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Genomic DNA in Eukaryotes00:58

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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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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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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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Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes
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The eukaryotic linear motif resource - 2018 update.

Marc Gouw1, Sushama Michael1, Hugo Sámano-Sánchez1

  • 1Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany.

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Summary
This summary is machine-generated.

The Eukaryotic Linear Motif (ELM) resource is updated with 32 new motif classes and enhanced features. This vital database aids in understanding short linear motifs (SLiMs) and their roles in cellular processes.

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Proteomics

Background:

  • Short linear motifs (SLiMs) are crucial for cellular processes but are challenging to identify.
  • The Eukaryotic Linear Motif (ELM) resource has been a primary source for SLiM research for 15 years.

Purpose of the Study:

  • To present the latest update of the ELM database, including new motif classes and features.
  • To provide biological insights into SLiM functions in various cellular contexts.

Main Methods:

  • Manual curation of SLiM data for the ELM database.
  • Development of a pipeline for discovering candidate SLiMs in protein sequences.
  • Integration of UniProt and Reactome databases.

Main Results:

  • Addition of 32 new motif classes to the ELM database.
  • Enhanced database features, including UniProt and Reactome integration.
  • Presentation of biological insights into SLiMs in cell cycle, bacterial pathogenicity, and the human kinome.

Conclusions:

  • The updated ELM resource provides a more comprehensive and integrated platform for SLiM research.
  • SLiMs play significant roles in diverse biological processes, including cell cycle regulation and disease.
  • Continued development of ELM is essential for advancing the study of SLiMs.