scholarly journals HiCoP, a simple and robust method for detecting interactions of regulatory regions

2020 ◽  
Author(s):  
Yan Zhang ◽  
Zhaoqiang Li ◽  
Shasha Bian ◽  
Hao Zhao ◽  
Delong Feng ◽  
...  
Keyword(s):  
Signal To Noise Ratio ◽  
Regulatory Elements ◽  
High Signal ◽  
Open Chromatin ◽  
Regulatory Regions ◽  
Essential Information ◽  
Histone H3k27 ◽  
Development And Differentiation ◽  
Physical Interactions ◽  
Accessible Chromatin

Abstract Background: Chromatin physical interactions provides essential information for understanding the regulation of cis -elements like enhancers, promoters, and insulators in cell development and differentiation. The Hi-C assay is a technique detecting chromatin structures of the whole genome but not sensitive to interactions of regulatory elements. Several methods, like HiChIP, DNase-C, and OCEAN-C, have been developed for enriching interactions of regulatory regions, but all of them have some shortcomings. New simple, efficient, and robust methods are still in need of detecting interactions of regulatory regions. Results: We developed a new, simple, and robust assay called CoP ( Co lumn P urified chromatin) for profiling of open chromatin regions by directly purifying fragmentized crosslinked chromatin with a DNA purification column. The open chromatin regions, including active enhancers, promoters, and insulators, were significantly enriched in CoP chromatin. The CoP-seq assay can efficiently detect open chromatin regions, especially active promoters, with a high signal-to-noise ratio. We integrated the CoP-seq and Hi-C technique (Hi-CoP) for the detection of interactions of accessible chromatin regions, which represent active cis -regulatory elements in cells. We observed that the HiCoP captured the peaks in the promoters-associated enhancer regions, and the chromatin features identified by HiCoP were similar to HiChIP of histone H3K27 acetylation rather than Hi-C. HiCoP detected more promoter-enhancer (P-E), promoter-promoter (P-P), and enhancer-enhancer (E-E) interactions within 20kb-5Mb than Hi-C. Most of the loops identified by HiCoP were associated with the expressed genes. Conclusion: CoP assay can efficiently enrich open chromatin regions. When CoP assay was integrated with Hi-C assay, it provides a simple, robust, alternative technique for profiling accessible chromatin regions and chromatin conformation simultaneously.

scholarly journals HiCoP, a simple and robust method for detecting interactions of regulatory regions

2020 ◽  
Author(s):  
Yan Zhang ◽  
Zhaoqiang Li ◽  
Shasha Bian ◽  
Hao Zhao ◽  
Delong Feng ◽  
...  
Keyword(s):  
Signal To Noise Ratio ◽  
Regulatory Elements ◽  
High Signal ◽  
Open Chromatin ◽  
Regulatory Regions ◽  
Essential Information ◽  
Histone H3k27 ◽  
Development And Differentiation ◽  
Physical Interactions ◽  
Accessible Chromatin

Abstract Background: Chromatin physical interactions provide essential information for understanding the regulation of cis-elements like enhancers, promoters, and insulators in cell development and differentiation. The Hi-C assay is a technique detecting chromatin structures of the whole genome but not sensitive to interactions of regulatory elements. Several methods, like HiChIP, DNase-C, and OCEAN-C, have been developed for enriching interactions of regulatory regions, but all of them have some shortcomings. New simple, efficient, and robust methods are still in need of detecting interactions of regulatory regions. Results: We developed a new, simple, and robust assay called CoP (Column Purified chromatin) for profiling of open chromatin regions by directly purifying fragmentized crosslinked chromatin with a DNA purification column. The accessible chromatin regions, including active enhancers, promoters, and insulators, were significantly enriched in CoP chromatin. The CoP-seq assay can efficiently detect open chromatin regions, especially active promoters, with a high signal-to-noise ratio. We integrated the CoP-seq and Hi-C technique (HiCoP) for the detection of interactions of accessible chromatin regions, which represent active cis-regulatory elements in cells. We observed that the HiCoP captured the peaks in the promoters-associated enhancer regions, and the chromatin features identified by HiCoP were similar to HiChIP of histone H3K27 acetylation rather than Hi-C. HiCoP detected more promoter-enhancer (P-E), promoter-promoter (P-P), and enhancer-enhancer (E-E) interactions within 20kb-5Mb than Hi-C. Most of the loops identified by HiCoP were associated with the expressed genes. Conclusion: CoP assay can efficiently enrich open chromatin regions. When CoP assay was integrated with Hi-C assay, it provides a simple, robust, alternative technique for profiling accessible chromatin regions and chromatin conformation simultaneously.

scholarly journals HiCoP, a simple and robust method for detecting interactions of regulatory regions

2020 ◽  
Author(s):  
Yan Zhang ◽  
Zhaoqiang Li ◽  
Shasha Bian ◽  
Hao Zhao ◽  
Delong Feng ◽  
...  
Keyword(s):  
Signal To Noise Ratio ◽  
Regulatory Elements ◽  
High Signal ◽  
Open Chromatin ◽  
Robust Methods ◽  
Regulatory Regions ◽  
Essential Information ◽  
Development And Differentiation ◽  
Physical Interactions ◽  
Accessible Chromatin

Abstract Background: Chromatin physical interactions provide essential information for understanding the regulation of cis-elements like enhancers, promoters, and insulators in cell development and differentiation. The Hi-C assay is a technique detecting chromatin structures of the whole genome but not sensitive to interactions of regulatory elements. Several methods, like HiChIP, DNase-C, and OCEAN-C, have been developed for enriching interactions of regulatory regions, but all of them have some shortcomings. New simple, efficient, and robust methods are still in need of detecting interactions of regulatory regions. Results: We developed a new, simple, and robust assay called CoP (Column Purified chromatin) for profiling of open chromatin regions by directly purifying fragmentized crosslinked chromatin with a DNA purification column. The accessible chromatin regions, including active enhancers, promoters, and insulators, were significantly enriched in CoP chromatin. The CoP-seq assay can efficiently detect open chromatin regions, especially active promoters, with a high signal-to-noise ratio. We integrated the CoP-seq and Hi-C technique (HiCoP) to detect interactions of accessible chromatin regions, which represent active cis-regulatory elements in cells. We observed that the HiCoP captured the peaks in the promoters-associated enhancer regions. HiCoP detected more promoter-enhancer (P-E), promoter-promoter (P-P), and enhancer-enhancer (E-E) interactions within 20kb-5Mb than Hi-C. Most of the loops identified by HiCoP are associated with the expressed genes. Conclusion: CoP assay can efficiently enrich open chromatin regions. When CoP assay was integrated with Hi-C assay, it provides a simple, robust, alternative technique for profiling accessible chromatin regions and chromatin conformation simultaneously.

scholarly journals CellWalkR: An R Package for integrating single-cell and bulk data to resolve regulatory elements

2021 ◽  
Author(s):  
Pawel F. Przytycki ◽  
Katherine S. Pollard
Keyword(s):  
Random Walk ◽  
Single Cell ◽  
R Package ◽  
Regulatory Elements ◽  
Random Walk Model ◽  
Open Chromatin ◽  
Cell Type ◽  
Regulatory Regions ◽  
Bulk Data ◽  
Cell Type Specific

AbstractWhile single-cell open chromatin (scATAC-seq) data allows for the identification of cell type-specific regulatory regions, it is much sparser than bulk data. CellWalkR is an R package that performs an integration of external labeling and bulk epigenetic data with scATAC-seq using a network-based random walk model to help overcome this sparsity. Outputs include cell type labels for individual cells and regulatory regions.Availability and implementationCellWalkR is freely available as an R package under a GNU GPL-2.0 License, and can be accessed from https://github.com/PFPrzytycki/CellWalkR with an accompanying vignette for analyzing example data.

scholarly journals BarkBase: Epigenomic Annotation of Canine Genomes

Genes ◽  
2019 ◽  
Vol 10 (6) ◽  
pp. 433 ◽  
Author(s):  
Kate Megquier ◽  
Diane P. Genereux ◽  
Jessica Hekman ◽  
Ross Swofford ◽  
Jason Turner-Maier ◽  
...  
Keyword(s):  
Regulatory Elements ◽  
Open Chromatin ◽  
Genetic Associations ◽  
Functional Studies ◽  
Genomic Annotation ◽  
File Formats ◽  
Causal Variants ◽  
Health And Disease ◽  
Differential Gene ◽  
Accessible Chromatin

Dogs are an unparalleled natural model for investigating the genetics of health and disease, particularly for complex diseases like cancer. Comprehensive genomic annotation of regulatory elements active in healthy canine tissues is crucial both for identifying candidate causal variants and for designing functional studies needed to translate genetic associations into disease insight. Currently, canine geneticists rely primarily on annotations of the human or mouse genome that have been remapped to dog, an approach that misses dog-specific features. Here, we describe BarkBase, a canine epigenomic resource available at barkbase.org. BarkBase hosts data for 27 adult tissue types, with biological replicates, and for one sample of up to five tissues sampled at each of four carefully staged embryonic time points. RNA sequencing is complemented with whole genome sequencing and with assay for transposase-accessible chromatin using sequencing (ATAC-seq), which identifies open chromatin regions. By including replicates, we can more confidently discern tissue-specific transcripts and assess differential gene expression between tissues and timepoints. By offering data in easy-to-use file formats, through a visual browser modeled on similar genomic resources for human, BarkBase introduces a powerful new resource to support comparative studies in dogs and humans.

scholarly journals Profiling of accessible chromatin regions across multiple plant species and cell types reveals common gene regulatory principles and new control modules

2017 ◽  
Author(s):  
Kelsey A. Maher ◽  
Marko Bajic ◽  
Kaisa Kajala ◽  
Mauricio Reynoso ◽  
Germain Pauluzzi ◽  
...  
Keyword(s):  
Hair Cell ◽  
Plant Species ◽  
Stress Responses ◽  
Binding Sites ◽  
Cell Types ◽  
Regulatory Elements ◽  
Open Chromatin ◽  
Cell Type ◽  
Cell Type Specific ◽  
Accessible Chromatin

ABSTRACTThe transcriptional regulatory structure of plant genomes remains poorly defined relative to animals. It is unclear how many cis-regulatory elements exist, where these elements lie relative to promoters, and how these features are conserved across plant species. We employed the Assay for Transposase-Accessible Chromatin (ATAC-seq) in four plant species (Arabidopsis thaliana, Medicago truncatula, Solanum lycopersicum, and Oryza sativa) to delineate open chromatin regions and transcription factor (TF) binding sites across each genome. Despite 10-fold variation in intergenic space among species, the majority of open chromatin regions lie within 3 kb upstream of a transcription start site in all species. We find a common set of four TFs that appear to regulate conserved gene sets in the root tips of all four species, suggesting that TF-gene networks are generally conserved. Comparative ATAC-seq profiling of Arabidopsis root hair and non-hair cell types revealed extensive similarity as well as many cell type-specific differences. Analyzing TF binding sites in differentially accessible regions identified a MYB-driven regulatory module unique to the hair cell, which appears to control both cell fate regulators and abiotic stress responses. Our analyses revealed common regulatory principles among species and shed light on the mechanisms producing cell type-specific transcriptomes during development.

ATAC-STARR-seq v2

2021 ◽  
Author(s):  
Tyler Hansen ◽  
Emily Hodges
Keyword(s):  
Regulatory Region ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
High Signal ◽  
Regulatory Pathways ◽  
Information Accessibility ◽  
Genome Wide ◽  
A Genome ◽  
Wide Scale ◽  
Accessible Chromatin

Massively parallel reporter assays test the capacity of putative cis-regulatory elements (CREs) to drive transcription on a genome-wide scale. In nearly all cases, chromatin accessibility is necessary to drive activity, so most CREs are inactive due to chromatin context rather than intrinsic DNA sequence properties. Here, we combined assay for transposase-accessible chromatin (ATAC-seq) with self-transcribing active regulatory region sequencing (STARR-seq) to selectively assay the regulatory potential of nucleosome-free DNA genome-wide. Our approach enabled high-resolution testing of ~50 million unique DNA fragments tiling ~101,000 accessible chromatin regions in human lymphoblastoid cells. To illustrate the application of our approach, we show that 30% of all accessible regions contain an activator, a silencer or both. Benchmarking against standard ATAC-seq, our approach faithfully captures chromatin accessibility and transcription factor (TF) footprints with high signal-to-noise. Integrating three layers of genomic information (accessibility, TF occupancy, and activity) provided by ATAC-STARR-seq, we stratified active and silent CREs by the presence of several TF footprints and show that CREs with specific TF combinations are associated with distinct gene regulatory pathways. Altogether, these data highlight the power of ATAC-STARR-seq to comprehensively investigate the regulatory landscape of the human genome from a single DNA source.

scholarly journals Profiling of open chromatin in developing pig (Sus scrofa) muscle to identify regulatory regions

2021 ◽  
Author(s):  
Mazdak Salavati ◽  
Shernae A. Woolley ◽  
Yennifer Cortés Araya ◽  
Michelle M. Halstead ◽  
Claire Stenhouse ◽  
...  
Keyword(s):  
Genetic Variants ◽  
Sus Scrofa ◽  
Prediction Models ◽  
Developmental Time ◽  
Open Chromatin ◽  
Regulatory Sequences ◽  
Specific Information ◽  
Regulatory Regions ◽  
Breeding Programmes ◽  
Accessible Chromatin

AbstractThere is very little species-specific information about how the genome is regulated in domestic pigs (Sus scrofa). This lack of knowledge hinders efforts to define and predict the effects of genetic variants in pig breeding programmes. In order to address this knowledge gap, we need to identify regulatory sequences in the pig genome starting with regions of open chromatin. We have optimised the ‘Improved Protocol for the Assay for Transposase-Accessible Chromatin (Omni-ATAC-seq)’ to profile regions of open chromatin in flash frozen pig muscle tissue samples. This protocol has allowed us to identify putative regulatory regions in semitendinosus muscle from 24 male piglets. We collected samples from the smallest, average, and largest sized male piglets from each litter through five developmental time points. The ATAC-Seq data were mapped to Sscrofa11.1 with Bowtie2 and Genrich were used for post-alignment peak-calling. Of the 4661 putative regions of accessible chromatin identified, >50% were within 1 kb of known transcription start sites. The size of each open chromatin region varied according to the developmental time point. At day 90 of gestation, we investigated chromatin openness relative to foetal piglet size. In parallel we measured genome-wide gene expression and allele-specific expression using RNA-Seq analysis of the same muscle samples. We found regions of open chromatin associated with down regulation of genes involved in muscle development in small sized foetal piglets. The dataset that we have generated here provides: i) a resource for studies of genome regulation in pigs, and ii) contributes valuable functional annotation information to filter genetic variants for use in genomic selection in pig breeding programmes. Future work could leverage the ATAC-Seq data with very large datasets of genetic variants from phenotyped pigs. This approach could inform chromatin aware genomic prediction models and determine whether regions of open chromatin are enriched for trait-linked variants, and especially for muscle and meat traits.

A compact guided-wave EMAT with pulsed electromagnet for ferromagnetic tube inspection

2020 ◽  
Vol 64 (1-4) ◽  
pp. 951-958
Author(s):  
Tianhao Liu ◽  
Yu Jin ◽  
Cuixiang Pei ◽  
Jie Han ◽  
Zhenmao Chen
Keyword(s):  
Power Plants ◽  
Signal To Noise Ratio ◽  
Small Diameter ◽  
Performance Testing ◽  
Guided Wave ◽  
High Signal ◽  
Receiver Coil ◽  
Signal To Noise ◽  
Corrosion Defects

Small-diameter tubes that are widely used in petroleum industries and power plants experience corrosion during long-term services. In this paper, a compact inserted guided-wave EMAT with a pulsed electromagnet is proposed for small-diameter tube inspection. The proposed transducer is noncontact, compact with high signal-to-noise ratio and unattractive to ferromagnetic tubes. The proposed EMAT is designed with coils-only configuration, which consists of a pulsed electromagnet and a meander pulser/receiver coil. Both the numerical simulation and experimental results validate its feasibility on generating and receiving L(0,2) mode guided wave. The parameters for driving the proposed EMAT are optimized by performance testing. Finally, feasibility on quantification evaluation for corrosion defects was verified by experiments.

Application of Novel Low Current OBIRCH Amplifier and Nanoprobing to Identify Subtle Leakages in Advanced Node Technologies

2018 ◽  
Author(s):  
Satish Kodali ◽  
Liangshan Chen ◽  
Yuting Wei ◽  
Tanya Schaeffer ◽  
Chong Khiam Oh
Keyword(s):  
Signal To Noise Ratio ◽  
Semiconductor Industry ◽  
Fault Isolation ◽  
Ring Oscillator ◽  
High Signal ◽  
The Novel ◽  
Resistance Change ◽  
Three Samples ◽  
Relative Threshold ◽  
First Time

Abstract Optical beam induced resistance change (OBIRCH) is a very well-adapted technique for static fault isolation in the semiconductor industry. Novel low current OBIRCH amplifier is used to facilitate safe test condition requirements for advanced nodes. This paper shows the differences between the earlier and novel generation OBIRCH amplifiers. Ring oscillator high standby leakage samples are analyzed using the novel generation amplifier. High signal to noise ratio at applied low bias and current levels on device under test are shown on various samples. Further, a metric to demonstrate the SNR to device performance is also discussed. OBIRCH analysis is performed on all the three samples for nanoprobing of, and physical characterization on, the leakage. The resulting spots were calibrated and classified. It is noted that the calibration metric can be successfully used for the first time to estimate the relative threshold voltage of individual transistors in advanced process nodes.

scholarly journals VS2 as saturable absorber for Q-switched pulse generation

Nanophotonics ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 2569-2576 ◽  
Author(s):  
Lu Li ◽  
Lihui Pang ◽  
Qiyi Zhao ◽  
Yao Wang ◽  
Wenjun Liu
Keyword(s):  
Saturable Absorber ◽  
Nonlinear Optical ◽  
Modulation Depth ◽  
Signal To Noise Ratio ◽  
Transition Metal Dichalcogenides ◽  
Laser Cavity ◽  
Pulse Generation ◽  
High Signal ◽  
Power Pulse ◽  
Metal Dichalcogenides

AbstractTransition metal dichalcogenides have been widely utilized as nonlinear optical materials for laser pulse generation applications. Herein, we study the nonlinear optical properties of a VS2-based optical device and its application as a new saturable absorber (SA) for high-power pulse generation. Few-layer VS2 nanosheets are deposited on the tapered region of a microfiber to form an SA device, which shows a modulation depth of 40.52%. After incorporating the microfiber-VS2 SA into an Er-doped fiber laser cavity, passively Q-switched pulse trains could be obtained with repetition rates varying from 95 to 233 kHz. Under the pump power of 890 mW, the largest output power and shortest pulse duration are measured to be 43 mW and 854 ns, respectively. The high signal-to-noise ratio of 60 dB confirms the excellent stability of the Q-switching state. To the best of our knolowdge, this is the first illustration of using VS2 as an SA. Our experimental results demonstrate that VS2 nanomaterials have a large potential for nonlinear optics applications.

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