nMOWChIP-seq: low-input genome-wide mapping of non-histone targets

Author:

Liu Zhengzhi1,Naler Lynette B2,Zhu Yan2,Deng Chengyu2,Zhang Qiang2,Zhu Bohan2,Zhou Zirui2,Sarma Mimosa2,Murray Alexander3,Xie Hehuang3ORCID,Lu Chang2ORCID

Affiliation:

1. Department of Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg, VA, USA

2. Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, USA

3. Department of Biomedical Sciences & Pathobiology, Virginia Tech, Blacksburg, VA, USA

Abstract

Abstract Genome-wide profiling of interactions between genome and various functional proteins is critical for understanding regulatory processes involved in development and diseases. Conventional assays require a large number of cells and high-quality data on tissue samples are scarce. Here we optimized a low-input chromatin immunoprecipitation followed by sequencing (ChIP-seq) technology for profiling RNA polymerase II (Pol II), transcription factor (TF), and enzyme binding at the genome scale. The new approach produces high-quality binding profiles using 1,000–50,000 cells. We used the approach to examine the binding of Pol II and two TFs (EGR1 and MEF2C) in cerebellum and prefrontal cortex of mouse brain and found that their binding profiles are highly reflective of the functional differences between the two brain regions. Our analysis reveals the potential for linking genome-wide TF or Pol II profiles with neuroanatomical origins of brain cells.

Funder

National Institutes of Health

Virginia Tech Institute

Publisher

Oxford University Press (OUP)

Subject

General Medicine

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