scholarly journals AMPure Purification Protocol v1

2020 ◽  
Author(s):  
Vasso Makrantoni ◽  
Daniel Robertson ◽  
Adele L. Marston
Keyword(s):  
Chromatin Immunoprecipitation ◽  
Binding Sites ◽  
Dna Recombination ◽  
Yeast Cells ◽  
Biological Processes ◽  
Technological Advancement ◽  
Entire Genome ◽  
Protein Dna Interactions ◽  
Generation Sequencing ◽  
Purification Protocol

A plethora of biological processes like gene transcription, DNA replication, DNA recombination, and chromosome segregation are mediated through protein–DNA interactions. A powerful method for investigating proteins within a native chromatin environment in the cell is chromatin immunoprecipitation (ChIP). Combined with the recent technological advancement in next generation sequencing, the ChIP assay can map the exact binding sites of a protein of interest across the entire genome. Here we describe a-step-by step protocol for ChIP followed by library preparation for ChIP-seq from yeast cells.

scholarly journals Cross-Linking and Cell Harvesting v1

2020 ◽  
Author(s):  
Vasso Makrantoni ◽  
Daniel Robertson ◽  
Adele L. Marston
Keyword(s):  
Chromatin Immunoprecipitation ◽  
Binding Sites ◽  
Dna Recombination ◽  
Yeast Cells ◽  
Biological Processes ◽  
Technological Advancement ◽  
Entire Genome ◽  
Cell Harvesting ◽  
Protein Dna Interactions ◽  
Generation Sequencing

A plethora of biological processes like gene transcription, DNA replication, DNA recombination, and chromosome segregation are mediated through protein–DNA interactions. A powerful method for investigating proteins within a native chromatin environment in the cell is chromatin immunoprecipitation (ChIP). Combined with the recent technological advancement in next generation sequencing, the ChIP assay can map the exact binding sites of a protein of interest across the entire genome. Here we describe a-step-by step protocol for ChIP followed by library preparation for ChIP-seq from yeast cells.

scholarly journals Bioinformatics Analysis v1

2020 ◽  
Author(s):  
Vasso Makrantoni ◽  
Daniel Robertson ◽  
Adele L. Marston
Keyword(s):  
Chromosome Segregation ◽  
Chromatin Immunoprecipitation ◽  
Binding Sites ◽  
Dna Recombination ◽  
Yeast Cells ◽  
Biological Processes ◽  
Technological Advancement ◽  
Entire Genome ◽  
Protein Dna Interactions ◽  
Generation Sequencing

A plethora of biological processes like gene transcription, DNA replication, DNA recombination, and chromosome segregation are mediated through protein–DNA interactions. A powerful method for investigating proteins within a native chromatin environment in the cell is chromatin immunoprecipitation (ChIP). Combined with the recent technological advancement in next generation sequencing, the ChIP assay can map the exact binding sites of a protein of interest across the entire genome. Here we describe a-step-by step protocol for ChIP followed by library preparation for ChIP-seq from yeast cells.

scholarly journals Analysis of the Chromosomal Localization of Yeast SMC Complexes by Chromatin Immunoprecipitation v1

2020 ◽  
Author(s):  
Vasso Makrantoni ◽  
Daniel Robertson ◽  
Adele L. Marston
Keyword(s):  
Chromosome Segregation ◽  
Chromatin Immunoprecipitation ◽  
Binding Sites ◽  
Dna Recombination ◽  
Yeast Cells ◽  
Biological Processes ◽  
Technological Advancement ◽  
Entire Genome ◽  
Protein Dna Interactions ◽  
Generation Sequencing

A plethora of biological processes like gene transcription, DNA replication, DNA recombination, and chromosome segregation are mediated through protein–DNA interactions. A powerful method for investigating proteins within a native chromatin environment in the cell is chromatin immunoprecipitation (ChIP). Combined with the recent technological advancement in next generation sequencing, the ChIP assay can map the exact binding sites of a protein of interest across the entire genome. Here we describe a-step-by step protocol for ChIP followed by library preparation for ChIP-seq from yeast cells.

scholarly journals Immunoprecipitation, Decross-linking, and DNA Extraction v1

2020 ◽  
Author(s):  
Vasso Makrantoni ◽  
Daniel Robertson ◽  
Adele L. Marston
Keyword(s):  
Chromosome Segregation ◽  
Chromatin Immunoprecipitation ◽  
Binding Sites ◽  
Dna Recombination ◽  
Yeast Cells ◽  
Biological Processes ◽  
Technological Advancement ◽  
Entire Genome ◽  
Protein Dna Interactions ◽  
Generation Sequencing

A plethora of biological processes like gene transcription, DNA replication, DNA recombination, and chromosome segregation are mediated through protein–DNA interactions. A powerful method for investigating proteins within a native chromatin environment in the cell is chromatin immunoprecipitation (ChIP). Combined with the recent technological advancement in next generation sequencing, the ChIP assay can map the exact binding sites of a protein of interest across the entire genome. Here we describe a-step-by step protocol for ChIP followed by library preparation for ChIP-seq from yeast cells.

scholarly journals ChIP-seq Library preparation v1

2020 ◽  
Author(s):  
Vasso Makrantoni ◽  
Daniel Robertson ◽  
Adele L. Marston
Keyword(s):  
Chromatin Immunoprecipitation ◽  
Binding Sites ◽  
Dna Recombination ◽  
Yeast Cells ◽  
Biological Processes ◽  
Technological Advancement ◽  
Library Preparation ◽  
Entire Genome ◽  
Protein Dna Interactions ◽  
Generation Sequencing

A plethora of biological processes like gene transcription, DNA replication, DNA recombination, and chromosome segregation are mediated through protein–DNA interactions. A powerful method for investigating proteins within a native chromatin environment in the cell is chromatin immunoprecipitation (ChIP). Combined with the recent technological advancement in next generation sequencing, the ChIP assay can map the exact binding sites of a protein of interest across the entire genome. Here we describe a-step-by step protocol for ChIP followed by library preparation for ChIP-seq from yeast cells.

scholarly journals Determine the Size of Sonicated Samples and the DNA Concentration v1

2020 ◽  
Author(s):  
Vasso Makrantoni ◽  
Daniel Robertson ◽  
Adele L. Marston
Keyword(s):  
Chromosome Segregation ◽  
Chromatin Immunoprecipitation ◽  
Binding Sites ◽  
Dna Recombination ◽  
Yeast Cells ◽  
Biological Processes ◽  
Technological Advancement ◽  
Entire Genome ◽  
Protein Dna Interactions ◽  
Generation Sequencing

A plethora of biological processes like gene transcription, DNA replication, DNA recombination, and chromosome segregation are mediated through protein–DNA interactions. A powerful method for investigating proteins within a native chromatin environment in the cell is chromatin immunoprecipitation (ChIP). Combined with the recent technological advancement in next generation sequencing, the ChIP assay can map the exact binding sites of a protein of interest across the entire genome. Here we describe a-step-by step protocol for ChIP followed by library preparation for ChIP-seq from yeast cells.

scholarly journals Cell Lysis and Sonication v1

2020 ◽  
Author(s):  
Vasso Makrantoni ◽  
Daniel Robertson ◽  
Adele L. Marston
Keyword(s):  
Chromosome Segregation ◽  
Chromatin Immunoprecipitation ◽  
Binding Sites ◽  
Dna Recombination ◽  
Yeast Cells ◽  
Biological Processes ◽  
Technological Advancement ◽  
Entire Genome ◽  
Protein Dna Interactions ◽  
Generation Sequencing

A plethora of biological processes like gene transcription, DNA replication, DNA recombination, and chromosome segregation are mediated through protein–DNA interactions. A powerful method for investigating proteins within a native chromatin environment in the cell is chromatin immunoprecipitation (ChIP). Combined with the recent technological advancement in next generation sequencing, the ChIP assay can map the exact binding sites of a protein of interest across the entire genome. Here we describe a-step-by step protocol for ChIP followed by library preparation for ChIP-seq from yeast cells.

Chromatin Immunoprecipitation of GFP-Tagged PML-Rara Coupled to High-Throughput Next Generation Sequencing.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 1276-1276
Author(s):  
Nicole R. Grieselhuber ◽  
Jahangheer S. Shaik ◽  
Li-Wei Chang ◽  
Sean McGrath ◽  
Lukas D. Wartman ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Dna Binding ◽  
Fusion Protein ◽  
Chromatin Immunoprecipitation ◽  
Binding Sites ◽  
Next Generation ◽  
High Confidence ◽  
Altered Expression ◽  
Dna Binding Sites ◽  
Generation Sequencing

Abstract Abstract 1276 Poster Board I-298 The PML-RARA fusion protein produced by the t(15;17) translocation is found in acute promyelocytic leukemia (APL) and acts as an aberrant transcription factor with oncogenic properties. To define the high affinity DNA binding sites of PML-RARA, we developed a novel system based upon chromatin immunoprecipitation of eGFP tagged PML-RARA (PR), coupled to next generation sequencing. Chromatin isolated from flow sorted, GFP+ PR9 cells (isolated 24 hours after electroporation with eGFP-PR) was immunoprecipitated with a highly specific anti-GFP monoclonal antibody, and massively parallel sequencing was performed using single-end read libraries generated from both input DNA and immunoprecipitated DNA. The sequenced reads were mapped to the reference human genome using the Burrows-Wheeler Alignment tool (BWA). Using the SamTools package, alignment files were then filtered to retain only reads with phred quality scores greater than 30. Finally, Model Based Analysis of ChIP-Seq (MACS) was used to obtain the predicted binding sites (approximately 13,000 for each replicate using a p value cutoff of 0.00001). To ensure the reproducibility of called peaks, we limited our analysis to 701 sites that occurred in replicate sequencing runs of the libraries, within a tolerance of ±50 bp at the peak. Visual inspection of graphically plotted peaks further filtered this list to 421 high quality sites. Using microarray expression data for 14 APL patients and 5 flow sorted, normal promyelocyte samples, we selected neighboring genes with at least a 3-fold difference between APL and promyelocyte expression. This step yielded a list of 82 neighboring genes whose expression may be altered by PML-RARA binding to adjacent DNA. While PML-RARA is often considered a transcriptional repressor, 68% of these genes were overexpressed in APL, suggesting that PML-RARA may also function as a transcriptional activator. Furthermore, 51 genes were dysregulated in the mCG-PML-RARA murine model of APL, 16 genes demonstrated expression changes following induction of PML-RARA expression in PR9 cells, and 12 genes had altered expression in both the PR9 and murine models. Collectively, these results demonstrate an association between the high confidence putative PR binding sites and gene expression changes. We next used the sequences found within the best 89 binding sites to define 6 potential in vivo consensus sites of PML-RARA using the CONSENSUS program. Three of these predicted sites were present in greater than 40% of the 421 high confidence sites. Two of these common motifs resemble the motifs found in retinoic acid response elements (RAREs), but have less stringent conservation at the 5' end while retaining the 3' TCA sequence. Taken together, our results suggest that PML-RARA has an extended repertoire of genomic DNA binding sites compared to wild-type RARA, reflecting novel gain-of-function properties of the fusion protein. Binding of some of these sites appears to have direct consequences for the expression of several tightly linked genes, which may themselves be involved in transcriptional regulatory networks that contribute to APL pathogenesis. Disclosures No relevant conflicts of interest to declare.

scholarly journals SDG712, a Putative H3K9-Specific Methyltransferase Encoding Gene, Delays Flowering through Repressing the Expression of Florigen Genes in Rice

Rice ◽  
2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Siju Zhang ◽  
Hongjiao Hao ◽  
Xiaonan Liu ◽  
Yingying Li ◽  
Xuan Ma ◽  
...  
Keyword(s):  
Chromatin Immunoprecipitation ◽  
Gene Expression Analysis ◽  
Regulatory Gene ◽  
Rhythmic Pattern ◽  
Biological Processes ◽  
Regulator Gene ◽  
Set Domain ◽  
Encoding Gene ◽  
Flowering Regulator ◽  
Functional Investigation

AbstractSET domain group (SDG) proteins have been identified to be involved in histone modification and participate in diverse biological processes. Rice contains 41 SDG genes, however, most of which have not been functionally characterized. Here, we report the identification and functional investigation of rice SDG712 gene. Phylogenic analysis revealed that SDG712 belongs to the H3K9-specific SDG subclade. SDG712 is highly expressed in leaves during reproductive growth stage with obvious circadian rhythmic pattern. Mutation of SDG712 promotes rice flowering, while overexpression of SDG712 delays rice flowering. Gene expression analysis suggested that SDG712 acts downstream of Hd1, while acts upstream of Ehd1, Hd3a and RFT1. Subcellular localization assay demonstrated that SDG712 is localized in the nucleus. Chromatin immunoprecipitation (ChIP) assay showed that the H3K9me2 levels at Hd3a and RFT1 loci were increased in SDG712 overexpression transgenic plants, indicating that SDG712 may mediate the H3K9 di-methylation on these loci to repress rice flowering. Taken together, our findings demonstrated that SDG712 is a negative flowering regulatory gene in rice, and it delays flowering through repressing key flowering regulator gene Ehd1 and the florigen genes Hd3a and RFT1.

scholarly journals Dynamic Association of the Replication Initiator and Transcription Factor DnaA with the Bacillus subtilis Chromosome during Replication Stress

2008 ◽  
Vol 191 (2) ◽  
pp. 486-493 ◽  
Author(s):  
Adam M. Breier ◽  
Alan D. Grossman
Keyword(s):  
Transcription Factor ◽  
Chromatin Immunoprecipitation ◽  
Binding Sites ◽  
Replication Fork ◽  
Replication Stress ◽  
Replication Initiation ◽  
Pass Through ◽  
Bacillus Subtilis Chromosome ◽  
Rapid Signaling ◽  
Replication Initiator

ABSTRACT DnaA functions as both a transcription factor and the replication initiator in bacteria. We characterized the DNA binding dynamics of DnaA on a genomic level. Based on cross-linking and chromatin immunoprecipitation data, DnaA binds at least 17 loci, 15 of which are regulated transcriptionally in response to inhibition of replication (replication stress). Six loci, each of which has a cluster of at least nine potential DnaA binding sites, had significant increases in binding by DnaA when replication was inhibited, indicating that the association of DnaA with at least some of its target sites is altered after replication stress. When replication resumed from oriC after inhibition of replication initiation, these high levels of binding decreased rapidly at origin-proximal and origin-distal regions, well before a replication fork could pass through each of the regulated regions. These findings indicate that there is rapid signaling to decrease activation of DnaA during replication and that interaction between DnaA bound at each site and the replication machinery is not required for regulation of DnaA activity in response to replication stress.

Sign in / Sign up

Export Citation Format

Share Document