DNA sequence-dependent activity and base flipping mechanisms of DNMT1 regulate genome-wide DNA methylation

AbstractTransgenerationally heritable epialleles are defined by the stable propagation of alternative transcriptional states through mitotic and meiotic cell cycles. Given that the propagation of DNA methylation at CpG sites, mediated in Arabidopsis by MET1, plays a central role in epigenetic inheritance, we examined genome-wide DNA methylation in partial and complete loss-of-function met1 mutants. We interpreted the data in relation to transgenerational epiallelic stability and provide evidence that DNA sequence features such as density of CpGs and genomic repetitiveness can be used to predict susceptibility to epiallelic switching. The importance of these rules was confirmed by analyses of common epialleles in natural Arabidopsis accessions and verified in rice.

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An Analysis of gRNA Sequence Dependent Cleavage Highlights the Importance of Genomic Context on CRISPR-Cas Activity

10.1101/2021.05.06.442929 ◽

2021 ◽

Author(s):

Eirik A Moreb ◽

Michael D Lynch

Keyword(s):

Dna Sequence ◽

Training Dataset ◽

Published Data ◽

Data Sets ◽

Target Sequence ◽

Genomic Context ◽

Sequence Dependent ◽

Dependent Activity ◽

Dna Editing ◽

Future Work

CRISPR-Cas9 is a powerful DNA editing tool. A gRNA directs Cas9 to cleave any DNA sequence with a PAM. However, some gRNA sequences mediate cleavage at higher efficiencies than others. To understand this, numerous studies have screened large gRNA libraries and developed algorithms to predict gRNA sequence dependent activity. These algorithms do not predict other datasets as well as their training dataset and do not predict well between species. To better understand these discrepancies, we retrospectively examine sequence features that impact gRNA activity in 39 published data sets. We find strong evidence that the genomic context, which can be defined as the DNA content outside of the gRNA/target sequence itself, greatly contributes to differences in gRNA dependent activity. Context underlies variation in activity often attributed to differences in gRNA sequence. This understanding will help guide future work to understand Cas9 activity as well as efforts to identify optimal gRNAs and improve Cas9 variants.

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Bisphenol A-associated alterations in genome-wide DNA methylation and gene expression patterns reveal sequence-dependent and non-monotonic effects in human fetal liver

Environmental Epigenetics ◽

10.1093/eep/dvv006 ◽

2015 ◽

Vol 1 (1) ◽

pp. dvv006 ◽

Cited By ~ 33

Author(s):

Christopher Faulk ◽

Jung H. Kim ◽

Tamara R. Jones ◽

Richard C. McEachin ◽

Muna S. Nahar ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Bisphenol A ◽

Fetal Liver ◽

Expression Patterns ◽

Gene Expression Patterns ◽

Human Fetal Liver ◽

Sequence Dependent ◽

Genome Wide

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Genome dependent Cas9/gRNA search time underlies sequence dependent gRNA activity

Nature Communications ◽

10.1038/s41467-021-25339-3 ◽

2021 ◽

Vol 12 (1) ◽

Cited By ~ 1

Author(s):

E. A. Moreb ◽

M. D. Lynch

Keyword(s):

Dna Sequence ◽

Search Time ◽

Target Site ◽

Training Dataset ◽

Published Data ◽

Data Sets ◽

Sequence Dependent ◽

Dependent Activity ◽

Dna Editing ◽

Future Work

AbstractCRISPR-Cas9 is a powerful DNA editing tool. A gRNA directs Cas9 to cleave any DNA sequence with a PAM. However, some gRNA sequences mediate cleavage at higher efficiencies than others. To understand this, numerous studies have screened large gRNA libraries and developed algorithms to predict gRNA sequence dependent activity. These algorithms do not predict other datasets as well as their training dataset and do not predict well between species. Here, to better understand these discrepancies, we retrospectively examine sequence features that impact gRNA activity in 44 published data sets. We find strong evidence that gRNA sequence dependent activity is largely influenced by the ability of the Cas9/gRNA complex to find the target site rather than activity at the target site and that this drives sequence dependent differences in gRNA activity between different species. This understanding will help guide future work to understand Cas9 activity as well as efforts to identify optimal gRNAs and improve Cas9 variants.

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