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Mary Gearing

Mary Gearing is a Scientist at Addgene. She got her start as a Science Communications Intern writing for the Addgene blog and website. As a full-time Addgenie, she still enjoys blogging about CRISPR and other cool plasmids!

Recent Posts

CRISPRainbow and Genome Visualization

Posted by Mary Gearing on Feb 28, 2017 10:30:00 AM

Colorful CRISPR technologies are helping researchers visualize the genome and its organization within the nucleus, also called the 4D nucleome. Visualizing specific loci has historically been difficult, as techniques like fluorescent in situ hybridization (FISH) and chromosome capture suffer from low resolution and can’t be used in vivo. Some researchers have used fluorescently tagged DNA-binding proteins to label certain loci, but this approach is not scalable for every locus...unlike CRISPR. Early CRISPR labeling techniques allowed researchers to visualize nearly any single genomic locus, and recent advances have allowed scientists to track multiple genomic loci over time using all the colors of the CRISPRainbow.

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Topics: CRISPR, Fluorescent Proteins

CRISPR 101: Editing the Epigenome

Posted by Mary Gearing on Feb 14, 2017 10:44:08 AM

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

Single Base Editing with CRISPR

Posted by Mary Gearing on Aug 16, 2016 10:30:00 AM

When we talk about CRISPR applications, one negative always comes up: the low editing efficiency of homology-directed repair (HDR). Compared to the random process of non-homologous end joining, HDR occurs at a relatively low frequency, and in nondividing cells, this pathway is further downregulated. Like all CRISPR applications that use wild-type Cas9, editing by HDR also has some potential for off-target cleavage even when gRNAs are well designed. Rather than try to improve HDR, Addgene depositor David Liu’s lab created new Cas9 fusion proteins that act as base editorsThese fusions, first described in Komor et al., contain dCas9 or Cas9 nickase and the rat cytidine deaminase APOBEC1, and can convert cytosine to uracil without cutting DNA. Uracil is subsequently converted to thymine through DNA replication or repair. Later work from Kim et al. and Rees et al. has improved base editor targeting flexibility and specificity, further demonstrating the utility of this method.

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Topics: Genome Engineering, CRISPR

Cpf1 Update: Comparison to Cas9 and NgAgo

Posted by Mary Gearing on Jul 14, 2016 10:30:00 AM

In 2015, Feng Zhang’s lab characterized two Cpf1 nucleases, distant cousins of well-known Cas9. Cpf1 cleaves DNA in a staggered pattern and requires only one RNA rather than the two (tracrRNA and crRNA) needed by Cas9 for cleavage. Now, two new studies show that Cpf1 displays lower off-target editing than Cas9, confirming that this protein is well suited for genome editing. 

Find Cpf1 Plasmids at Addgene

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Topics: Genome Engineering, CRISPR

Comparing Cas9 to NgAgo: Can the Argonautes Best CRISPR?

Posted by Mary Gearing on Jun 9, 2016 10:30:00 AM

THE ORIGINAL NgAgo ARTICLE DISCUSSED IN THIS POST HAS BEEN RETRACTED AND FOLLOW UP STUDIES HAVE FAILED TO REPEAT THE RESULTS DISCUSSED BELOW

Biologists are going gaga over the newest gene-editing protein - a DNA-cleaving Argonaute from Natronobacterium gregoryi, or NgAgo for short. Addgene has already distributed this plasmid all over the world, and the question on everyone’s minds is: could NgAgo replace CRISPR? Such a drastic shift won’t happen overnight, but there are a few reasons why you might choose NgAgo over CRISPR proteins Cas9 or Cpf1 - keep reading to learn more!

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Topics: Plasmid Technology, Genome Engineering, CRISPR

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