Genome-wide localization of chromatin and transcription regulators can be detected by a variety of techniques. Here, we describe a novel method ‘greenCUT&RUN’ for genome-wide profiling of transcription regulators, which has a very high sensitivity, resolution, accuracy and reproducibility, whilst assuring specificity.

Our strategy begins with tagging of the protein of interest with GFP and utilizes a GFP-specific nanobody fused to MNase to profile genome-wide binding events.

By using a GFP-nanobody the greenCUT&RUN approach eliminates antibody dependency and variability. Robust genomic profiles were obtained with greenCUT&RUN, which are accurate and unbiased towards open chromatin.

By integrating greenCUT&RUN with nanobody-based affinity purification mass spectrometry, ‘piggy-back’ DNA binding events can be identified on a genomic scale.

The unique design of greenCUT&RUN grants target protein flexibility and yields high resolution footprints. In addition, greenCUT&RUN allows rapid profiling of mutants of chromatin and transcription proteins. In conclusion, greenCUT&RUN is a widely applicable and versatile genome-mapping technique.

[maxbutton id=”4″ url=”″ text=”Read more” linktitle=”Nucleic Acids Research: Integrating quantitative proteomics with accurate genome profiling of transcription factors by greenCUT&RUN” ]


Sheikh Nizamuddin, Stefanie Koidl, Tanja Bhuiyan, Tamara V Werner, Martin L Biniossek, Alexandre M J J Bonvin, Silke Lassmann, HThMarc Timmers (2022):
Integrating quantitative proteomics with accurate genome profiling of transcription factors by greenCUT&RUN.
Nucleic Acids Research 49(9)

About the author

Stian works in School of Computer Science, at the University of Manchester in Carole Goble‘s eScience Lab as a technical software architect and researcher. In addition to BioExcel, Stian’s involvements include Open PHACTS (pharmacological data warehouse), Common Workflow Language (CWL), Apache Taverna (scientific workflow system), Linked Data and identifiers, research objects (open science) and digital preservation, myExperiment (sharing scientific workflows), provenance (where did things come from and who did it) and annotations (who said what).