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Related Experiment Video

Updated: Aug 9, 2025

Formaldehyde-assisted Isolation of Regulatory Elements to Measure Chromatin Accessibility in Mammalian Cells
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Universal NicE-Seq: A Simple and Quick Method for Accessible Chromatin Detection in Fixed Cells.

Hang Gyeong Chin1, Udayakumar S Vishnu1, Zhiyi Sun1

  • 1New England Biolabs Inc., Ipswich, MA, USA.

Methods in Molecular Biology (Clifton, N.J.)
|February 22, 2023
PubMed
Summary
This summary is machine-generated.

This study introduces universal NicE-seq, a method for preparing sequencing libraries from low cell numbers. This technique efficiently maps accessible chromatin regions, even from formaldehyde-fixed samples.

Keywords:
Biotin-14-dCTP/dATPDNA library preparationEpigenetic profilingFormaldehyde-crosslinked cellsMethyl-dCTPNicking enzymeNucleosomeOpen chromatin labeling

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Area of Science:

  • Epigenetics
  • Genomics
  • Molecular Biology

Background:

  • Genome-wide accessible chromatin sequencing reveals crucial epigenetic information like promoter and enhancer activity.
  • Formaldehyde crosslinking is a common initial step for analyzing chromatin accessibility.
  • Current methods can be challenging with limited cell numbers.

Purpose of the Study:

  • To develop a robust method for accessible chromatin library preparation from low cell numbers.
  • To adapt the method for formaldehyde-crosslinked and FFPE samples.
  • To streamline the library preparation process for next-generation sequencing (NGS).

Main Methods:

  • A modified nick translation method using a nicking enzyme and biotin-conjugated nucleotides.
  • Incorporation of biotin-conjugated nucleotides for DNA labeling.
  • Universal NicE-seq (nicking enzyme-assisted sequencing) for library preparation.

Main Results:

  • Successful accessible chromatin library preparation from low numbers of formaldehyde-crosslinked cells.
  • Demonstration of a single-tube method for direct NGS library preparation without DNA purification.
  • Validation of universal NicE-seq on FFPE tissue section samples.

Conclusions:

  • Universal NicE-seq provides an efficient approach for analyzing accessible chromatin from limited or challenging samples.
  • The method simplifies library preparation, enabling broader application of chromatin accessibility studies.
  • This technique is applicable to various sample types, including FFPE tissues.