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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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Related Experiment Video

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Immunofluorescence Analysis of Endogenous and Exogenous Centromere-kinetochore Proteins
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The string decomposition problem and its applications to centromere analysis and assembly.

Tatiana Dvorkina1, Andrey V Bzikadze2, Pavel A Pevzner3

  • 1Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg 199034, Russia.

Bioinformatics (Oxford, England)
|July 14, 2020
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Summary
This summary is machine-generated.

A new algorithm, StringDecomposer, translates centromeric DNA reads into repeat units, simplifying the assembly of complex human centromeres and identifying novel genetic elements.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Assembling complex genomic regions like human centromeres is challenging due to long, error-prone DNA reads.
  • Centromeres consist of chromosome-specific high-order repeats (HORs) formed by monomers.
  • Translating nucleotide sequences into repeat unit alphabets is a key hurdle.

Purpose of the Study:

  • To develop and apply an algorithm for translating centromeric reads into a repeat unit alphabet.
  • To identify novel monomers and assess the completeness of known human centromeric sequences.
  • To facilitate the complete assembly of the human genome.

Main Methods:

  • Modeling the translation of centromeric reads as a String Decomposition Problem.
  • Developing the StringDecomposer (SD) algorithm to solve this problem.
  • Benchmarking SD on Oxford Nanopore and Pacific Biosciences HiFi reads.

Main Results:

  • SD successfully translates long, error-prone reads into a monomer alphabet.
  • A novel, rare X-chromosome specific monomer was identified.
  • Analysis revealed that known human monomers and HORs are incomplete.
  • SD facilitates the identification of all human monomers and HORs.

Conclusions:

  • The StringDecomposer algorithm simplifies centromere assembly by enabling translation of nucleotide reads.
  • The study highlights the incompleteness of current human centromere and HOR datasets.
  • SD is crucial for future efforts in generating complete human genome assemblies and evolutionary studies.