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Related Concept Videos

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
The enzyme histone acetyltransferase adds acetyl group to the histones. Another enzyme, histone...
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Histone Modification02:32

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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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Peptide Bonds02:43

Peptide Bonds

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A peptide bond covalently attaches amino acids through a dehydration reaction. One amino acid's carboxyl group and another amino acid's amino group combine, releasing a water molecule. The resulting bond is the peptide bond. The products that such linkages form are peptides. As more amino acids join this growing chain, the resulting chain is a polypeptide. Each polypeptide has a free amino group at one end. This end has the N-terminal, or the amino-terminal, and the other end has a free...
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Spreading of Chromatin Modifications02:25

Spreading of Chromatin Modifications

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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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Chromatin Modification in iPS Cells01:32

Chromatin Modification in iPS Cells

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Chromatin modification alters gene expression; therefore, scientists can add histone-modifying enzymes, histone variants, and chromatin remodeling complexes to somatic cells to aid reprogramming into pluripotent stem (iPS) cells.
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Related Experiment Video

Updated: Jan 21, 2026

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
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Sequence Variant and Posttranslational Modification Analysis During Cell Line Selection via High-Throughput Peptide

Chong-Feng Xu1, Yan Wang2, Pete Bryngelson2

  • 1Analytical Development, Biogen, Cambridge, MA, USA. chongfeng.xu@biogen.com.

Advances in Experimental Medicine and Biology
|July 27, 2019
PubMed
Summary

A new high-throughput peptide mapping workflow enables early detection of sequence variants and PTMs in cell line development for protein therapeutics, reducing project timelines.

Keywords:
Amino acid misincorporationAmino acid substitutionAntibodyClone selectionHigh throughput peptide mappingMass spectrometryMutationPosttranslational modificationSequence variant

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Area of Science:

  • Biotechnology
  • Protein Therapeutics Development
  • Analytical Chemistry

Background:

  • Cell line development for protein therapeutics requires selecting high-producing clones with accurate primary structures.
  • Conventional methods like mass spectrometry (MS) and next-generation sequencing (NGS) for variant analysis are time-consuming and limited in sample throughput.
  • These limitations often restrict their use to late stages, risking significant project delays.

Purpose of the Study:

  • To present a high-throughput (HT) peptide mapping workflow for early-stage cell line selection.
  • To enable rapid analysis of sequence variants and post-translational modifications (PTMs) in a large number of clones.
  • To reduce risks and improve predictability in cell line development timelines.

Main Methods:

  • Development and application of a high-throughput peptide mapping workflow.
  • Analysis of sequence variants, including unknown peptide ions and PTMs.
  • Quantitation of PTMs, such as N-glycan profiles.
  • Demonstration on two monoclonal antibody (mAb) programs.

Main Results:

  • Identified and removed multiple clones based on upregulated unknown peptide ions and critical PTMs for mAb-1.
  • Detected light chain sequence extensions (up to 11%) and a heavy chain Q to H mutation (undetectable by intact mass analysis) in mAb-2 clones.
  • Facilitated selection of clones with desirable quality attributes, including N-glycan profiles.

Conclusions:

  • The HT peptide mapping workflow allows for early-stage detection of abnormal clones.
  • This risk-reducing strategy significantly shortens and enhances the predictability of cell line development timelines.
  • Enables informed selection of lead and backup cell lines with high-fidelity primary structures and desired quality attributes.