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Related Concept Videos

Genomic DNA in Eukaryotes00:58

Genomic DNA in Eukaryotes

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Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
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The eukaryotic promoter region is a segment of DNA located upstream of a gene. It contains an RNA polymerase binding site, a transcription start site, and several cis-regulatory sequences.  The proximal promoter region is located in the vicinity of the gene and has cis-regulatory sequences and the core promoter. The core promoter is the binding site for RNA polymerase and is usually located between -35 and +35 nucleotides from the transcription start site. The distal promoter regions are...
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While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
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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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RNA Polymerase (RNAP) is conserved in all animals, with bacterial, archaeal, and eukaryotic RNAPs sharing significant sequence, structural, and functional similarities. Among the three eukaryotic RNAPs, RNA Polymerase II is most similar to bacterial RNAP in terms of both structural organization and folding topologies of the enzyme subunits. However, these similarities are not reflected in their mechanism of action.
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Novel Sequence Discovery by Subtractive Genomics
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Identifying Sequenced Eukaryotic Genomes and Transcriptomes with diArk.

Martin Kollmar1, Dominic Simm2,3

  • 1Group Systems Biology of Motor Proteins, Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany. mako@nmr.mpibpc.mpg.de.

Methods in Molecular Biology (Clifton, N.J.)
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Summary

The diArk Eukaryotic Genome Database provides curated eukaryotic genome data. This guide helps researchers navigate diArk for comparative genomics and species discovery.

Keywords:
EukaryotesGenome assemblySequenced genomesTranscriptome assembly

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Area of Science:

  • Genomics
  • Bioinformatics
  • Comparative Genomics

Background:

  • The number of sequenced eukaryotic genomes is rapidly increasing.
  • Researchers require efficient tools for accessing and analyzing genomic data.
  • Comparative genomics necessitates comprehensive and up-to-date databases.

Purpose of the Study:

  • To describe the navigation of the diArk Eukaryotic Genome Database.
  • To provide a user-friendly guide for first-time users.
  • To highlight diArk as a resource for comparative eukaryotic genomics.

Main Methods:

  • Manual curation and updating of eukaryotic genome and transcriptome assemblies.
  • Development of sophisticated search and data presentation tools.
  • Focus on user-centric navigation for new users.

Main Results:

  • diArk serves as a central repository for eukaryotic genomic data.
  • The database facilitates browsing of sequenced eukaryotes.
  • It enables identification of closely related species for research.

Conclusions:

  • diArk is an essential resource for comparative eukaryotic genomics research.
  • Effective navigation tools are crucial for managing large-scale genomic data.
  • The database supports researchers in exploring eukaryotic diversity and evolutionary relationships.