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CpG Islands

Overview of attention for book
Cover of 'CpG Islands'

Table of Contents

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    Book Overview
  2. Altmetric Badge
    Chapter 1 CpG Islands: A Historical Perspective
  3. Altmetric Badge
    Chapter 2 Biochemical Identification of Nonmethylated DNA by BioCAP-Seq
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    Chapter 3 Prediction of CpG Islands as an Intrinsic Clustering Property Found in Many Eukaryotic DNA Sequences and Its Relation to DNA Methylation
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    Chapter 4 CpG Islands in Cancer: Heads, Tails, and Sides
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    Chapter 5 Infinium DNA Methylation Microarrays on Formalin-Fixed, Paraffin-Embedded Samples
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    Chapter 6 The Use of Methylation-Sensitive Multiplex Ligation-Dependent Probe Amplification for Quantification of Imprinted Methylation
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    Chapter 7 The Pancancer DNA Methylation Trackhub: A Window to The Cancer Genome Atlas Epigenomics Data
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    Chapter 8 Methylation-Sensitive Amplification Length Polymorphism (MS-AFLP) Microarrays for Epigenetic Analysis of Human Genomes
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    Chapter 9 Genome-Wide Profiling of DNA Methyltransferases in Mammalian Cells
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    Chapter 10 Experimental Design and Bioinformatic Analysis of DNA Methylation Data
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    Chapter 11 Assay for Transposase Accessible Chromatin (ATAC-Seq) to Chart the Open Chromatin Landscape of Human Pancreatic Islets
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    Chapter 12 Defining Regulatory Elements in the Human Genome Using Nucleosome Occupancy and Methylome Sequencing (NOMe-Seq)
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    Chapter 13 Genome-Wide Mapping of Protein–DNA Interactions on Nascent Chromatin
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    Chapter 14 Analysis of Chromatin Interactions Mediated by Specific Architectural Proteins in Drosophila Cells
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    Chapter 15 High-Throughput Single-Cell RNA Sequencing and Data Analysis
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    Chapter 16 Functional Insulator Scanning of CpG Islands to Identify Regulatory Regions of Promoters Using CRISPR
  18. Altmetric Badge
    Chapter 17 An Application-Directed, Versatile DNA FISH Platform for Research and Diagnostics
Attention for Chapter 16: Functional Insulator Scanning of CpG Islands to Identify Regulatory Regions of Promoters Using CRISPR
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Chapter title
Functional Insulator Scanning of CpG Islands to Identify Regulatory Regions of Promoters Using CRISPR
Chapter number 16
Book title
CpG Islands
Published in
Methods in molecular biology, January 2018
DOI 10.1007/978-1-4939-7768-0_16
Pubmed ID
Book ISBNs
978-1-4939-7767-3, 978-1-4939-7768-0
Authors

Alice Grob, Masue Marbiah, Mark Isalan

Abstract

The ability to mutate a promoter in situ is potentially a very useful approach for gaining insights into endogenous gene regulation mechanisms. The advent of CRISPR/Cas systems has provided simple, efficient, and targeted genetic manipulation in eukaryotes, which can be applied to studying genome structure and function.The basic CRISPR toolkit comprises an endonuclease, Cas9, and a short DNA-targeting sequence, made up of a single guide RNA (sgRNA). The catalytic domains of Cas9 are rendered active upon dimerization of Cas9 with sgRNA, resulting in targeted double stranded DNA breaks. Among other applications, this method of DNA cleavage can be coupled to endogenous homology-directed repair (HDR) mechanisms for the generation of site-specific editing or knockin mutations, at both promoter regulatory and gene coding sequences.A well-characterized regulatory feature of promoter regions is the high abundance of CpGs. These CpG islands tend to be unmethylated, ensuring a euchromatic environment that promotes gene transcription. Here, we demonstrate CRISPR-mediated editing of two CpG islands located within the promoter region of the MDR1 gene (Multi Drug Resistance 1). Cas9 is used to generate double stranded breaks across multiple target sites, which are then repaired while inserting the beta globin (β-globin) insulator, 5'HS5. Thus, we are screening through promoter regulatory sequences with a chromatin barrier element to identify functional regions via "insulator scanning." Transcriptional and functional assessment of MDR1 expression provides evidence of genome engineering. Overall, this method allows the scanning of CpG islands to identify their promoter functions.

Twitter Demographics

The data shown below were collected from the profiles of 8 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 14 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 14 100%

Demographic breakdown

Readers by professional status Count As %
Student > Master 2 14%
Professor 1 7%
Student > Bachelor 1 7%
Student > Doctoral Student 1 7%
Researcher 1 7%
Other 1 7%
Unknown 7 50%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 4 29%
Agricultural and Biological Sciences 2 14%
Environmental Science 1 7%
Unknown 7 50%

Attention Score in Context

This research output has an Altmetric Attention Score of 2. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 16 May 2019.
All research outputs
#8,324,502
of 15,123,815 outputs
Outputs from Methods in molecular biology
#2,134
of 8,925 outputs
Outputs of similar age
#129,559
of 278,201 outputs
Outputs of similar age from Methods in molecular biology
#6
of 7 outputs
Altmetric has tracked 15,123,815 research outputs across all sources so far. This one is in the 43rd percentile – i.e., 43% of other outputs scored the same or lower than it.
So far Altmetric has tracked 8,925 research outputs from this source. They receive a mean Attention Score of 2.6. This one has done well, scoring higher than 75% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 278,201 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 51% of its contemporaries.
We're also able to compare this research output to 7 others from the same source and published within six weeks on either side of this one.