensional (3D) architecture of chromatin and its relation to gene expression and regulation is fundamental to understanding how the genome functions. Advances in Hi-C technology now permit us to study 3D genome organization, but we still lack an understanding of the structural dynamics of chromosomes. The dynamic couplings between regions separated by large genomic distances (>50 Mb) have yet to be characterized. We adapted a well-established protein-modeling framework, the Gaussian Network Model (GNM), to model chromatin dynamics using Hi-C data...
April 20, 2017: Nucleic Acids Research
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