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Related Concept Videos

Chromatin Structure Regulates pre-mRNA Processing02:41

Chromatin Structure Regulates pre-mRNA Processing

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In eukaryotic cells, nascent mRNA transcripts need to undergo many post-transcriptional modifications to reach the cell cytoplasm and translate into functional proteins. For a long time, transcription and pre-mRNA processing were considered two independent events that occur sequentially in the cell. However, it has now been well established that transcription and pre-mRNA processing are two simultaneous processes that are precisely regulated inside the cell.
The chromatin structure, especially...
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Spreading of Chromatin Modifications02:25

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The histone proteins in the nucleosomes are post-translationally modified (PTM) to increase or decrease access to DNA. The commonly observed PTMs are methylation, acetylation, phosphorylation, and ubiquitination of lysine amino acids in the histone H3 tail region. These histone modifications have specific meaning for the cell. Hence, they are called "histone code". The protein complex involved in histone modification is termed as "reader-writer" complex.
Writers
The writer...
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Histone Modification02:32

Histone Modification

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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.
Acetylation
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Histone Variants at the Centromere02:30

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Histone variants are the histone proteins with structural and sequence variations. These variants may be regarded as “mutant” forms that replace their canonical histone counterparts in the nucleosomes. Specific post-translational modifications on the histone variants enable further chromatin complexity and regulate tissue-specific gene expression. The most common histone variants are from histone H2A, H2B, and linker histone H1 families. However, several variants of histone H3...
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Inheritance of Chromatin Structures03:17

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Epigenetics is the study of inherited changes in a cell's phenotype without changing the DNA sequences. It provides a form of memory for the differential gene expression pattern to maintain cell lineage, position-effect variegation, dosage compensation, and maintenance of chromatin structures such as telomeres and centromeres. For example, the structure and location of the centromere on chromosomes are epigenetically inherited. Its functionality is not dictated or ensured by the underlying...
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Exon Recombination02:32

Exon Recombination

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The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes. 
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Related Experiment Video

Updated: Jun 7, 2025

Complete Workflow for Analysis of Histone Post-translational Modifications Using Bottom-up Mass Spectrometry: From Histone Extraction to Data Analysis
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Inferring causal relationships among histone modifications in exon skipping event.

Pengmian Feng1, Yuanfang Tian2, Wei Chen2

  • 1School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.

Methods (San Diego, Calif.)
|November 11, 2024
PubMed
Summary

Histone modifications significantly influence alternative splicing, a key gene expression process. Distinct patterns mark alternative splicing events, providing insights into gene regulation.

Keywords:
Alternative splicingBayesian networkCausal relationshipExon skippingHistone modification

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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

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Area of Science:

  • Molecular Biology
  • Genetics
  • Epigenetics

Background:

  • Alternative splicing is a vital gene expression mechanism, with over 90% of human multi-exonic genes undergoing this process.
  • Existing models of the splicing code do not fully explain tissue-specific alternative splicing.
  • Histone modifications, alongside other regulatory elements, have been implicated in co-transcriptional RNA processing and alternative splicing.

Purpose of the Study:

  • To investigate the role of histone modifications in alternative splicing.
  • To analyze the associations among 27 types of histone modifications in H1 human embryonic stem cells.
  • To elucidate the causal relationships between histone modifications and alternative splicing patterns.

Main Methods:

  • Analysis of 27 distinct histone modifications in H1 human embryonic stem cells.
  • Construction of a Bayesian network to model causal relationships.
  • Validation of the Bayesian network using cross-validation tests.

Main Results:

  • Identified associations among various histone modifications relevant to alternative splicing.
  • Developed a robust Bayesian network model to illustrate causal links.
  • Observed distinct histone modification patterns in alternatively spliced exons and adjacent introns.

Conclusions:

  • Histone modifications play a substantial role in marking alternative splicing events.
  • The findings contribute to a deeper understanding of the regulatory mechanisms governing alternative splicing.
  • This study highlights the importance of epigenetic modifications in gene expression complexity.