scholarly journals Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs

2018 ◽  
Author(s):  
Jonas Ibn-Salem ◽  
Miguel A. Andrade-Navarro
Keyword(s):  
Protein Binding ◽  
Genomic Sequence ◽  
Three Dimensional ◽  
Chromosome Conformation Capture ◽  
Computational Method ◽  
Dimensional Structure ◽  
Bioconductor Package ◽  
Chromosome Conformation ◽  
Cross Links ◽  
Genomic Regions

AbstractWe present a computational method to gain knowledge of the three-dimensional structure of the genome from ChIP-seq datasets. While not designed to detect contacts, the ChIP-seq protocol cross-links proteins with each other and with DNA. Consequently, genomic regions that interact with the protein binding-site via chromatin looping are coimmunoprecipitated and sequenced. This produces minor ChIP-seq signals around CTCF motif pairs at loop anchor regions. Together with genomic sequence features, these signals predict whether loop anchors interact or not. Our method, Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs (7C), is available as an R/Bioconductor package: http://bioconductor.org/packages/sevenC

scholarly journals 7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Jonas Ibn-Salem ◽  
Miguel A. Andrade-Navarro
Keyword(s):  
Three Dimensional ◽  
Prediction Method ◽  
Cell Types ◽  
Chromosome Conformation Capture ◽  
Dimensional Structure ◽  
Single Chip ◽  
Chromosome Conformation ◽  
Chromatin Looping ◽  
Chromatin Interactions ◽  
Cross Links

Abstract Background Knowledge of the three-dimensional structure of the genome is necessary to understand how gene expression is regulated. Recent experimental techniques such as Hi-C or ChIA-PET measure long-range chromatin interactions genome-wide but are experimentally elaborate, have limited resolution and such data is only available for a limited number of cell types and tissues. Results While ChIP-seq was not designed to detect chromatin interactions, the formaldehyde treatment in the ChIP-seq protocol cross-links proteins with each other and with DNA. Consequently, also regions that are not directly bound by the targeted TF but interact with the binding site via chromatin looping are co-immunoprecipitated and sequenced. This produces minor ChIP-seq signals at loop anchor regions close to the directly bound site. We use the position and shape of ChIP-seq signals around CTCF motif pairs to predict whether they interact or not. We implemented this approach in a prediction method, termed Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs (7C). We applied 7C to all CTCF motif pairs within 1 Mb in the human genome and validated predicted interactions with high-resolution Hi-C and ChIA-PET. A single ChIP-seq experiment from known architectural proteins (CTCF, Rad21, Znf143) but also from other TFs (like TRIM22 or RUNX3) predicts loops accurately. Importantly, 7C predicts loops in cell types and for TF ChIP-seq datasets not used in training. Conclusion 7C predicts chromatin loops which can help to associate TF binding sites to regulated genes. Furthermore, profiling of hundreds of ChIP-seq datasets results in novel candidate factors functionally involved in chromatin looping. Our method is available as an R/Bioconductor package: http://bioconductor.org/packages/sevenC.

scholarly journals The DLO Hi-C Tool for Digestion-Ligation-Only Hi-C Chromosome Conformation Capture Data Analysis

Genes ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 289 ◽  
Author(s):  
Ping Hong ◽  
Hao Jiang ◽  
Weize Xu ◽  
Da Lin ◽  
Qian Xu ◽  
...  
Keyword(s):  
Target Genes ◽  
High Efficiency ◽  
New Technology ◽  
Three Dimensional ◽  
Large Data ◽  
Regulatory Elements ◽  
Chromosome Conformation Capture ◽  
Genome Chromosome ◽  
Chromosome Conformation ◽  
3D Genome

It is becoming increasingly important to understand the mechanism of regulatory elements on target genes in long-range genomic distance. 3C (chromosome conformation capture) and its derived methods are now widely applied to investigate three-dimensional (3D) genome organizations and gene regulation. Digestion-ligation-only Hi-C (DLO Hi-C) is a new technology with high efficiency and cost-effectiveness for whole-genome chromosome conformation capture. Here, we introduce the DLO Hi-C tool, a flexible and versatile pipeline for processing DLO Hi-C data from raw sequencing reads to normalized contact maps and for providing quality controls for different steps. It includes more efficient iterative mapping and linker filtering. We applied the DLO Hi-C tool to different DLO Hi-C datasets and demonstrated its ability in processing large data with multithreading. The DLO Hi-C tool is suitable for processing DLO Hi-C and in situ DLO Hi-C datasets. It is convenient and efficient for DLO Hi-C data processing.

scholarly journals Heat Shock Protein Genes Undergo Dynamic Alteration in Their Three-Dimensional Structure and Genome Organization in Response to Thermal Stress

2017 ◽  
Vol 37 (24) ◽  
Author(s):  
Surabhi Chowdhary ◽  
Amoldeep S. Kainth ◽  
David S. Gross
Keyword(s):  
Thermal Stress ◽  
Heat Shock ◽  
Heat Shock Protein ◽  
Rna Polymerase Ii ◽  
De Novo ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Chromosome Conformation ◽  
Coding Regions ◽  
Response To Stress

ABSTRACT Three-dimensional (3D) chromatin organization is important for proper gene regulation, yet how the genome is remodeled in response to stress is largely unknown. Here, we use a highly sensitive version of chromosome conformation capture in combination with fluorescence microscopy to investigate Heat Shock Protein (HSP) gene conformation and 3D nuclear organization in budding yeast. In response to acute thermal stress, HSP genes undergo intense intragenic folding interactions that go well beyond 5′-3′ gene looping previously described for RNA polymerase II genes. These interactions include looping between upstream activation sequence (UAS) and promoter elements, promoter and terminator regions, and regulatory and coding regions (gene “crumpling”). They are also dynamic, being prominent within 60 s, peaking within 2.5 min, and attenuating within 30 min, and correlate with HSP gene transcriptional activity. With similarly striking kinetics, activated HSP genes, both chromosomally linked and unlinked, coalesce into discrete intranuclear foci. Constitutively transcribed genes also loop and crumple yet fail to coalesce. Notably, a missense mutation in transcription factor TFIIB suppresses gene looping, yet neither crumpling nor HSP gene coalescence is affected. An inactivating promoter mutation, in contrast, obviates all three. Our results provide evidence for widespread, transcription-associated gene crumpling and demonstrate the de novo assembly and disassembly of HSP gene foci.

A structural proteomics filter: prediction of the quaternary structural type of hetero-oligomeric proteins on the basis of their sequences

2007 ◽  
Vol 40 (6) ◽  
pp. 986-989 ◽  
Author(s):  
Oliviero Carugo
Keyword(s):  
Structural Biology ◽  
Three Dimensional ◽  
Structural Type ◽  
Computational Method ◽  
Structural Proteomics ◽  
Dimensional Structure ◽  
Protein Chain ◽  
Oligomeric Proteins ◽  
Single Protein ◽  
A Chain

A protein chain can correspond to a monomeric protein or it can form, together with other chains, oligomeric assemblies, which can be either homo-oligomers or hetero-oligomers. In the latter case, the three-dimensional structure of the single protein chain is unlikely to be determined, since it will probably be difficult to express and crystallize. A computational method is presented here that allows one to predict if a chain participates in hetero-oligomeric assemblies, on the basis of its amino acid composition, with accuracy close to 80%. Such a technique should improve the success rate of structural biology projects.

scholarly journals Investigation of the Basic Steps in the Chromosome Conformation Capture Procedure

2021 ◽  
Vol 12 ◽  
Author(s):  
Oleg V. Bylino ◽  
Airat N. Ibragimov ◽  
Anna E. Pravednikova ◽  
Yulii V. Shidlovskii
Keyword(s):  
Biochemical Analysis ◽  
Enzyme Digestion ◽  
Chromosome Conformation Capture ◽  
Restriction Enzyme Digestion ◽  
Optimal Conditions ◽  
Chromosome Conformation ◽  
Depth Study ◽  
Cross Links ◽  
Triton X ◽  
Extraction Treatment

A constellation of chromosome conformation capture methods (С-methods) are an important tool for biochemical analysis of the spatial interactions between DNA regions that are separated in the primary sequence. All these methods are based on the long sequence of basic steps of treating cells, nuclei, chromatin, and finally DNA, thus representing a significant technical challenge. Here, we present an in-depth study of the basic steps in the chromatin conformation capture procedure (3С), which was performed using Drosophila Schneider 2 cells as a model. We investigated the steps of cell lysis, nuclei washing, nucleoplasm extraction, chromatin treatment with SDS/Triton X-100, restriction enzyme digestion, chromatin ligation, reversion of cross-links, DNA extraction, treatment of a 3C library with RNases, and purification of the 3C library. Several options were studied, and optimal conditions were found. Our work contributes to the understanding of the 3C basic steps and provides a useful guide to the 3C procedure.

scholarly journals Three-dimensional reconstruction of the Z disk of sectioned bee flight muscle.

1989 ◽  
Vol 108 (5) ◽  
pp. 1761-1774 ◽  
Author(s):  
N Q Cheng ◽  
J F Deatherage
Keyword(s):  
Central Region ◽  
Actin Filaments ◽  
Flight Muscle ◽  
Three Dimensional ◽  
Opposite Polarity ◽  
Dimensional Structure ◽  
Three Dimensional Reconstruction ◽  
Thin Sections ◽  
Dimensional Reconstruction ◽  
Cross Links

The three-dimensional structure of the central region of the Z disk of honeybee flight muscle has been determined to a resolution of 70 A by three-dimensional reconstruction from electron micrographs of tilted thin sections. The reconstructions show a complex assembly in which actin filaments terminate and are cross-linked together; a number of structural domains of this network are resolved in quantitative three-dimensional detail. The central region of the Z disk contains two sets of overlapping actin filaments of opposite polarity, which originate in the sarcomeres adjacent to the Z disk, and connections between these filaments. The filaments are deflected by the attachment of cross-links; spacing between filaments change by greater than 100 A during their passage through the Z disk. Each actin filament is linked by connecting structures to four filaments of opposite polarity and two filaments are of the same polarity. Four types of connecting density domain are observed in association with pairs of filaments of opposite polarity: C1, C2, C3, and C5. Two of these, C3 and C5, are associated with the ends of actin filaments. Another connection, C4, is associated with three filaments of the same polarity; C4 is threefold symmetric.

scholarly journals The three-dimensional structure of the nemaline rod Z-band.

1990 ◽  
Vol 111 (6) ◽  
pp. 2961-2978 ◽  
Author(s):  
E P Morris ◽  
G Nneji ◽  
J M Squire
Keyword(s):  
Actin Filaments ◽  
Three Dimensional ◽  
Nemaline Myopathy ◽  
Opposite Polarity ◽  
Three Dimensions ◽  
Dimensional Structure ◽  
Filament Axis ◽  
Correct Alignment ◽  
Cardiac Muscles ◽  
Cross Links

In nemaline myopathy and some cardiac muscles, the Z-band becomes greatly enlarged and contains multiple layers of a zigzag structure similar to that seen in normal muscle. Because of the additional periodicity in the direction of the filament axis, these structures are particularly favorable for three-dimensional analysis since it becomes possible to average the data in all three dimensions and thus improve the reliability of the reconstruction. Individual views of the structure corresponding to tilted longitudinal and transverse sections were combined by matching the phases of common reflections. Examination of the tilted views strongly suggested that to the available resolution, the structure possesses fourfold screw symmetry along the actin filament axes. This symmetry could be used both in establishing the correct alignment for the combination of individual tilted views and to generate additional views not readily accessible in a single tilt series. The reconstruction shows actin filaments from one sarcomere surrounded by an array of four actin filaments with opposite polarity from the adjacent sacormere. The actin filaments show a right-handed twist and are connected by a structure that links adjacent filaments with the same polarity at the same axial level, then runs parallel to the filaments, and finally forms a link between two actin filaments whose polarity is opposite to that of the first pair. The connecting structure is probably composed of alpha-actinin which is located in Z-bands and cross-links actin filaments. The connecting structure may consist of two alpha-actinin molecules linking actin filaments of opposite polarity.

Cloning and Characterization of an Agglutinin Gene from Arisaema lobatum

2005 ◽  
Vol 25 (5-6) ◽  
pp. 345-362 ◽  
Author(s):  
Juan Lin ◽  
Xuanwei Zhou ◽  
Yongzhen Pang ◽  
Han Gao ◽  
Jiong Fei ◽  
...  
Keyword(s):  
Genomic Sequence ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Regulation Mechanism ◽  
Amino Acid Residues ◽  
Reading Frame ◽  
Mannose Binding ◽  
Pcr Technology ◽  
Plant Families ◽  
Race Pcr

A novel agglutinin gene was cloned from Arisaema lobatum using SMART RACE-PCR technology. The full-length cDNA of Arisaema lobatum agglutinin (ala) was 1078 bp and contained a 774 bp open reading frame encoding a lectin precursor (proproprotein) of 258 amino acid residues with a 23 aa signal peptide. ALA contained three mannose-binding sites (QXDXNXVXY) with two-conserved domains of 45% identity, ALA-DOM1 and ALA-DOM2. The three-dimensional structure of ALA was very similar to that of GNA (Galanthus nivalis agglutinin). ALA shared varying identities, ranging from 40% to 85%, with mannose-binding lectins from other species of plant families, such as Araceae, Alliaceae, Iridaceae, Lillaceae, Amaryllidaceae and Bromeliaceae. Genomic sequence of ala was also cloned using genomic walker technology, and it was found to contain three putative TATA boxes and eight possible CAAT boxes in the 5′-flanking region. No intron was found within the region of genomic sequence. Southern blot analysis indicated that the ala belonged to a multi-copy gene family. Expression pattern analysis revealed that the ala preferentially expressed in the tissues with the higher expression being found in spadix, bud, leaf, spathe and tuber. The cloning of the ala gene not only provides a basis for further investigation of its structure, expression and regulation mechanism, but also enables us to test its potential role in controlling pests and fungal diseases by transferring the gene into plants in the future.

scholarly journals GenomeDISCO: A concordance score for chromosome conformation capture experiments using random walks on contact map graphs

2017 ◽  
Author(s):  
Oana Ursu ◽  
Nathan Boley ◽  
Maryna Taranova ◽  
Y.X. Rachel Wang ◽  
Galip Gurkan Yardimci ◽  
...  
Keyword(s):  
Random Walks ◽  
Critical Role ◽  
Three Dimensional ◽  
Cell Types ◽  
Chromosome Conformation Capture ◽  
Supplementary Information ◽  
Contact Map ◽  
Chromosome Conformation ◽  
Contact Maps ◽  
Map Graphs

AbstractMotivationThe 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.ResultsWe introduce a concordance measure called GenomeDISCO (DIfferences between Smoothed COntact maps) for assessing the similarity of a pair of contact maps obtained from chromosome conformation capture experiments. The key idea is to smooth contact maps using random walks on the contact map graph, before estimating concordance. We use simulated datasets to benchmark GenomeDISCO’s sensitivity to different types of noise that affect chromatin contact maps. When applied to a large collection of Hi-C datasets, GenomeDISCO accurately distinguishes biological replicates from samples obtained from different cell types. GenomeDISCO also generalizes to other chromosome conformation capture assays, such as HiChIP.AvailabilitySoftware implementing GenomeDISCO is available at https://github.com/kundajelab/[email protected] informationSupplementary data are available at Bioinformatics online.

scholarly journals Cross-linking of bovine rhodopsin with sulfosuccinimidyl 4-(N maleimidomethyl)cyclohexane-1-carboxylate affects its functionality

2020 ◽  
Vol 477 (12) ◽  
pp. 2295-2312
Author(s):  
Rafael Medina ◽  
Deisy Perdomo ◽  
Carolina Möller ◽  
José Bubis
Keyword(s):  
Conformational Changes ◽  
Polyacrylamide Gel Electrophoresis ◽  
Three Dimensional ◽  
Binding Activity ◽  
Dimensional Structure ◽  
Cross Linking ◽  
Bovine Rhodopsin ◽  
Rhodopsin Kinase ◽  
Cross Links ◽  
Guanine Nucleotide Binding

Rhodopsin is the photoreceptor protein involved in visual excitation in retinal rods. The functionality of bovine rhodopsin was determined following treatment with sulfosuccinimidyl 4-(N maleimidomethyl)cyclohexane-1-carboxylate (sulfo-SMCC), a bifunctional reagent capable of forming covalent cross-links between suitable placed lysines and cysteines. Denaturing polyacrylamide gel electrophoresis showed that rhodopsin incubated with sulfo-SMCC generated intermolecular dimers, trimers, and higher oligomers, although most of the sulfo-SMCC-treated protein remained as a monomer. Minor alterations on the absorption spectrum of light-activated sulfo-SMCC-treated rhodopsin were observed. However, only ∼2% stimulation of the guanine nucleotide binding activity of transducin was measured in the presence of sulfo-SMCC-cross-linked photolyzed rhodopsin. Moreover, rhodopsin kinase was not able of phosphorylating sulfo-SMCC-cross-linked rhodopsin after illumination. Rhodopsin was purified in the presence of either 0.1% or 1% n-dodecyl β-d-maltoside, to obtain dimeric and monomeric forms of the protein, respectively. Interestingly, no generation of the regular F1 and F2 thermolytic fragments was perceived with sulfo-SMCC-cross-linked rhodopsin either in the dimeric or monomeric state, implying the formation of intramolecular connections in the protein that might thwart the light-induced conformational changes required for interaction with transducin and rhodopsin kinase. Structural analysis of the rhodopsin three-dimensional structure suggested that the following lysine and cysteine pairs: Lys66/Lys67 and Cys316, Cys140 and Lys141, Cys140 and Lys248, Lys311 and Cys316, and/or Cys316 and Lys325 are potential candidates to generate intramolecular cross-links in the protein. Yet, the lack of fragmentation of sulfo-SMCC-treated Rho with thermolysin is consistent with the formation of cross-linking bridges between Lys66/Lys67 and Cys316, and/or Cys140 and Lys248.

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