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Related Concept Videos

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

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.
The Spindle Assembly Checkpoint02:19

The Spindle Assembly Checkpoint

The spindle assembly checkpoint is a molecular surveillance mechanism ensuring the fidelity of chromosome segregation during anaphase. The checkpoint monitors the completion of all the prerequisite steps before chromosome segregation to determine whether the segregation process should proceed or be delayed.
Many proteins function together to control the spindle assembly checkpoint. Mutations affecting these proteins may allow cells to proceed into anaphase prematurely, resulting in the...
Spindle Assembly02:50

Spindle Assembly

Spindle assembly occurs through three, often coexisting, pathways – the centrosome-mediated pathway, the chromatin-mediated pathway, and the microtubule-mediated pathway – collectively contributing to form a robust spindle apparatus.
In most cells, centrosomes are the primary microtubule nucleation centers. In the centrosome-mediated pathway, the G2-prophase transition triggers centrosome maturation and increased microtubule nucleation. Progressive nucleation results in a microtubule array...
Attachment of Sister Chromatids02:57

Attachment of Sister Chromatids

As cells progress into mitosis, the nuclear envelope breaks down, and the condensed chromosomes are exposed to the array of bipolar microtubules of the mitotic spindle. The kinetochore, a large, disc-shaped protein complex, is present at the centromere region of the sister chromatids and acts as a binding site for the microtubules.  Usually, the plus-end of a single microtubule is embedded within the kinetochore. However, some kinetochores first establish lateral contact with the side-wall of a...
Homologous Recombination02:31

Homologous Recombination

The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
Separation of Sister Chromatids02:17

Separation of Sister Chromatids

At the transition from prophase to metaphase, there is a reduction in cohesion along the chromosomal arms, resulting in the resolution of sister chromatids. However, residual cohesin connections remain to hold the sister chromatids together until the transition from metaphase to anaphase. The residual connection prevents any premature separation of sister chromatids, blocking the risks of aneuploidy within the daughter cells.
At the onset of anaphase, separase, a proteolytic enzyme, is...

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Related Experiment Video

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Associated Chromosome Trap for Identifying Long-range DNA Interactions
14:49

Associated Chromosome Trap for Identifying Long-range DNA Interactions

Published on: April 23, 2011

Reference-assisted chromosome assembly.

Jaebum Kim1, Denis M Larkin, Qingle Cai

  • 1Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.

Proceedings of the National Academy of Sciences of the United States of America
|January 12, 2013
PubMed
Summary
This summary is machine-generated.

Assembling full-length chromosomes from next-generation sequencing (NGS) data is challenging. Reference-assisted chromosome assembly (RACA) reliably orders and orients sequence scaffolds, significantly improving genome assembly accuracy for evolutionary studies.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Assembling full-length chromosomes from next-generation sequencing (NGS) data presents a significant challenge in modern genomics.
  • Existing de novo assembly methods often produce fragmented genomes, hindering comprehensive analysis.

Purpose of the Study:

  • To develop and evaluate a novel algorithm, Reference-Assisted Chromosome Assembly (RACA), for improving genome assembly by ordering and orienting sequence scaffolds.
  • To enhance the accuracy and contiguity of genome assemblies, particularly for species lacking genetic or physical maps.

Main Methods:

  • RACA utilizes comparative genomics information and paired-end reads to order and orient sequence scaffolds.
  • The algorithm was evaluated using simulated and real genome assemblies, alongside experimental validation via PCR.

Main Results:

  • RACA substantially improves genome assemblies generated by various de novo assemblers when a closely related reference genome is available.
  • The algorithm successfully reconstructed 60 Tibetan antelope chromosome fragments, with 16 showing homology to cattle chromosomes.
  • Experimental validation confirmed the high accuracy of RACA's predictions.

Conclusions:

  • RACA offers a robust solution for chromosome assembly from NGS data, especially for non-model organisms.
  • This approach significantly facilitates the study of chromosome evolution and genome rearrangements.
  • RACA is a valuable tool for analyzing the vast number of genomes being sequenced by NGS without pre-existing maps.