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Related Concept Videos

Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
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Cis-regulatory Sequences02:02

Cis-regulatory Sequences

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...
Cis-regulatory Sequences02:02

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Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
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Conserved Binding Sites01:49

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An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

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Published on: July 12, 2022

Short sequence motifs, overrepresented in mammalian conserved non-coding sequences.

Simon Minovitsky1, Philip Stegmaier, Alexander Kel

  • 1Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. sminovitsky@lbl.gov

BMC Genomics
|October 20, 2007
PubMed
Summary

Conserved non-coding sequences (CNSs) in the human genome show compositional biases, not specific short motif overrepresentation. Their properties are shaped by mutation patterns, indicating variable selective pressures.

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Area of Science:

  • Genomics
  • Evolutionary Biology
  • Bioinformatics

Background:

  • A significant portion of eukaryotic genomes comprises conserved non-coding sequences (CNSs).
  • These CNSs exhibit distinct nucleotide compositions and presumed functional roles, largely uncharacterized.
  • Approximately 5% of the human genome is classified as CNSs.

Purpose of the Study:

  • To investigate the relative abundance of short sequence motifs within human CNSs.
  • To compare motif frequencies in CNSs against various background sequence sets.
  • To elucidate the underlying compositional properties and functional implications of CNSs.

Main Methods:

  • Comparative analysis of short sequence motif abundances in human CNSs.
  • Utilized human/mouse whole-genome alignments for CNS identification.
  • Compared CNS motifs against non-coding sequences (non-CNSs), near-promoter regions, and compositionally matched random sequences.

Main Results:

  • Human CNSs exhibit an excess of AT-rich motifs compared to non-CNSs and promoter regions.
  • CNSs show an overrepresentation of GC-rich motifs lacking CpG dinucleotides when compared to random sequences.
  • The overall motif landscape in CNSs is primarily dictated by compositional properties like high AT-content, nucleotide clumping, GC-rich regions, and CpG avoidance, rather than specific motif enrichment.

Conclusions:

  • Human CNSs, as a broad category, lack distinct short sequence-specific functional footprints.
  • Functional subclasses of CNSs, potentially linked to gene expression patterns, require focused study.
  • Mutation patterns influence CNS properties, suggesting that selective conservation pressures can vary significantly.