Issue 17, 2018

A droplet microfluidic platform for efficient enzymatic chromatin digestion enables robust determination of nucleosome positioning

Abstract

The first step in chromatin-based epigenetic assays involves the fragmentation of chromatin to facilitate precise genomic localization of the associated DNA. Here, we report the development of a droplet microfluidic device that can rapidly and efficiently digest chromatin into single nucleosomes starting from whole-cell input material offering simplified and automated processing compared to conventional manual preparation. We demonstrate the digestion of chromatin from 2500–125 000 Jurkat cells using micrococcal nuclease for enzymatic processing. We show that the yield of mononucleosomal DNA can be optimized by controlling enzyme concentration and incubation time, with resulting mononucleosome yields exceeding 80%. Bioinformatic analysis of sequenced mononucleosomal DNA (MNase-seq) indicated a high degree of reproducibility and concordance (97–99%) compared with conventionally processed preparations. Our results demonstrate the feasibility of robust and automated nucleosome preparation using a droplet microfluidic platform for nucleosome positioning and downstream epigenomic assays.

Graphical abstract: A droplet microfluidic platform for efficient enzymatic chromatin digestion enables robust determination of nucleosome positioning

Supplementary files

Article information

Article type
Paper
Submitted
11 Jun 2018
Accepted
09 Jul 2018
First published
26 Jul 2018

Lab Chip, 2018,18, 2583-2592

A droplet microfluidic platform for efficient enzymatic chromatin digestion enables robust determination of nucleosome positioning

Y. Xu, J. Lee, Z. Li, L. Wang, T. Ordog and R. C. Bailey, Lab Chip, 2018, 18, 2583 DOI: 10.1039/C8LC00599K

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