scholarly journals HiC-bench: comprehensive and reproducible Hi-C data analysis designed for parameter exploration and benchmarking

2016 ◽  
Author(s):  
Charalampos Lazaris ◽  
Stephen Kelly ◽  
Panagiotis Ntziachristos ◽  
Iannis Aifantis ◽  
Aristotelis Tsirigos
Keyword(s):  
Quality Assessment ◽  
Genome Organization ◽  
Three Dimensional ◽  
Sequencing Data ◽  
Topological Domains ◽  
Resolution Analysis ◽  
Reproducible Analysis ◽  
Computationally Intensive ◽  
Capture Techniques ◽  
Computational Platform

AbstractBackgroundChromatin conformation capture techniques have evolved rapidly over the last few years and have provided new insights into genome organization at an unprecedented resolution. Analysis of Hi-C data is complex and computationally intensive involving multiple tasks and requiring robust quality assessment. This has led to the development of several tools and methods for processing Hi-C data. However, most of the existing tools do not cover all aspects of the analysis and only offer few quality assessment options. Additionally, availability of a multitude of tools makes scientists wonder how these tools and associated parameters can be optimally used, and how potential discrepancies can be interpreted and resolved. Most importantly, investigators need to be ensured that slight changes in parameters and/or methods do not affect the conclusions of their studies.ResultsTo address these issues (compare, explore and reproduce), we introduce HiC-bench, a configurable computational platform for comprehensive and reproducible analysis of Hi-C sequencing data. HiC-bench performs all common Hi-C analysis tasks, such as alignment, filtering, contact matrix generation and normalization, identification of topological domains, scoring and annotation of specific interactions using both published tools and our own. We have also embedded various tasks that perform quality assessment and visualization. HiC-bench is implemented as a data flow platform with an emphasis on analysis reproducibility. Additionally, the user can readily perform parameter exploration and comparison of different tools in a combinatorial manner that takes into account all desired parameter settings in each pipeline task. This unique feature facilitates the design and execution of complex benchmark studies that may involve combinations of multiple tool/parameter choices in each step of the analysis. To demonstrate the usefulness of our platform, we performed a comprehensive benchmark of existing and new TAD callers exploring different matrix correction methods, parameter settings and sequencing depths. Users can extend our pipeline by adding more tools as they become available.ConclusionsHiC-bench consists an easy-to-use and extensible platform for comprehensive analysis of Hi-C datasets. We expect that it will facilitate current analyses and help scientists formulate and test new hypotheses in the field of three-dimensional genome organization.

scholarly journals The three-dimensional genome organization of Drosophila melanogaster through data integration

2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Qingjiao Li ◽  
Harianto Tjong ◽  
Xiao Li ◽  
Ke Gong ◽  
Xianghong Jasmine Zhou ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Data Integration ◽  
Genome Organization ◽  
Genome Structure ◽  
Three Dimensional ◽  
Structural Features ◽  
Embryonic Cells ◽  
Data Types ◽  
Chromosome Conformation ◽  
Topological Domains

Abstract Background Genome structures are dynamic and non-randomly organized in the nucleus of higher eukaryotes. To maximize the accuracy and coverage of three-dimensional genome structural models, it is important to integrate all available sources of experimental information about a genome’s organization. It remains a major challenge to integrate such data from various complementary experimental methods. Here, we present an approach for data integration to determine a population of complete three-dimensional genome structures that are statistically consistent with data from both genome-wide chromosome conformation capture (Hi-C) and lamina-DamID experiments. Results Our structures resolve the genome at the resolution of topological domains, and reproduce simultaneously both sets of experimental data. Importantly, this data deconvolution framework allows for structural heterogeneity between cells, and hence accounts for the expected plasticity of genome structures. As a case study we choose Drosophila melanogaster embryonic cells, for which both data types are available. Our three-dimensional genome structures have strong predictive power for structural features not directly visible in the initial data sets, and reproduce experimental hallmarks of the D. melanogaster genome organization from independent and our own imaging experiments. Also they reveal a number of new insights about genome organization and its functional relevance, including the preferred locations of heterochromatic satellites of different chromosomes, and observations about homologous pairing that cannot be directly observed in the original Hi-C or lamina-DamID data. Conclusions Our approach allows systematic integration of Hi-C and lamina-DamID data for complete three-dimensional genome structure calculation, while also explicitly considering genome structural variability.

scholarly journals Understanding 3D Genome Organization and Its Effect on Transcriptional Gene Regulation Under Environmental Stress in Plant: A Chromatin Perspective

2021 ◽  
Vol 9 ◽  
Author(s):  
Suresh Kumar ◽  
Simardeep Kaur ◽  
Karishma Seem ◽  
Santosh Kumar ◽  
Trilochan Mohapatra
Keyword(s):  
Gene Expression ◽  
Environmental Stress ◽  
Genome Organization ◽  
Regulation Of Gene Expression ◽  
Three Dimensional ◽  
Regulatory Elements ◽  
Chromosome Conformation ◽  
3D Genome ◽  
Chromatin Architecture ◽  
Capture Techniques

The genome of a eukaryotic organism is comprised of a supra-molecular complex of chromatin fibers and intricately folded three-dimensional (3D) structures. Chromosomal interactions and topological changes in response to the developmental and/or environmental stimuli affect gene expression. Chromatin architecture plays important roles in DNA replication, gene expression, and genome integrity. Higher-order chromatin organizations like chromosome territories (CTs), A/B compartments, topologically associating domains (TADs), and chromatin loops vary among cells, tissues, and species depending on the developmental stage and/or environmental conditions (4D genomics). Every chromosome occupies a separate territory in the interphase nucleus and forms the top layer of hierarchical structure (CTs) in most of the eukaryotes. While the A and B compartments are associated with active (euchromatic) and inactive (heterochromatic) chromatin, respectively, having well-defined genomic/epigenomic features, TADs are the structural units of chromatin. Chromatin architecture like TADs as well as the local interactions between promoter and regulatory elements correlates with the chromatin activity, which alters during environmental stresses due to relocalization of the architectural proteins. Moreover, chromatin looping brings the gene and regulatory elements in close proximity for interactions. The intricate relationship between nucleotide sequence and chromatin architecture requires a more comprehensive understanding to unravel the genome organization and genetic plasticity. During the last decade, advances in chromatin conformation capture techniques for unravelling 3D genome organizations have improved our understanding of genome biology. However, the recent advances, such as Hi-C and ChIA-PET, have substantially increased the resolution, throughput as well our interest in analysing genome organizations. The present review provides an overview of the historical and contemporary perspectives of chromosome conformation capture technologies, their applications in functional genomics, and the constraints in predicting 3D genome organization. We also discuss the future perspectives of understanding high-order chromatin organizations in deciphering transcriptional regulation of gene expression under environmental stress (4D genomics). These might help design the climate-smart crop to meet the ever-growing demands of food, feed, and fodder.

scholarly journals Transcription-dependent domain-scale three-dimensional genome organization in the dinoflagellate Breviolum minutum

2021 ◽  
Author(s):  
Georgi K. Marinov ◽  
Alexandro E. Trevino ◽  
Tingting Xiang ◽  
Anshul Kundaje ◽  
Arthur R. Grossman ◽  
...  
Keyword(s):  
Genome Organization ◽  
Crystalline State ◽  
Liquid Crystalline ◽  
Gene Array ◽  
Three Dimensional ◽  
Topological Domains ◽  
Transcriptional Inhibition ◽  
Topologically Associating Domains ◽  
Condensed Liquid ◽  
Dependent Domain

AbstractDinoflagellate chromosomes represent a unique evolutionary experiment, as they exist in a permanently condensed, liquid crystalline state; are not packaged by histones; and contain genes organized into tandem gene arrays, with minimal transcriptional regulation. We analyze the three-dimensional genome of Breviolum minutum, and find large topological domains (dinoflagellate topologically associating domains, which we term ‘dinoTADs’) without chromatin loops, which are demarcated by convergent gene array boundaries. Transcriptional inhibition disrupts dinoTADs, implicating transcription-induced supercoiling as the primary topological force in dinoflagellates.

Acoustic and Photoacoustic Inspection of Through-Silicon Vias in the GHz-Frequency Band

2017 ◽  
Author(s):  
Sebastian Brand ◽  
Michael Kögel ◽  
Frank Altmann ◽  
Ingrid DeWolf ◽  
Ahmad Khaled ◽  
...  
Keyword(s):  
Quality Assessment ◽  
Frequency Band ◽  
Process Development ◽  
Three Dimensional ◽  
Non Destructive Testing ◽  
Destructive Testing ◽  
Vertical Interconnection ◽  
Testing Techniques ◽  
Silicon Vias ◽  
Non Destructive

Abstract Through Silicon Via (TSV) is the most promising technology for vertical interconnection in novel three-dimensional chip architectures. Reliability and quality assessment necessary for process development and manufacturing require appropriate non-destructive testing techniques to detect cracks and delamination defects with sufficient penetration and imaging capabilities. The current paper presents the application of two acoustically based methods operating in the GHz-frequency band for the assessment of the integrity of TSV structures.

scholarly journals BIGpre: A Quality Assessment Package for Next-Generation Sequencing Data

2011 ◽  
Vol 9 (6) ◽  
pp. 238-244 ◽  
Author(s):  
Tongwu Zhang ◽  
Yingfeng Luo ◽  
Kan Liu ◽  
Linlin Pan ◽  
Bing Zhang ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Quality Assessment ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Sequencing Data ◽  
Generation Sequencing

scholarly journals A Survey of Computational Tools to Analyze and Interpret Whole Exome Sequencing Data

2016 ◽  
Vol 2016 ◽  
pp. 1-16 ◽  
Author(s):  
Jennifer D. Hintzsche ◽  
William A. Robinson ◽  
Aik Choon Tan
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Sequencing Data ◽  
Disease Treatment ◽  
Computational Tools ◽  
Whole Exome ◽  
Data Production ◽  
Whole Exome Sequencing Data ◽  
Computationally Intensive ◽  
Generation Technology

Whole Exome Sequencing (WES) is the application of the next-generation technology to determine the variations in the exome and is becoming a standard approach in studying genetic variants in diseases. Understanding the exomes of individuals at single base resolution allows the identification of actionable mutations for disease treatment and management. WES technologies have shifted the bottleneck in experimental data production to computationally intensive informatics-based data analysis. Novel computational tools and methods have been developed to analyze and interpret WES data. Here, we review some of the current tools that are being used to analyze WES data. These tools range from the alignment of raw sequencing reads all the way to linking variants to actionable therapeutics. Strengths and weaknesses of each tool are discussed for the purpose of helping researchers make more informative decisions on selecting the best tools to analyze their WES data.

scholarly journals Centromeric Localization of Dispersed Pol III Genes in Fission Yeast

2010 ◽  
Vol 21 (2) ◽  
pp. 254-265 ◽  
Author(s):  
Osamu Iwasaki ◽  
Atsunari Tanaka ◽  
Hideki Tanizawa ◽  
Shiv I.S. Grewal ◽  
Ken-ichi Noma
Keyword(s):  
Genome Organization ◽  
Gene Locus ◽  
Mitotic Chromosome ◽  
Three Dimensional ◽  
Rrna Genes ◽  
Mitotic Chromosomes ◽  
Gene Encoding ◽  
5S Rrna Genes ◽  
Pol Iii ◽  
Mitotic Chromosome Condensation

The eukaryotic genome is a complex three-dimensional entity residing in the nucleus. We present evidence that Pol III–transcribed genes such as tRNA and 5S rRNA genes can localize to centromeres and contribute to a global genome organization. Furthermore, we find that ectopic insertion of Pol III genes into a non-Pol III gene locus results in the centromeric localization of the locus. We show that the centromeric localization of Pol III genes is mediated by condensin, which interacts with the Pol III transcription machinery, and that transcription levels of the Pol III genes are negatively correlated with the centromeric localization of Pol III genes. This centromeric localization of Pol III genes initially observed in interphase becomes prominent during mitosis, when chromosomes are condensed. Remarkably, defective mitotic chromosome condensation by a condensin mutation, cut3-477, which reduces the centromeric localization of Pol III genes, is suppressed by a mutation in the sfc3 gene encoding the Pol III transcription factor TFIIIC subunit, sfc3-1. The sfc3-1 mutation promotes the centromeric localization of Pol III genes. Our study suggests there are functional links between the process of the centromeric localization of dispersed Pol III genes, their transcription, and the assembly of condensed mitotic chromosomes.

A High Fidelity Quality Assessment of High Pressure Turbine Blades Using Surface Curvature and Gradient-Based Adjoint

2018 ◽  
Author(s):  
Akhil Mulloth ◽  
Gabriel Banks ◽  
Giulio Zamboni ◽  
Simon Bather
Keyword(s):  
Quality Assessment ◽  
Turbine Blades ◽  
Three Dimensional ◽  
Surface Curvature ◽  
Assessment Process ◽  
Screening Process ◽  
Profile Tolerance ◽  
Gradient Based ◽  
Parts Manufacturing ◽  
The Impact

Gas turbine performance is highly dependent on the quality of the manufactured parts. Manufacturing variations in the parts can significantly alter the performance, especially efficiency and thus SFC. The legacy process is to accept variations within predefined profile tolerance limits and a few other qualitative parameters, mostly at a few, key two-dimensional aerofoil sections. With the widespread use of White light scans and other similar three-dimensional scans, this has improved to include the three-dimensional profile. The future however may lie with performance based quality assessment of manufactured parts, combined with quantitative surface quality assessment to implement an intelligent screening process for the parts. The adjoint method, typically used for shape optimization is adapted to provide a prediction of the impact on performance due to manufacturing variations. The work presented outlines a three stage quality assessment process for manufactured parts, involving three-dimensional profile tolerance based screening, followed by a surface curvature based screening and finally an Adjoint based performance prediction.

scholarly journals Quality assessment of single-cell RNA sequencing data by coverage skewness analysis

2019 ◽  
Author(s):  
Imad Abugessaisa ◽  
Shuhei Noguchi ◽  
Melissa Cardon ◽  
Akira Hasegawa ◽  
Kazuhide Watanabe ◽  
...  
Keyword(s):  
Quality Assessment ◽  
Single Cell ◽  
Rna Sequencing ◽  
Single Cells ◽  
Assessment Method ◽  
Poor Quality ◽  
Sequencing Data ◽  
Single Cell Rna Sequencing ◽  
Gene Coverage ◽  
The Impact

AbstractAnalysis and interpretation of single-cell RNA-sequencing (scRNA-seq) experiments are compromised by the presence of poor quality cells. For meaningful analyses, such poor quality cells should be excluded to avoid biases and large variation. However, no clear guidelines exist. We introduce SkewC, a novel quality-assessment method to identify poor quality single-cells in scRNA-seq experiments. The method is based on the assessment of gene coverage for each single cell and its skewness as a quality measure. To validate the method, we investigated the impact of poor quality cells on downstream analyses and compared biological differences between typical and poor quality cells. Moreover, we measured the ratio of intergenic expression, suggesting genomic contamination, and foreign organism contamination of single-cell samples. SkewC is tested in 37,993 single-cells generated by 15 scRNA-seq protocols. We envision SkewC as an indispensable QC method to be incorporated into scRNA-seq experiment to preclude the possibility of scRNA-seq data misinterpretation.

scholarly journals Three-dimensional Resolution Analysis for Geosynchronous Circular SAR

2012 ◽  
Vol 1 (3) ◽  
pp. 314-322
Author(s):  
Bing-nan Wang ◽  
Mao-sheng Xiang
Keyword(s):  
Three Dimensional ◽  
Resolution Analysis
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