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Related Experiment Video

Updated: Dec 8, 2025

Chromatin Immunoprecipitation ChIP Protocol for Low-abundance Embryonic Samples
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Tracking Histone Modifications in Embryos and Low-Input Samples Using Ultrasensitive STAR ChIP-Seq.

Bingjie Zhang1, Xu Peng2, Feng Xu2

  • 1Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.

Methods in Molecular Biology (Clifton, N.J.)
|September 18, 2020
PubMed
Summary

We developed STAR ChIP-seq, a low-input method for detecting histone modifications. This technique enables robust epigenomic profiling from a few hundred cells, ideal for limited samples like mammalian embryos.

Keywords:
Early embryosEpigenome profilingLow-input ChIP-seqNative chromatin

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Area of Science:

  • Epigenetics
  • Molecular Biology
  • Developmental Biology

Background:

  • Chromatin immunoprecipitation sequencing (ChIP-seq) identifies protein and epigenetic modification localization in chromatin.
  • Conventional ChIP-seq requires millions of cells, limiting its use with scarce biological samples.
  • Mammalian embryonic development involves significant epigenetic reprogramming, crucial for development but challenging to study with low cell numbers.

Purpose of the Study:

  • To develop a low-input ChIP-seq method for epigenomic profiling.
  • To enable the study of epigenetic reprogramming in limited cell populations, such as early embryos.
  • To provide a robust method for histone modification detection using minimal experimental material.

Main Methods:

  • Optimization of a ChIP-seq protocol for reduced cell input.
  • Development of the STAR (Small-scale TELP-Assisted Rapid) ChIP-seq method.
  • Application of the method to histone modification detection in both embryonic and cultured cells.

Main Results:

  • The STAR ChIP-seq method successfully detects histone modifications using only a few hundred cells.
  • The method demonstrates robustness in epigenomic profiling.
  • Successful application in analyzing histone modifications in mammalian embryos and cultured cells.

Conclusions:

  • STAR ChIP-seq significantly lowers the cell input requirement for ChIP-seq analysis.
  • This method is instrumental for deciphering molecular mechanisms of epigenetic reprogramming in low-cell-number systems.
  • The developed technique offers a powerful tool for epigenomic profiling in various biological contexts, especially where material is limited.