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The histone proteins have a flexible N-terminal tail extending out from the nucleosome. These histone tails are often subjected to post-translational modifications such as acetylation, methylation, phosphorylation, and ubiquitination. Particular combinations of these modifications form “histone codes” that influence the chromatin folding and tissue-specific gene expression.
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Chromatin Immunoprecipitation ChIP to Assay Dynamic Histone Modification in Activated Gene Expression in Human Cells
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Reprogramming histone modification patterns to coordinate gene expression in early zebrafish embryos.

Wei Zhu1,2, Xiaocui Xu1,2, Xinxin Wang1,2

  • 1CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.

BMC Genomics
|March 30, 2019
PubMed
Summary
This summary is machine-generated.

Histone modifications like H3K4me3/H3K27me3 are reprogrammed in zebrafish early embryos, with patterns conserved across vertebrates. This epigenetic reprogramming coordinates gene expression during zygotic genome activation (ZGA).

Keywords:
ConservationEarly embryoEpigeneticsHistone modificationReprogramming

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Area of Science:

  • Epigenetics
  • Developmental Biology
  • Genomics

Background:

  • Precise gene regulation is crucial for multicellular development, with epigenetic modifications like DNA methylation and histone modification playing key roles.
  • While DNA methylation reprogramming is understood in vertebrates, histone modification inheritance from gametes to early embryos remains unclear.
  • The conservation of histone modification reprogramming across species is not well established.

Purpose of the Study:

  • To investigate the patterns of H3K4me3 and H3K27me3 modifications in zebrafish gametes and early embryos.
  • To determine how these histone modifications are reprogrammed and transmitted during early development.
  • To assess the conservation of histone modification reprogramming in vertebrates and its coordination with gene expression during zygotic genome activation (ZGA).

Main Methods:

  • Profiling of H3K4me3 and H3K27me3 modifications in zebrafish gametes and early embryos.
  • Analysis of histone modification patterns in gene promoter regions.
  • Comparative analysis across vertebrate species.
  • Correlation of histone modification reprogramming with DNA methylation and gene expression dynamics.

Main Results:

  • Histone modification patterns (H3K4me3/H3K27me3) are largely established in gametes and inherited by early embryos.
  • Active H3K4me3 states are largely restored in early embryos, resembling sperm patterns before zygotic genome activation (ZGA).
  • Repressive H3K27me3 modifications are removed from promoters, and genes initiating ZGA are converted to non-repressive states.
  • Stage-specific gene promoters show independent erasure of histone modifications, distinct from DNA methylation reprogramming.
  • Functional and age-related conservation of gamete-derived histone modification patterns (co-occupied and active) is observed in vertebrates.

Conclusions:

  • Provides foundational data on H3K4me3/H3K27me3 modifications in early zebrafish embryos.
  • Demonstrates that histone modification reprogramming is conserved in vertebrates.
  • Highlights the coordination between histone modification reprogramming and gene expression during ZGA.