scholarly journals HIPPIE2: a method for fine-scale identification of physically interacting chromatin regions

2019 ◽  
Author(s):  
Pavel P. Kuksa ◽  
Alexandre Amlie-Wolf ◽  
Yih-Chii Hwang ◽  
Otto Valladares ◽  
Brian D. Gregory ◽  
...  
Keyword(s):  
High Resolution ◽  
Cell Line ◽  
Cell Lines ◽  
Dna Looping ◽  
Open Chromatin ◽  
Fine Scale ◽  
Long Distance ◽  
Chromosome Conformation ◽  
Chromatin Interactions ◽  
Distance Regulation

AbstractMost regulatory chromatin interactions are mediated by various transcription factors (TFs) and involve physically-interacting elements such as enhancers, insulators, or promoters. To map these elements and interactions, we developed HIPPIE2 which analyzes raw reads from high-throughput chromosome conformation (Hi-C) experiments to identify fine-scale physically-interacting regions (PIRs). Unlike standard genome binning approaches (e.g., 10K-1Mbp bins), HIPPIE2 dynamically calls physical locations of PIRs with better precision and higher resolution based on the pattern of restriction events and relative locations of interacting sites inferred from the sequencing readout.We applied HIPPIE2 to in situ Hi-C datasets across 6 human cell lines (GM12878, IMR90, K562, HMEC, HUVEC, NHEK) with matched ENCODE and Roadmap functional genomic data. HIPPIE2 detected 1,042,738 distinct PIRs across cell lines, with high resolution (average PIR length of 1,006bps) and high reproducibility (92.3% in GM12878 replicates). 32.8% of PIRs were shared among cell lines. PIRs are enriched for epigenetic marks (H3K27ac, H3K4me1) and open chromatin, suggesting active regulatory roles. HIPPIE2 identified 2.8M significant intrachromosomal PIR–PIR interactions, 27.2% of which were enriched for TF binding sites. 50,608 interactions were enhancer–promoter interactions and were enriched for 33 TFs (31 in enhancers/29 in promoters), several of which are known to mediate DNA looping/long-distance regulation. 29 TFs were enriched in >1 cell line and 4 were cell line-specific. These findings demonstrate that the dynamic approach used in HIPPIE2 (https://bitbucket.com/wanglab-upenn/HIPPIE2) characterizes PIR–PIR interactions with high resolution and reproducibility.

scholarly journals HIPPIE2: a method for fine-scale identification of physically interacting chromatin regions

2020 ◽  
Vol 2 (2) ◽  
Author(s):  
Pavel P Kuksa ◽  
Alexandre Amlie-Wolf ◽  
Yih-Chii Hwang ◽  
Otto Valladares ◽  
Brian D Gregory ◽  
...  
Keyword(s):  
High Resolution ◽  
Dna Looping ◽  
Open Chromatin ◽  
The Novel ◽  
Fine Scale ◽  
Chromosome Conformation ◽  
Chromatin Interactions ◽  
Restriction Sites

Abstract Most regulatory chromatin interactions are mediated by various transcription factors (TFs) and involve physically interacting elements such as enhancers, insulators or promoters. To map these elements and interactions at a fine scale, we developed HIPPIE2 that analyzes raw reads from high-throughput chromosome conformation (Hi-C) experiments to identify precise loci of DNA physically interacting regions (PIRs). Unlike standard genome binning approaches (e.g. 10-kb to 1-Mb bins), HIPPIE2 dynamically infers the physical locations of PIRs using the distribution of restriction sites to increase analysis precision and resolution. We applied HIPPIE2 to in situ Hi-C datasets across six human cell lines (GM12878, IMR90, K562, HMEC, HUVEC, NHEK) with matched ENCODE/Roadmap functional genomic data. HIPPIE2 detected 1042 738 distinct PIRs, with high resolution (average PIR length of 1006 bp) and high reproducibility (92.3% in GM12878). PIRs are enriched for epigenetic marks (H3K27ac, H3K4me1) and open chromatin, suggesting active regulatory roles. HIPPIE2 identified 2.8 million significant PIR–PIR interactions, 27.2% of which were enriched for TF binding sites. 50 608 interactions were enhancer–promoter interactions and were enriched for 33 TFs, including known DNA looping/long-range mediators. These findings demonstrate that the novel dynamic approach of HIPPIE2 (https://bitbucket.com/wanglab-upenn/HIPPIE2) enables the characterization of chromatin and regulatory interactions with high resolution and reproducibility.

Pharmacogenetic 3C interaction associated with the PDGFRA gene as a chromatin conformation marker for treatment with tyrosine kinase inhibitors.

2017 ◽  
Vol 35 (15_suppl) ◽  
pp. e23054-e23054
Author(s):  
Alexandre Akoulitchev ◽  
Aroul Ramadass ◽  
Jayne Green ◽  
Ulku Uzun ◽  
Jane Mellor ◽  
...  
Keyword(s):  
High Resolution ◽  
Tyrosine Kinase ◽  
Cell Line ◽  
Cell Lines ◽  
Kinase Inhibitors ◽  
Kinase Inhibitor ◽  
Leukemia Cell ◽  
Single Step ◽  
Chromosome Conformation ◽  
Insulator Function

e23054 Background: IDH1 mutations detected in glioma cells impair the insulator function between FIPL1L1 and PDGFRA at 4q12 ( Flavahan et al. 2016). We have used a high-resolution chromosome-conformation capture 3C analysis platform, EpiSwitch, and quantitative PCR, to map, evaluate, and quantify the TKI-sensitive conformational juxtaposition between FIP1L1 and PDGFRA. Loss of the insulator function in glioma prompted us to investigate the same interaction in the context of insulator loss with interstitial deletions at 4q12 in eosinophilic leukemias and AML. Methods: We tested a total of 72 primers in temperature gradient PCRs, with concentration matched negative controls, using the AML cell lines EOL-1 and HL-60. Products were sequenced in forward and reverse order. Dual label 5’FAM-BHQ1-3’hydrolysis probe assays, entirely specific for the PCR products, targeted the junction region of the 3C fragments. A reference 3C interaction was used as an internal copy number control for 3C library production. Results: EpiSwitch predicted and identified six 3C FIP1L1-PDGFRA interactions in different sequence orientations, within the 3D organization of the PDGFRA locus. The interaction D7 identified by the EpiSwitch qPCR assay was detected reproducibly in EOL-1 cells and glioblastoma tissue using both single step PCR and qPCR. An imatinib-sensitive AML cell line EOL-1 was used as a positive control for qPCR assays. Both AML and glioma cell lines tested positive using the assay as did glioma patient biopsies. The glioblastoma cell line DBTRG-05MG also tested positive for the D7 interaction at a maximum of 8.92 copies per 20 ng of the template. Conclusions: We confirmed and characterized, at high resolution, the conformational deregulation of FIP1L1 and PDGFRA in glioma. Additionally, our group detected the interaction in TKI-sensitive leukemia cell lines. The analysis of 3C microstructural alterations is consistent with latest insights into epigenetic regulation of PDGFRA. It provides a promising approach to the stratification of patients for tyrosine kinase inhibitor treatment, which could not be provided diagnostically with conventional sequencing approaches.

scholarly journals An integrative approach for fine-mapping chromatin interactions

2019 ◽  
Vol 36 (6) ◽  
pp. 1704-1711
Author(s):  
Artur Jaroszewicz ◽  
Jason Ernst
Keyword(s):  
Gene Regulation ◽  
High Resolution ◽  
Biological Significance ◽  
Computational Method ◽  
Supplementary Information ◽  
Integrative Approach ◽  
Genome Architecture ◽  
Open Chromatin ◽  
Chromatin Interactions ◽  
Genome Wide

Abstract Motivation Chromatin interactions play an important role in genome architecture and gene regulation. The Hi-C assay generates such interactions maps genome-wide, but at relatively low resolutions (e.g. 5-25 kb), which is substantially coarser than the resolution of transcription factor binding sites or open chromatin sites that are potential sources of such interactions. Results To predict the sources of Hi-C-identified interactions at a high resolution (e.g. 100 bp), we developed a computational method that integrates data from DNase-seq and ChIP-seq of TFs and histone marks. Our method, χ-CNN, uses this data to first train a convolutional neural network (CNN) to discriminate between called Hi-C interactions and non-interactions. χ-CNN then predicts the high-resolution source of each Hi-C interaction using a feature attribution method. We show these predictions recover original Hi-C peaks after extending them to be coarser. We also show χ-CNN predictions enrich for evolutionarily conserved bases, eQTLs and CTCF motifs, supporting their biological significance. χ-CNN provides an approach for analyzing important aspects of genome architecture and gene regulation at a higher resolution than previously possible. Availability and implementation χ-CNN software is available on GitHub (https://github.com/ernstlab/X-CNN). Supplementary information Supplementary data are available at Bioinformatics online.

Chromosomes 2q, 4q and 13q21 Are Preferential Targets of Epstein-Barr Virus (EBV) Integration In Burkitt's Lymphoma Cell Lines

Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 4452-4452
Author(s):  
Eva Maria Murga Penas ◽  
Juliane Hinke ◽  
Petra Behrmann ◽  
Snjezana Janjetovic ◽  
Georgia Schilling ◽  
...  
Keyword(s):  
Cell Line ◽  
Cell Lines ◽  
Epstein Barr Virus ◽  
Burkitt’S Lymphoma ◽  
Burkitt's Lymphoma ◽  
Long Distance ◽  
Exact Integration ◽  
Barr Virus ◽  
Ebv Dna ◽  
Epstein Barr

Abstract Abstract 4452 The Epstein-Barr virus (EBV) was first described in 1964 as a possible cause of Burkitt's lymphoma (BL), the most common childhood cancer in equatorial Africa. EBV is an oncogenic virus found in about 95% of the endemic BL. In latently infected cells, the EBV DNA can be maintained in episomal form, but integrated EBV could also be present. Data on the exact integration loci of EBV in BL are very rare, however, integration of EBV-DNA into the human genome has been pointed as an important mechanism in malignant cellular transformation. We have investigated the EBV integration loci (EBV-IL) in 20 BL cell lines using fluorescence in situ hybridization (FISH). FISH was performed using, as EBV-DNA probe, a biotinylated 3,000 bp fragment amplified by long distance-PCR from DNA of the EBV-positive BL cell line Raji. FISH on metaphase spreads of the BL cell line Namalwa was performed to validate the quality of the EBV-FISH probe. Negative controls were performed on EBV-negative BL cell lines CA-46, CW698, and Tanoue. Integration of EBV was defined by the presence of symmetrical doublet hybridization signals at the same chromosomal loci in both sister chromatids. A minimum of 15 well-conserved and complete metaphases was evaluated in each case. As expected, Namalwa showed symmetrical doublet hybridization signals of our EBV-FISH probe on chromosome 1p35. EBV-negative cell lines did not show hybridization signals of the probe. We detected 632 EBV-IL in the total of metaphases analyzed in 20 BL cell lines. Integration of EBV was seen in all chromosomal arms except Yp, 8p, 14p, 20q, 21p, and 22p. An analysis of the chromosomal distribution of all EBV-IL revealed a pattern of preferential insertion for EBV-IL on chromosomes 13q (14% of the metaphases), 2q and 4q (12%, respectively), 7q (10,5%), 3q (9%), and 17q (6,5%). Regarding the recurrency of EBV-IL, the BL cell lines were divided in 4 groups. The first group consisted of 8 cell lines with high-recurrent EBV-IL at a specific chromosomal band (75%-100% of the metaphases analyzed). This first group showed specific EBV-IL at a precise chromosomal location on homologous chromatids on 2p23 (Seraphine), 2q21~31 (Switzer), 22q12 (PA-682), 7p22 and 13q21 (AG876), 7q11 and 17q25 (Naliaka), and 7q21 and 13q21 (LY-67). Interestingly, in BL60 and Maku, the unique EBV-IL visualized was localized near the translocation breakpoint junction of a der(19)t(17;19) and a der(13)t(3;13), respectively. The second group contained 5 cell lines with medium-recurrent EBV-IL (27%-50%). In this group, we observed metaphases with 1 to 3 recurrent EBV-IL localized on 2p12 (Rael), 15q11~14 (JI), 15q13~15 (JBL2), 4q21 and 4q32 (BL16), and 3q21~26, 4p12, and 13q21 (Akuba). The third and fourth groups comprised 4 cell lines with low-recurrent EBV-IL (13%-20%) and 3 cell lines with absence of recurrent EBV-IL, respectively. Non-recurrently integrated EBV-DNA signals on additional chromosomes were observed in cell lines of all 4 groups, except in 4 of the high-recurrent group. We further investigated the distribution of the EBV-IL of groups 3 and 4, of those in groups 1 and 2 with a recurrency less than 27% of the metaphases, and of those that were non-recurrently integrated. We observed again that the viral integration targeted preferentially chromosomes 2q (21%), 4q (14%), and 3q (11%). Our results identify for the first time the integration loci of EBV in BL cell lines and that this integration succeed preferentially on chromosomes 2q, 3q, and 4q. Moreover, in 12 cell lines, this integration ocurred non-randomly at a specific chromosomal sites, targeting 13q21 recurrently. Whether the integration of EBV in these loci affects the expression of genes important for the pathogenesis of BL or whether the EBV integration contributes to an enhanced chromosomal instability remains to be elucidated. Disclosures: No relevant conflicts of interest to declare.

scholarly journals HiCORE: Hi-C analysis for identification of core chromatin loops with higher resolution and reliability

2020 ◽  
Author(s):  
Hongwoo Lee ◽  
Pil Joon Seo
Keyword(s):  
High Resolution ◽  
High Throughput Sequencing ◽  
Stochastic Noise ◽  
3D Interaction ◽  
Chromosome Conformation ◽  
Genome Coverage ◽  
Chromatin Loops ◽  
Chromatin Interactions ◽  
Genome Wide ◽  
Physical Interactions

AbstractGenome-wide chromosome conformation capture (3C)-based high-throughput sequencing (Hi-C) has enabled identification of genome-wide chromatin loops. Because the Hi-C map with restriction fragment resolution is intrinsically associated with sparsity and stochastic noise, Hi-C data are usually binned at particular intervals; however, the binning method has limited reliability, especially at high resolution. Here, we describe a new method called HiCORE, which provides simple pipelines and algorithms to overcome the limitations of single-layered binning and predict core chromatin regions with 3D physical interactions. In this approach, multiple layers of binning with slightly shifted genome coverage are generated, and interacting bins at each layer are integrated to infer narrower regions of chromatin interactions. HiCORE predicts chromatin looping regions with higher resolution and contributes to the identification of the precise positions of potential genomic elements.Author SummaryThe Hi-C analysis has enabled to obtain information on 3D interaction of genomes. While various approaches have been developed for the identification of reliable chromatin loops, binning methods have been limitedly improved. We here developed HiCORE algorithm that generates multiple layers of bin-array and specifies core chromatin regions with 3D interactions. We validated our algorithm and provided advantages over conventional binning method. Overall, HiCORE facilitates to predict chromatin loops with higher resolution and reliability, which is particularly relevant in analysis of small genomes.

scholarly journals An Integrative Approach for Fine-Mapping Chromatin Interactions

2019 ◽  
Author(s):  
Artur Jaroszewicz ◽  
Jason Ernst
Keyword(s):  
High Resolution ◽  
Binding Sites ◽  
Biological Significance ◽  
Computational Method ◽  
Integrative Approach ◽  
Genome Architecture ◽  
Open Chromatin ◽  
Chromatin Interactions ◽  
Genome Wide ◽  
Evolutionarily Conserved

AbstractChromatin interactions play an important role in genome architecture and regulation. The Hi-C assay generates such interactions maps genome-wide, but at relatively low resolutions (e.g., 5-25kb), which is substantially larger than the resolution of transcription factor binding sites or open chromatin sites that are potential sources of such interactions. To predict the sources of Hi-C identified interactions at a high resolution (e.g., 100bp), we developed a computational method that integrates ChIP-seq data of transcription factors and histone marks and DNase-seq data. Our method,χ-SCNN, uses this data to first train a Siamese Convolutional Neural Network (SCNN) to discriminate between called Hi-C interactions and non-interactions.χ-SCNN then predicts the high-resolution source of each Hi-C interaction using a feature attribution method. We show these predictions recover original Hi-C peaks after extending them to be coarser. We also showχ-SCNN predictions enrich for evolutionarily conserved bases, eQTLs, and CTCF motifs, supporting their biological significance.χ-SCNN provides an approach for analyzing important aspects of genome architecture and regulation at a higher resolution than previously possible.χ-SCNN software is available on GitHub (https://github.com/ernstlab/X-SCNN).

scholarly journals Positional cues governing cell migration in leech neurogenesis

Development ◽  
1991 ◽  
Vol 111 (4) ◽  
pp. 993-1005 ◽  
Author(s):  
S.A. Torrence
Keyword(s):  
Nervous System ◽  
Cell Line ◽  
Cell Lines ◽  
Embryonic Cell ◽  
Long Distance ◽  
Mesodermal Cell ◽  
Selective Ablation ◽  
Embryonic Cell Lines ◽  
Migration Pathways ◽  
Glial Precursor

The stereotyped distribution of identified neurons and glial cells in the leech nervous system is the product of stereotyped cell migrations and rearrangements during embryogenesis. To examine the dependence of long-distance cell migrations on positional cues provided by other tissues, embryos of Theromyzon rude were examined for the effects of selective ablation of various embryonic cell lines on the migration and final distribution of neural and glial precursor cells descended from the bilaterally paired ectodermal cell lines designated q bandlets. The results suggest that neither the commitment of q-bandlet cells to migrate nor the general lateral-to-medial direction of their migration depend on interactions with any other cell line. However, the ability of the migrating cells to follow their normal pathways and to find their normal destinations does depend on interactions with cells of the mesodermal cell line, which appears to provide positional cues that specify the migration pathways.

scholarly journals Algorithmic considerations when analysing capture Hi-C data

2020 ◽  
Vol 5 ◽  
pp. 289
Author(s):  
Linden Disney-Hogg ◽  
Ben Kinnersley ◽  
Richard Houlston
Keyword(s):  
Gene Regulation ◽  
Cell Lines ◽  
Chromosome Conformation Capture ◽  
Chromosome Conformation ◽  
Targeting Efficiency ◽  
Chromatin Interactions ◽  
Genomic Architecture ◽  
Insight Into ◽  
Recent Extension

Chromosome conformation capture methodologies have provided insight into the effect of 3D genomic architecture on gene regulation. Capture Hi-C (CHi-C) is a recent extension of Hi-C that improves the effective resolution of chromatin interactions by enriching for defined regions of biological relevance. The varying targeting efficiency between capture regions, however, introduces bias not present in conventional Hi-C, making analysis more complicated. Here we consider salient features of an algorithm that should be considered in evaluating the performance of a program used to analyse CHi-C data in order to infer meaningful interactions. We use the program CHICAGO to analyse promotor capture Hi-C data generated on 28 different cell lines as a case study.

Tri-C

2019 ◽  
Author(s):  
A. Marieke Oudelaar ◽  
Jim R. Hughes ◽  
Damien J. Downes
Keyword(s):  
Quantitative Analysis ◽  
High Resolution ◽  
High Throughput ◽  
Illumina Sequencing ◽  
Great Depth ◽  
Sequencing Data ◽  
Chromosome Conformation ◽  
Chromatin Interactions ◽  
Pcr Duplicates ◽  
Illumina Sequencing Data

Abstract Tri-C is a Chromosome Conformation Capture \(3C) approach, which can very efficiently identify multi-way chromatin interactions at individual alleles with selected viewpoints of interest at high resolution. Tri-C allows for multiplexing both viewpoints and samples. As identification of multi-way interactions relies on Illumina sequencing, data can be generated at great depth and PCR duplicates \(based on identical sonication ends) can accurately be removed, allowing for high-throughput, quantitative analysis of multi-way chromatin interactions.

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