Genome-wide Analysis of Histone Modifications Distribution using the Chromatin Immunoprecipitation Sequencing Method in Magnaporthe oryzae

10.3791/62423 ◽  
2021 ◽  
Author(s):  
Zechi Wu ◽  
Wanyu Sun ◽  
Sida Zhou ◽  
Li Zhang ◽  
Xinyu Zhao ◽  
...  
Keyword(s):  
Histone Modifications ◽  
Magnaporthe Oryzae ◽  
Chromatin Immunoprecipitation ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Sequencing Method ◽  
Chromatin Immunoprecipitation Sequencing

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 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 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.

Genome-wide analysis of T-DNA integration into the chromosomes of Magnaporthe oryzae

2007 ◽  
Vol 66 (3) ◽  
pp. 826-826 ◽  
Author(s):  
Jaehyuk Choi ◽  
Jongsun Park ◽  
Junhyun Jeon ◽  
Myoung-Hwan Chi ◽  
Jaeduk Goh ◽  
...  
Keyword(s):  
Magnaporthe Oryzae ◽  
Dna Integration ◽  
Genome Wide Analysis ◽  
Genome Wide

scholarly journals Genome-Wide Analysis of Hypoxia-Responsive Genes in the Rice Blast Fungus, Magnaporthe oryzae

PLoS ONE ◽  
2015 ◽  
Vol 10 (8) ◽  
pp. e0134939 ◽  
Author(s):  
Jaehyuk Choi ◽  
Hyunjung Chung ◽  
Gir-Won Lee ◽  
Sun-Ki Koh ◽  
Suhn-Kee Chae ◽  
...  
Keyword(s):  
Magnaporthe Oryzae ◽  
Rice Blast ◽  
Rice Blast Fungus ◽  
Genome Wide Analysis ◽  
Blast Fungus ◽  
Genome Wide
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