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Related Concept Videos

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

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...
Conserved Binding Sites01:49

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.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Exon Recombination02:32

Exon Recombination

The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes. 
Exon shuffling follows “splice frame rules.” Each exon has three reading...
Genetic Screens02:46

Genetic Screens

Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing  genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which result in visible changes...

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Related Experiment Video

Updated: May 10, 2026

An in vivo Crosslinking Approach to Isolate Protein Complexes From Drosophila Embryos
08:51

An in vivo Crosslinking Approach to Isolate Protein Complexes From Drosophila Embryos

Published on: April 23, 2014

Drosophila functional elements are embedded in structurally constrained sequences.

Ephraim Kenigsberg1, Amos Tanay

  • 1Department of Computer Science and Applied Mathematics and Department of Biological Regulation, Weizmann Institute, Rehovot, Israel.

Plos Genetics
|June 11, 2013
PubMed
Summary
This summary is machine-generated.

Conserved sequence elements in fly genomes act as anchors for broader genomic regions with altered nucleotide frequencies. This pattern reflects evolutionary shifts influencing genome structure and function.

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Single Nucleotide Polymorphism-sensitive FISH Detection of Locus-specific Ribosomal RNA Transcription in Drosophila melanogaster
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Single Nucleotide Polymorphism-sensitive FISH Detection of Locus-specific Ribosomal RNA Transcription in Drosophila melanogaster

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Last Updated: May 10, 2026

An in vivo Crosslinking Approach to Isolate Protein Complexes From Drosophila Embryos
08:51

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Published on: April 23, 2014

Single Nucleotide Polymorphism-sensitive FISH Detection of Locus-specific Ribosomal RNA Transcription in Drosophila melanogaster
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Single Nucleotide Polymorphism-sensitive FISH Detection of Locus-specific Ribosomal RNA Transcription in Drosophila melanogaster

Published on: March 28, 2025

Area of Science:

  • Genomics
  • Evolutionary Biology
  • Molecular Biology

Background:

  • Metazoan genomes contain numerous functional elements, but most non-exonic regions lack direct coding function.
  • A significant portion of the non-exonic genome shows evolutionary constraints, implying weak functionality.

Purpose of the Study:

  • To investigate the relationship between conserved sequence elements and broader genomic patterns in flies.
  • To understand the evolutionary mechanisms shaping non-exonic genome function and structure.

Main Methods:

  • Analysis of conserved sequence elements (30-70 bp) in fly genomes.
  • Examination of G/C nucleotide frequency patterns and their correlation with epigenetic states.
  • Investigation of evolutionary dynamics using SNP allele frequencies and compensatory evolution.

Main Results:

  • Local conserved elements are associated with punctuated regional increases in G/C nucleotide frequencies, spanning larger areas.
  • This pattern results from an evolutionary shift in the balance of G/C nucleotide gain and loss.
  • The observed pattern correlates with nucleosome occupancy and epigenetic states, suggesting non-neutral evolutionary processes.

Conclusions:

  • Sparse, functionally important sequence elements are embedded within structural sequences that influence the epigenomic context.
  • This model helps explain current gaps in understanding genome function and evolutionary dynamics.
  • Evolutionary shifts in nucleotide balance around functional elements shape genome structure and function.