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CRISPR 101: Epigenetics and Editing the Epigenome

Posted by Mary Gearing on Jun 24, 2020 1:45:00 PM

Originally published Feb 14, 2017 and updated Jun 24, 2020.

Epigenetic modifications are an additional layer of control over gene expression that go beyond genomic sequence. Dysregulation of the epigenome (the sum of epigenetic modifications across the genome) has been implicated in disease states, and targeting the epigenome may make certain processes, like cellular reprogramming of iPSCs, more efficient. In general, epigenetic chromatin modifications are correlated with alterations in gene expression, but causality and mechanisms remain unclear. Today, targeted epigenetic modification at specific genomic loci is possible using CRISPR, and Addgene has a number of tools for this purpose.

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Topics: CRISPR, CRISPR 101

Fluorescent CRISPR Reporters: SRIRACCHA and GEmCherry2

Posted by Alyssa Cecchetelli on May 26, 2020 9:15:00 AM

If you’re using CRISPR to make a genome edit, how do you know if your CRISPR experiment was successful in your organism or cell type? You can use DNA sequencing or other molecular cloning techniques to determine CRISPR/sgRNA efficiency of an experiment and confirm the correct edit was made to the genome without any off target effects. However, these methods can be labor intensive and quite time consuming.  

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Topics: CRISPR, Other CRISPR Tools

A New Generation of Adenine Base Editors Improves Editing in Primary Human Cells

Posted by Susanna Bachle on May 7, 2020 9:15:00 AM

Adenine base editors (ABE) mediate A•T-to-G•C base changes (Figure 1), but it can be challenging to make these base changes, especially in primary human cells. Now, scientists at Beam Therapeutics have found a way to improve editing in primary human cells (Gaudelli et al., 2020).

One of the widely used base editing systems, ABE7.10 (and the starting point for a new generation of ABEs), consists of 3 components: 

  • a deaminase (TadA, originally from E.coli, named TadA7.10 in ABE7.10) 
  • a catalytically impaired Cas protein (dCas or Cas nickase) 
  • a guide RNA that targets the complex of TadA and dCas to the genomic DNA of interest 
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Topics: CRISPR, Base Editing

SARS-CoV-2/COVID-19 Detection Methods Based on CRISPR/Cas

Posted by Guest Blogger on May 5, 2020 9:15:00 AM

This post was contributed by Shravanti Suresh from Iowa State University.

Since its appearance, SARS-CoV-2 has spread to almost every part of the world manifesting as a full-fledged pandemic. Containing the spread of this virus has become an utmost priority for countries around the world and to do so, the WHO recommends one strategy: testing, tracking, and social distancing.

With countries like South Korea, one of the earlier epicenters of the outbreak ultimately flattening the curve, it has become evident that widespread testing is crucial in controlling this pandemic. Currently, the CDC uses RT-qPCR tests to diagnose COVID-19 and some serological tests to determine past exposure. However, the limited availability of reagents and equipment and the long turnaround times, have led researchers to turn to other technologies like CRISPR.

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Topics: CRISPR, Cas Proteins, COVID-19

Finding nucleic acids with SHERLOCK and DETECTR

Posted by Alyssa Cecchetelli on Apr 16, 2020 9:00:09 AM

Originally published Aug 30, 2018 and updated April 16, 2020.

Sensitive and specific nucleic acid detection is crucial for clinical diagnostics, genotyping, and biotechnological advancements. Many methods of nucleic acid detection however, either lack the sensitivity or the specificity to detect nucleic acids at low concentrations and/or are too expensive, time-consuming, and complex to use outside of standard laboratories. In the case of the COVID-19 pandemic, qPCR can be used to diagnose the presence of SARS-CoV-2 RNA, but inadequate access to reagents and equipment has become a bottleneck.

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Topics: CRISPR, Cas Proteins, Other CRISPR Tools, COVID-19

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