Chromatin immunoprecipitation sequencing (ChIP-Seq) on the SOLiD™ system

Shah, Anjali

doi:10.1038/nmeth.f.247

Cited by 6 publications

(6 citation statements)

References 1 publication

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“…The DNA undergoes PCR amplification using primers targeting a particular genomic locus. These DNA sequences can be subjected to a number of downstream analysis techniques, including targeted approaches, like semiquantitative PCR and quantitative PCR, and genome-wide analyses using microarrays (ChIP–chip) and deep sequencing (ChIP-seq), ChIP-on-chip ( Shah, 2009 ; Vinckevicius and Chakravarti, 2012 ).…”

Section: Conventional Methods For Detecting Protein–dna Interaction Amentioning

confidence: 99%

Choosing a suitable method for the identification of replication origins in microbial genomes

2015

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As the replication of genomic DNA is arguably the most important task performed by a cell and given that it is controlled at the initiation stage, the events that occur at the replication origin play a central role in the cell cycle. Making sense of DNA replication origins is important for improving our capacity to study cellular processes and functions in the regulation of gene expression, genome integrity in much finer detail. Thus, clearly comprehending the positions and sequences of replication origins which are fundamental to chromosome organization and duplication is the first priority of all. In view of such important roles of replication origins, tremendous work has been aimed at identifying and testing the specificity of replication origins. A number of computational tools based on various skew types have been developed to predict replication origins. Using various in silico approaches such as Ori-Finder, and databases such as DoriC, researchers have predicted the locations of replication origins sites for thousands of bacterial chromosomes and archaeal genomes. Based on the predicted results, we should choose an effective method for identifying and confirming the interactions at origins of replication. Here we describe the main existing experimental methods that aimed to determine the replication origin regions and list some of the many the practical applications of these methods.

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Section: Conventional Methods For Detecting Protein–dna Interaction Amentioning

confidence: 99%

Choosing a suitable method for the identification of replication origins in microbial genomes

2015

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“…As to why ABI themselves successfully performed ChIP-Seq with input DNA fragment length exceeding the suggested 60-90 bp, even going up to 300 bp [11], one reason is that SOLiD v3 system supports these larger size ranges, but how ABI upgrades SOLiD is beyond the issue discussed here. If a transcription factor binds two adjacent sites along the promoter region, the slightly larger sizes (200-300 bp) may uncover such complexity.…”

Section: Superiority Of Shorter Fragments From a Further Sonication Imentioning

confidence: 99%

“…Lately, an application note of ChIP-Seq on SOLiD system from ABI themselves came into publication. In the application note, the initial quantity of IPed DNA was as much as 0.5 μg [11] which is hard to obtain for most ChIP-Seq experiments. In addition, the experimental process chose DNA fragment length in three different ranges (150-200, 200-250, 250-300 bp) [8] which is generally the same size-selection step for the Solexa system, obviously not optimal for subsequent library preparations on SOLiD v2 system.…”

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confidence: 99%

Simulation of ChIP-Seq based on extra-sonication of IPed DNA fragments

Wang

Shi

2010

Chin. Sci. Bull.

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The combination of chromatin immunoprecipitation with sequencing (ChIP-Seq) is an effective method for obtaining an in vivo genome-wide profile of the interaction of a protein with DNA. With the dramatic development of high-throughput short sequencing technologies, several new algorithms have been developed to process ChIP-Seq. However, the reported analytical tools for ChIP-Seq based on size selection of immunoprecipitated (IPed) DNA fragments are mainly adopted on the Solexa system. As a sequencer with the highest throughput, few studies of ChIP-Seq based on SOLiD system have been reported. The main difference of the SOLiD and Solexa systems exists in the length of DNA fragments during preparing sequencing libraries. The SOLiD system has relatively short DNA fragments if it processes a further sonication of IPed DNA fragments in order to meet the length requirement of DNA fragments for emulsion-PCR (ePCR). This work aims to investigate the influences of DNA fragment length on data analysis from ChIP-Seq. Previous studies show that typical bimodal peaks can be observed in Solexa ChIP-Seq data, but based on the analysis of the real SOLiD ChIP-Seq data in this study, we found that there were no double peaks with apparent reads shift in a local enriched region and the local reads distribution of peaks were tested by normal distribution. Using real and simulated ChIP-Seq data, three main ChIP-Seq algorithms (CisGenome, SISSRs and MACS) have been investigated. We found that algorithms developed for processing ChIP-Seq data generated from Solexa library protocol, cannot efficiently capture the feature of the ChIP-Seq data from SOLiD library. Misuse of those analytical tools would be a possible reason for failure of ChIP-Seq on the SOLiD system. Therefore, a new ChIP-Seq analytical strategy for an extra-sonication of IPed DNA fragments needs to be developed.protein-DNA interaction, ChIP-Seq, next generation sequencing, reads directionality, ePCR, SOLiD Citation:Wang W, Shi X L, Lu Z H. Simulation of ChIP-Seq based on extra-sonication of IPed DNA fragments.

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“…These fragments are of varying size, typically a couple of hundred bases in length, and do not accurately represent the typical 6–20-bp interaction site of trans -acting proteins. Nevertheless, a large number of factors have been assayed to date across many organisms, including RNA polymerase II (PolII) [23], STAT1 [24], CCCTC-binding factor (CTCF) [23,25], GABP [26], SRF [26], neuron-restrictive silencer factor (NRSF) [26,27], FoxA2 [28] and FoxA3 [29] in human cell lines. Kim et al provided comprehensive maps of CTCF binding, a factor known to act as an insulator influencing both chromatin structure and gene regulation, in human primary fibroblasts [25].…”

Section: Trans-acting Factorsmentioning

confidence: 99%

High-resolution mapping studies of chromatin and gene regulatory elements

Boyle

Furey

2009

Epigenomics

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Microarray and high-throughput sequencing technologies have enabled the development of comprehensive assays to identify locations of particular chromatin structures and regulatory elements. It is now possible to create genome-wide maps of DNA methylation, trans-factor binding sites, histone variants and histone tail modifications, nucleosome positions, regions of open chromatin, and chromosome locations and interactions. This review provides a summary of these new assays that are changing the way in which molecular biology research is being performed. While the generation of large amounts of data from these experiments is becoming increasingly easier, the development of corresponding analysis methods has progressed more slowly. It will likely be years before the full extent of the information contained in these data is fully appreciated.

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Chromatin immunoprecipitation sequencing (ChIP-Seq) on the SOLiD™ system

Cited by 6 publications

References 1 publication

Choosing a suitable method for the identification of replication origins in microbial genomes

Choosing a suitable method for the identification of replication origins in microbial genomes

Simulation of ChIP-Seq based on extra-sonication of IPed DNA fragments

High-resolution mapping studies of chromatin and gene regulatory elements

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