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https://www.readbyqxmd.com/read/28433605/stability-of-patient-specific-features-of-altered-dna-replication-timing-in-xenografts-of-primary-human-acute-lymphoblastic-leukemia
#1
Takayo Sasaki, Juan Carlos Rivera-Mulia, Daniel Vera, Jared Zimmerman, Sunny Das, Michelle Padget, Naoto Nakamichi, Bill H Chang, Jeff Tyner, Brian J Druker, Andrew P Weng, Curt I Civin, Connie J Eaves, David M Gilbert
Genome-wide DNA replication timing (RT) profiles reflect the global 3D chromosome architecture of cells. They also provide a comprehensive and unique megabase-scale picture of the cellular epigenetic state. Thus normal differentiation involves reproducible changes in RT and transformation generally perturbs these, although the potential effects of altered RT on the properties of transformed cells remain largely unknown. A major challenge to interrogating these issues in human acute lymphoid leukemia (ALL) is the low proliferative activity of most of the cells, which may be further reduced in cryopreserved samples and difficult to overcome in vitro...
April 19, 2017: Experimental Hematology
https://www.readbyqxmd.com/read/28429758/intracellular-lipid-binding-protein-family-diversity-from-oyster-crassostrea-gigas-genomic-and-structural-features-of-invertebrate-lipid-transporters
#2
Guilherme de Toledo-Silva, Guilherme Razzera, Flavia Lucena Zacchi, Nestor Cubas Wendt, Jacó Joaquim Mattos, Afonso Celso Dias Bainy
Intracellular lipid binding proteins (iLBPs) play a role in the transport and cellular uptake of fatty acids and gene expression regulation. The aim of this work was to characterize the iLBP gene family of the Pacific oyster Crassostrea gigas, one of the most cultivated marine bivalves in the world, using bioinformatics and molecular biology approaches. A total of 26 different iLBPs transcripts were identified in the Pacific oyster genome, including alternative splicing and gene duplication events. The oyster iLBP gene family seems to be more expanded than in other invertebrates...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28428791/genome-wide-association-study-for-pre-harvest-sprouting-resistance-in-a-large-germplasm-collection-of-chinese-wheat-landraces
#3
Yong Zhou, Hao Tang, Meng-Ping Cheng, Kwame O Dankwa, Zhong-Xu Chen, Zhan-Yi Li, Shang Gao, Ya-Xi Liu, Qian-Tao Jiang, Xiu-Jin Lan, Zhi-En Pu, Yu-Ming Wei, You-Liang Zheng, Lee T Hickey, Ji-Rui Wang
Pre-harvest sprouting (PHS) is mainly caused by the breaking of seed dormancy in high rainfall regions, which leads to huge economic losses in wheat. In this study, we evaluated 717 Chinese wheat landraces for PHS resistance and carried out genome-wide association studies (GWAS) using to 9,740 DArT-seq and 178,803 SNP markers. Landraces were grown across six environments in China and germination testing of harvest-ripe grain was used to calculate the germination rate (GR) for each accession at each site. GR was highly correlated across all environments...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28426659/three-distinct-mechanisms-of-long-distance-modulation-of-gene-expression-in-yeast
#4
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/28426555/creating-artificial-lymphoid-tissues-to-study-immunity-and-hematological-malignancies
#5
Shivem B Shah, Ankur Singh
PURPOSE OF REVIEW: The specialized microenvironments of lymphoid tissue affect immune cell function and progression of disease. However, current animal models are low throughput and a large number of human diseases are difficult to model in animals. Animal models are less amenable to manipulation of tissue niche components, signalling pathways, epigenetics, and genome editing than ex vivo models. On the other hand, conventional 2D cultures lack the physiological relevance to study precise microenvironmental interactions...
April 19, 2017: Current Opinion in Hematology
https://www.readbyqxmd.com/read/28424353/constrained-release-of-lamina-associated-enhancers-and-genes-from-the-nuclear-envelope-during-t-cell-activation-facilitates-their-association-in-chromosome-compartments
#6
Michael I Robson, Jose I de Las Heras, Rafal Czapiewski, Aishwarya Sivakumar, Alastair R W Kerr, Eric Schirmer
The 3D organization of the genome changes concomitantly with expression changes during hematopoiesis and immune activation. Studies have focused either on lamina-associated domains (LADs) or on topologically-associated domains (TADs), defined by preferential local chromatin interactions, and chromosome compartments, defined as higher-order interactions between TADs sharing functionally similar states. However, few studies have investigated how these affect one another. To address this, we mapped LADs using Lamin B1-DamID during Jurkat T-cell activation, finding significant genome re-organization at the nuclear periphery dominated by release of loci frequently important for T-cell function...
April 19, 2017: Genome Research
https://www.readbyqxmd.com/read/28424341/alterations-in-three-dimensional-organization-of-the-cancer-genome-and-epigenome
#7
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/28420610/the-diversity-of-dna-fragment-editing-by-crispr-cas9-in-highly-homologous-or-repetitive-sequences
#8
Wang Leyang, Huang Haiyan, Wu Qiang
In complex genomes, there are a large number of duplicated genes in the coding regions and many more repetitive sequences in the non-coding regions. Repetitive sequences can exert great impacts on the heredity and evolution of the organisms, as well as their genome 3D architecture and transcriptional regulation. The high homology nature of repetitive sequences renders their editing by CRISPR/Cas9 very complex. At diploid or polyploid situations, such repetitive sequences could be edited differently on each chromosome or chromatid...
April 20, 2017: Yi Chuan, Hereditas
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
#9
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/28419324/improving-data-workflow-systems-with-cloud-services-and-use-of-open-data-for-bioinformatics-research
#10
Md Rezaul Karim, Audrey Michel, Achille Zappa, Pavel Baranov, Ratnesh Sahay, Dietrich Rebholz-Schuhmann
Data workflow systems (DWFSs) enable bioinformatics researchers to combine components for data access and data analytics, and to share the final data analytics approach with their collaborators. Increasingly, such systems have to cope with large-scale data, such as full genomes (about 200 GB each), public fact repositories (about 100 TB of data) and 3D imaging data at even larger scales. As moving the data becomes cumbersome, the DWFS needs to embed its processes into a cloud infrastructure, where the data are already hosted...
April 16, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28401144/insights-into-the-activity-change-of-spore-photoproduct-lyase-induced-by-mutations-at-a-peripheral-glycine-residue
#11
Linlin Yang, Lei Li
UV radiation triggers the formation of 5-thyminyl-5,6-dihydrothymine, i.e., the spore photoproduct (SP), in the genomic DNA of bacterial endospores. These SPs, if not repaired in time, may lead to genome instability and cell death. SP is mainly repaired by spore photoproduct lyase (SPL) during spore outgrowth via an unprecedented protein-harbored radical transfer pathway that is composed of at least a cysteine and two tyrosine residues. This mechanism is consistent with the recently solved SPL structure that shows all three residues are located in proximity and thus able to participate in the radical transfer process during the enzyme catalysis...
2017: Frontiers in Chemistry
https://www.readbyqxmd.com/read/28399397/genome-architecture-from-a-different-angle
#12
Elizabeth H Finn, Tom Misteli
The study of genome architecture has recently been advanced by new techniques combining nuclear proximity ligation and high-throughput sequencing, but independent methods to validate them have been lacking. Reporting in Nature, Beagrie et al. (2017) describe such an orthogonal technique, called genome architecture mapping, to map genomes in 3D space.
April 10, 2017: Developmental Cell
https://www.readbyqxmd.com/read/28381300/linkages-between-changes-in-the-3d-organization-of-the-genome-and-transcription-during-myotube-differentiation-in-vitro
#13
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/28373416/on-site-cytology-for-development-of-patient-derived-three-dimensional-organoid-cultures-a-pilot-study
#14
Verena Sailer, Chantal Pauli, Elyze C Merzier, Juan Miguel Mosquera, Himisha Beltran, Mark A Rubin, Rema A Rao
BACKGROUND/AIM: Development of patient-derived three-dimensional (3D) organoid cultures is an emerging technique in the field of precision oncology. We aimed to integrate on-site adequacy evaluation using cytology into the tumor organoid development workflow to ensure precise characterization and growth of these cultures. PATIENTS AND METHODS: Cancer patients were consented to a Precision Medicine trial. Fresh tissue was procured for genomic analyses as well as organoid development...
April 2017: Anticancer Research
https://www.readbyqxmd.com/read/28369658/tracking-the-evolution-of-3d-gene-organization-demonstrates-its-connection-to-phenotypic-divergence
#15
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/28369339/hic-spector-a-matrix-library-for-spectral-and-reproducibility-analysis-of-hi-c-contact-maps
#16
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/28349175/characterization-of-the-temporal-and-spatial-expression-of-wheat-triticum-aestivum-l-plant-height-at-the-qtl-level-and-their-influence-on-yield-related-traits
#17
Na Zhang, Xiaoli Fan, Fa Cui, Chunhua Zhao, Wei Zhang, Xueqiang Zhao, Lijuan Yang, Ruiqing Pan, Mei Chen, Jie Han, Jun Ji, Dongcheng Liu, Zongwu Zhao, Yiping Tong, Aimin Zhang, Tao Wang, Junming Li
The temporal and spatial expression patterns of stable QTL for plant height and their influences on yield were characterized. Plant height (PH) is a complex trait in wheat (Triticum aestivum L.) that includes the spike length (SL) and the internode lengths from the first to the fifth internode, which are counted from the top and abbreviated as FIRITL, SECITL, THIITL, FOUITL, and FIFITL, respectively. This study identified eight putative additive quantitative trait loci (QTL) for PH. In addition, unconditional and conditional QTL mapping were used to analyze the temporal and spatial expression patterns of five stable QTL for PH...
March 27, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28343999/a-genome-wide-analysis-of-human-pluripotent-stem-cell-derived-endothelial-cells-in-2d-or-3d-culture
#18
Jue Zhang, Michael P Schwartz, Zhonggang Hou, Yongsheng Bai, Hamisha Ardalani, Scott Swanson, John Steill, Victor Ruotti, Angela Elwell, Bao Kim Nguyen, Jennifer Bolin, Ron Stewart, James A Thomson, William L Murphy
A defined protocol for efficiently deriving endothelial cells from human pluripotent stem cells was established and vascular morphogenesis was used as a model system to understand how synthetic hydrogels influence global biological function compared with common 2D and 3D culture platforms. RNA sequencing demonstrated that gene expression profiles were similar for endothelial cells and pericytes cocultured in polyethylene glycol (PEG) hydrogels or Matrigel, while monoculture comparisons identified distinct vascular signatures for each cell type...
April 11, 2017: Stem Cell Reports
https://www.readbyqxmd.com/read/28334818/chromosomal-dynamics-predicted-by-an-elastic-network-model-explains-genome-wide-accessibility-and-long-range-couplings
#19
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
https://www.readbyqxmd.com/read/28333290/evolution-of-the-genome-3d-organization-comparison-of-fused-and-segregated-globin-gene-clusters
#20
Anastasia P Kovina, Natalia V Petrova, Ekaterina S Gushchanskaya, Konstantin V Dolgushin, Evgeny S Gerasimov, Aleksandra A Galitsyna, Alexey A Penin, Ilya M Flyamer, Elena S Ioudinkova, Alexey A Gavrilov, Yegor S Vassetzky, Sergey V Ulianov, Olga V Iarovaia, Sergey V Razin
The genomes are folded in a complex three-dimensional (3D) structure. Some features of this organization are common for all eukaryotes, but little is known about its evolution. Here we have studied the 3D organization and regulation of zebrafish globin domain and compared its organization and regulation with those of other vertebrate species. In birds and mammals, the alpha- and beta-globin genes are segregated into separate clusters located on different chromosomes and organized into chromatin domains of different types, whereas in cold-blooded vertebrates, including Danio rerio, alpha- and beta-globin genes are organized into common clusters...
March 7, 2017: Molecular Biology and Evolution
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