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Related Concept Videos

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

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The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
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Related Experiment Video

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Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.
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Improving 3D Genome Reconstructions Using Orthologous and Functional Constraints.

Alon Diament1, Tamir Tuller2

  • 1Dept. of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel.

Plos Computational Biology
|May 23, 2015
PubMed
Summary

This study validates 3D genomic reconstructions using sparse Hi-C data and introduces a novel method to enhance accuracy by incorporating predicted interactions, improving 3D genome models.

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Area of Science:

  • Genomics and Molecular Biology
  • Computational Biology
  • Bioinformatics

Background:

  • Advancements in understanding chromosome 3D architecture are rapid.
  • Existing 3D genomic reconstruction methods often use diverse data representations.
  • Reproducibility of previous findings in Saccharomyces cerevisiae using 3D reconstructions is explored.

Purpose of the Study:

  • To reproduce established 3D genomic organization results for Saccharomyces cerevisiae.
  • To investigate the properties of 3D genomic models generated from sparse Hi-C data.
  • To develop and validate a novel method for enhancing 3D genome reconstruction accuracy.

Main Methods:

  • Analysis of 3D reconstructions from Hi-C data.
  • Generation and evaluation of sparse reconstructions using a fraction (5%) of experimental data.
  • Integration of predicted physical and functional interactions to improve reconstruction accuracy.

Main Results:

  • Many previously reported 3D genomic organization findings can be reproduced using sparse reconstructions.
  • Properties of models derived from limited Hi-C data were characterized.
  • The novel approach significantly improved the accuracy of 3D genome reconstructions.

Conclusions:

  • Sparse Hi-C data is sufficient for reproducing key 3D genomic organization insights.
  • Incorporating predicted orthologous and functional interactions enhances 3D genome model fidelity.
  • This study presents a promising strategy for more accurate and robust 3D genome modeling.