scholarly journals GoPeaks: Histone Modification Peak Calling for CUT&Tag

2022 ◽  
Author(s):  
William M Yashar ◽  
Garth Kong ◽  
Jake VanCampen ◽  
Brittany M Smith ◽  
Daniel J Coleman ◽  
...  
Keyword(s):  
Histone Modification ◽  
Histone Modifications ◽  
Chromatin Immunoprecipitation ◽  
Binomial Distribution ◽  
Read Count ◽  
Peak Calling ◽  
Genome Wide ◽  
Chromatin Immunoprecipitation Sequencing ◽  
Genomic Regions ◽  
Covalent Histone Modifications

Genome-wide mapping of the histone modification landscape is critical to understanding tran-scriptional regulation. Cleavage Under Targets and Tagmentation (CUT&Tag) is a new method for profiling the localization of covalent histone modifications, offering improved sensitivity and decreased cost compared with Chromatin Immunoprecipitation Sequencing (ChIP-seq). Here, we present GoPeaks, a peak calling method specifically designed for histone modification CUT&Tag data. GoPeaks implements a Binomial distribution and stringent read count cut-off to nominate candidate genomic regions. We compared the performance of GoPeaks against com-monly used peak calling algorithms to detect H3K4me3, H3K4me1, and H3K27Ac peaks from CUT&Tag data. These histone modifications display a range of peak profiles and are frequently used in epigenetic studies. We found GoPeaks robustly detects genome-wide histone modifica-tions and, notably, identifies H3K27Ac with improved sensitivity compared to other standard peak calling algorithms.

scholarly journals Fast Detection of Differential Chromatin Domains with SCIDDO

2018 ◽  
Author(s):  
Peter Ebert ◽  
Marcel H. Schulz
Keyword(s):  
Histone Modifications ◽  
Chromatin Immunoprecipitation ◽  
Regulatory Elements ◽  
Differential Analysis ◽  
Chromatin Domains ◽  
Chromatin Dynamics ◽  
Fast Detection ◽  
Genome Wide ◽  
Chromatin Immunoprecipitation Sequencing

AbstractThe generation of genome-wide maps of histone modifications using chromatin immunoprecipitation sequencing (ChIP-seq) is a common approach to dissect the complexity of the epigenome. However, interpretation and differential analysis of histone ChIP-seq datasets remains challenging due to the genomic co-occurrence of several marks and their difference in genomic spread. Here we present SCIDDO, a fast statistical method for the detection of differential chromatin domains (DCDs) from chromatin state maps. DCD detection simplifies relevant tasks such as the characterization of chromatin changes in differentially expressed genes or the examination of chromatin dynamics at regulatory elements. SCIDDO is available at github.com/ptrebert/sciddo

scholarly journals Binding of an X-Specific Condensin Correlates with a Reduction in Active Histone Modifications at Gene Regulatory Elements

Genetics ◽  
2019 ◽  
Vol 212 (3) ◽  
pp. 729-742 ◽  
Author(s):  
Lena Annika Street ◽  
Ana Karina Morao ◽  
Lara Heermans Winterkorn ◽  
Chen-Yu Jiao ◽  
Sarah Elizabeth Albritton ◽  
...  
Keyword(s):  
Gene Expression ◽  
Histone Modifications ◽  
Chromatin Immunoprecipitation ◽  
Protein Complexes ◽  
Regulatory Elements ◽  
Evolutionarily Conserved ◽  
Chromatin Immunoprecipitation Sequencing ◽  
Gene Regulatory Elements ◽  
Gene Regulatory ◽  
Regulatory Sites

Condensins are evolutionarily conserved protein complexes that are required for chromosome segregation during cell division and genome organization during interphase. In Caenorhabditis elegans, a specialized condensin, which forms the core of the dosage compensation complex (DCC), binds to and represses X chromosome transcription. Here, we analyzed DCC localization and the effect of DCC depletion on histone modifications, transcription factor binding, and gene expression using chromatin immunoprecipitation sequencing and mRNA sequencing. Across the X, the DCC accumulates at accessible gene regulatory sites in active chromatin and not heterochromatin. The DCC is required for reducing the levels of activating histone modifications, including H3K4me3 and H3K27ac, but not repressive modification H3K9me3. In X-to-autosome fusion chromosomes, DCC spreading into the autosomal sequences locally reduces gene expression, thus establishing a direct link between DCC binding and repression. Together, our results indicate that DCC-mediated transcription repression is associated with a reduction in the activity of X chromosomal gene regulatory elements.

scholarly journals Rapid and Low-Input Profiling of Histone Marks in Plants Using Nucleus CUT&Tag

2021 ◽  
Vol 12 ◽  
Author(s):  
Weizhi Ouyang ◽  
Xiwen Zhang ◽  
Yong Peng ◽  
Qing Zhang ◽  
Zhilin Cao ◽  
...  
Keyword(s):  
Histone Modifications ◽  
Chromatin Immunoprecipitation ◽  
Binding Sites ◽  
Protein A ◽  
Transcriptional Factor ◽  
Experimental Procedure ◽  
Histone Marks ◽  
Genome Wide ◽  
Efficient Alternative ◽  
Tn5 Transposase

Characterizing genome-wide histone posttranscriptional modifications and transcriptional factor occupancy is crucial for deciphering their biological functions. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a powerful method for genome-wide profiling of histone modifications and transcriptional factor-binding sites. However, the current ChIP-seq experimental procedure in plants requires significant material and several days for completion. CUT&Tag is an alternative method of ChIP-seq for low-sample and single-cell epigenomic profiling using protein A-Tn5 transposase fusion proteins (PAT). In this study, we developed a nucleus CUT&Tag (nCUT&Tag) protocol based on the live-cell CUT&Tag technology. Our results indicate that nCUT&Tag could be used for histone modifications profiling in both monocot rice and dicot rapeseed using crosslinked or fresh tissues. In addition, both active and repressive histone marks such as H3K4me3 and H3K9me2 can be identified using our nCUT&Tag. More importantly, all the steps in nCUT&Tag can be finished in only 1 day, and the assay can be performed with as little as 0.01 g of plant tissue as starting materials. Therefore, our results demonstrate that nCUT&Tag is an efficient alternative strategy for plant epigenomic studies.

scholarly journals Genome-wide dysregulation of histone acetylation in the Parkinson’s disease brain

2019 ◽  
Author(s):  
Lilah Toker ◽  
Gia T Tran ◽  
Janani Sundaresan ◽  
Ole-Bjørn Tysnes ◽  
Guido Alves ◽  
...  
Keyword(s):  
Histone Acetylation ◽  
Chromatin Immunoprecipitation ◽  
Genetic Risk ◽  
Neurodegenerative Disorder ◽  
Unknown Etiology ◽  
Transcriptomic Data ◽  
Genome Wide ◽  
A Genome ◽  
Chromatin Immunoprecipitation Sequencing ◽  
Epigenetic Signatures

AbstractParkinson disease (PD) is a complex neurodegenerative disorder of largely unknown etiology. While several genetic risk factors have been identified, the involvement of epigenetics in the pathophysiology of PD is mostly unaccounted for. We conducted a histone acetylome-wide association study in PD, using brain tissue from two independent cohorts of cases and controls. Immunoblotting revealed increased acetylation at several histone sites in PD, with the most prominent change observed for H3K27, a marker of active promoters and enhancers. Chromatin immunoprecipitation sequencing (ChIP-seq) further indicated that H3K27 hyperacetylation in the PD brain is a genome-wide phenomenon, with a strong predilection for genes implicated in the disease, including SNCA, PARK7, PRKN and MAPT. Integration of the ChIP-seq with transcriptomic data revealed that the correlation between promoter H3K27 acetylation and gene expression is attenuated in PD patients, suggesting that H3K27 acetylation may be decoupled from transcription in the PD brain. Our findings strongly suggest that dysregulation of histone acetylation plays an important role in the pathophysiology of PD and identify novel epigenetic signatures associated with the disease.

scholarly journals CSA: a web service for the complete process of ChIP-Seq analysis

2019 ◽  
Vol 20 (S15) ◽  
Author(s):  
Min Li ◽  
Li Tang ◽  
Fang-Xiang Wu ◽  
Yi Pan ◽  
Jianxin Wang
Keyword(s):  
Web Service ◽  
Protein Interactions ◽  
Chromatin Immunoprecipitation ◽  
Peak Calling ◽  
Web Interface ◽  
Whole Process ◽  
Graphical Interfaces ◽  
Chromatin Immunoprecipitation Sequencing ◽  
Downstream Analysis ◽  
User Friendly

Abstract Background Chromatin immunoprecipitation sequencing (ChIP-seq) is a technology that combines chromatin immunoprecipitation (ChIP) with next generation of sequencing technology (NGS) to analyze protein interactions with DNA. At present, most ChIP-seq analysis tools adopt the command line, which lacks user-friendly interfaces. Although some web services with graphical interfaces have been developed for ChIP-seq analysis, these sites cannot provide a comprehensive analysis of ChIP-seq from raw data to downstream analysis. Results In this study, we develop a web service for the whole process of ChIP-Seq Analysis (CSA), which covers mapping, quality control, peak calling, and downstream analysis. In addition, CSA provides a customization function for users to define their own workflows. And the visualization of mapping, peak calling, motif finding, and pathway analysis results are also provided in CSA. For the different types of ChIP-seq datasets, CSA can provide the corresponding tool to perform the analysis. Moreover, CSA can detect differences in ChIP signals between ChIP samples and controls to identify absolute binding sites. Conclusions The two case studies demonstrate the effectiveness of CSA, which can complete the whole procedure of ChIP-seq analysis. CSA provides a web interface for users, and implements the visualization of every analysis step. The website of CSA is available at http://CompuBio.csu.edu.cn

scholarly journals Genome-wide Profiling of Histone Lysine Butyrylation Reveals its Role in the Positive Regulation of Gene Transcription in Rice

Rice ◽  
2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Shuai Liu ◽  
Guanqing Liu ◽  
Peifeng Cheng ◽  
Chao Xue ◽  
Yong Zhou ◽  
...  
Keyword(s):  
Gene Expression ◽  
Histone Modifications ◽  
Rice Genome ◽  
Enrichment Analysis ◽  
Carbon Chain ◽  
Main Body ◽  
Rice Varieties ◽  
Genome Wide ◽  
Chromatin Immunoprecipitation Sequencing ◽  
Intergenic Regions

Abstract Background Histone modifications play important roles in growth and development of rice (Oryza sativa L.). Lysine butyrylation (Kbu) with a four-carbon chain is a newly-discovered histone acylation modification in rice. Main Body In this study, we performed chromatin immunoprecipitation sequencing (ChIP-seq) analyses, the result showed that major enrichment of histone Kbu located in genebody regions of rice genome, especially in exons. The enrichment level of Kbu histone modification is positively correlated with gene expression. Furthermore, we compared Kbu with DNase-seq and other histone modifications in rice. We found that 60.06% Kub enriched region co-located with DHSs in intergenic regions. The similar profiles were detected among Kbu and several acetylation modifications such as H3K4ac, H3K9ac, and H3K23ac, indicating that Kbu modification is an active signal of transcription. Genes with both histone Kbu and one other acetylation also had significantly increased expression compared with genes with only one acetylation. Gene Ontology (GO) enrichment analysis revealed that these genes with histone Kbu can regulate multiple metabolic process in different rice varieties. Conclusion Our study showed that the lysine butyrylation modificaiton may promote gene expression as histone acetylation and will provide resources for futher studies on histone Kbu and other epigenetic modifications in plants.

scholarly journals HERON: A Novel Tool Enables Identification of Long, Weakly Enriched Genomic Domains in ChIP-seq Data

2021 ◽  
Vol 22 (15) ◽  
pp. 8123
Author(s):  
Anna Macioszek ◽  
Bartek Wilczynski
Keyword(s):  
Chromatin Immunoprecipitation ◽  
Hidden Markov ◽  
Histone Variants ◽  
Molecular Signatures ◽  
Peak Calling ◽  
Genome Wide ◽  
Sequencing Technique ◽  
Genome Wide Data ◽  
Novel Method ◽  
Generation Sequencing

The explosive development of next-generation sequencing-based technologies has allowed us to take an unprecedented look at many molecular signatures of the non-coding genome. In particular, the ChIP-seq (Chromatin ImmunoPrecipitation followed by sequencing) technique is now very commonly used to assess the proteins associated with different non-coding DNA regions genome-wide. While the analysis of such data related to transcription factor binding is relatively straightforward, many modified histone variants, such as H3K27me3, are very important for the process of gene regulation but are very difficult to interpret. We propose a novel method, called HERON (HiddEn MaRkov mOdel based peak calliNg), for genome-wide data analysis that is able to detect DNA regions enriched for a certain feature, even in difficult settings of weakly enriched long DNA domains. We demonstrate the performance of our method both on simulated and experimental data.

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