A CRISPR-based approach for proteomic analysis of a single genomic locus

Waldrip, Zachary J; Byrum, Stephanie D.; Storey, Aaron J.; Gao, Jun; Byrd, Alicia K.; Mackintosh, Samuel G.; Wahls, Wayne P.; Taverna, Sean D.; Raney, Kevin D.; Tackett, Alan J.

doi:10.4161/epi.29919

Cited by 70 publications

(68 citation statements)

References 18 publications

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“…The stochasticity of transcription observed in single-cell studies provides a very intriguing viewpoint, suggesting that there may be far more levels of regulation in play that lead to the deterministic pattern of expression observed at the population level [57,58]. In addition, effort has been put into developing methods facilitating unbiased identification of proteins and histone marks at a single genomic locus, although these approaches are still constrained to using populations of cells to obtain enough material [59][60][61][62]. Both single-cell and single-locus approaches have the potential to offer more details about the behaviour of the Sin3A/B, N-CoR/SMRT and NuRD complexes.…”

Section: Data Interpretation and Future Directionsmentioning

confidence: 99%

Perspective on unraveling the versatility of ‘co-repressor’ complexes

Baymaz

Karemaker

Vermeulen

2015

Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanism

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Section: Data Interpretation and Future Directionsmentioning

confidence: 99%

Perspective on unraveling the versatility of ‘co-repressor’ complexes

Baymaz

Karemaker

Vermeulen

2015

Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanism

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“…For example, fusions of epigenome-modifying enzymes to programmable DNA-binding proteins hold promise for targeting DNA methylation (Maeder et al 2013) as well as histone acetylation (Hilton et al 2015) and epiproteomes (Waldrip et al 2014) at specific loci; but they have drawbacks, for example, because every zinc-finger domain must be custom evolved to target a specific sequence, and target motifs are size limited. One recent innovation in the field of target specific DNA methylation is the development of a suite of tools, based on the Piwi-interacting RNA (piRNA) system, to accurately induce DNA methylation of targeted loci in adult tissues (work presently being done under NIH grant ES026877; https://directorsblog.nih.gov/tag/pirna/).…”

Section: Investigating the Functional Relevance Of Replicated Locimentioning

confidence: 99%

Small-Magnitude Effect Sizes in Epigenetic End Points are Important in Children’s Environmental Health Studies: The Children’s Environmental Health and Disease Prevention Research Center’s Epigenetics Working Group

Breton

Marsit

Faustman

et al. 2017

Environ Health Perspect

241

159

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Background:Characterization of the epigenome is a primary interest for children’s environmental health researchers studying the environmental influences on human populations, particularly those studying the role of pregnancy and early-life exposures on later-in-life health outcomes.Objectives:Our objective was to consider the state of the science in environmental epigenetics research and to focus on DNA methylation and the collective observations of many studies being conducted within the Children’s Environmental Health and Disease Prevention Research Centers, as they relate to the Developmental Origins of Health and Disease (DOHaD) hypothesis.Methods:We address the current laboratory and statistical tools available for epigenetic analyses, discuss methods for validation and interpretation of findings, particularly when magnitudes of effect are small, question the functional relevance of findings, and discuss the future for environmental epigenetics research.Discussion:A common finding in environmental epigenetic studies is the small-magnitude epigenetic effect sizes that result from such exposures. Although it is reasonable and necessary that we question the relevance of such small effects, we present examples in which small effects persist and have been replicated across populations and across time. We encourage a critical discourse on the interpretation of such small changes and further research on their functional relevance for children’s health.Conclusion:The dynamic nature of the epigenome will require an emphasis on future longitudinal studies in which the epigenome is profiled over time, over changing environmental exposures, and over generations to better understand the multiple ways in which the epigenome may respond to environmental stimuli.Citation:Breton CV, Marsit CJ, Faustman E, Nadeau K, Goodrich JM, Dolinoy DC, Herbstman J, Holland N, LaSalle JM, Schmidt R, Yousefi P, Perera F, Joubert BR, Wiemels J, Taylor M, Yang IV, Chen R, Hew KM, Freeland DM, Miller R, Murphy SK. 2017. Small-magnitude effect sizes in epigenetic end points are important in children’s environmental health studies: the Children’s Environmental Health and Disease Prevention Research Center’s Epigenetics Working Group. Environ Health Perspect 125:–526; http://dx.doi.org/10.1289/EHP595

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“…This tool will also be useful to define in detail the set of chromatin readers/effectors primarily recruited in the context of mRNA transcription, the secondary chromatin marks derived thereafter, and the effectors directly responsible for gene silencing or activation. These goals can be facilitated by characterizing the molecules associated with the target genomic sequence upon targeted chromatin modifications, utilizing dCas9-based ChIP (Fujita and Fujii, 2013, 2015) and chromatin affinity purification coupled with mass spectrometry (Byrum et al, 2012; Waldrip et al, 2014). …”

Section: Applications In Stem Cell Biology and Regenerative Medicinementioning

confidence: 99%

CRISPR/Cas9-Based Engineering of the Epigenome

et al. 2017

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Determining causal relationships between distinct chromatin features and gene expression, and ultimately cell behavior, remains a major challenge. Recent developments in targetable epigenome-editing tools enables us to assign direct transcriptional and functional consequences to locus-specific chromatin modifications. This review discusses the unprecedented opportunity that CRISPR/(d)Cas9 technology offers for investigating and manipulating the epigenome to facilitate further understanding of stem cell biology and engineering of stem cells for therapeutic applications. We also provide technical considerations for standardization and further improvement of the CRISPR/(d)Cas9 tools.

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A CRISPR-based approach for proteomic analysis of a single genomic locus

Cited by 70 publications

References 18 publications

Perspective on unraveling the versatility of ‘co-repressor’ complexes

Perspective on unraveling the versatility of ‘co-repressor’ complexes

Small-Magnitude Effect Sizes in Epigenetic End Points are Important in Children’s Environmental Health Studies: The Children’s Environmental Health and Disease Prevention Research Center’s Epigenetics Working Group

CRISPR/Cas9-Based Engineering of the Epigenome

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