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Related Concept Videos

Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

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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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The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
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Cis-regulatory Sequences02:02

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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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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. 
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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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In 1928, a German botanist Emil Heitz observed the moss nuclei with a DNA binding dye. He observed that while some chromatin regions decondense and spread out in the interphase nucleus, others do not. He termed them euchromatin and heterochromatin, respectively. He proposed that the heterochromatin regions reflect a functionally inactive state of the genome. It was later confirmed that heterochromatin is transcriptionally repressed, and euchromatin is transcriptionally active chromatin.
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Differentially Active and Conserved Neural Enhancers Define Two Forms of Adaptive Noncoding Evolution in Humans.

Jason Pizzollo1,2, Trisha M Zintel1,2, Courtney C Babbitt2

  • 1Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA 01003, USA.

Genome Biology and Evolution
|July 22, 2022
PubMed
Summary

Human and chimpanzee genomes differ in neural traits due to gene expression changes. This study identifies specific regulatory elements linked to human brain evolution and neuropsychiatric diseases.

Keywords:
Cis-regulationhuman brain evolutioninduced pluripotent stem cellsmassively parallel enhancer assay

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Area of Science:

  • Evolutionary biology
  • Neuroscience
  • Genomics

Background:

  • Human and chimpanzee genomes show high similarity, yet exhibit significant differences in neural phenotypes.
  • Changes in gene expression, potentially driven by adaptive evolution, are hypothesized to underlie these neural differences.
  • The precise location and evolutionary impact of functional regulatory changes in the human genome remain unclear.

Purpose of the Study:

  • To investigate the location and function of cis-regulatory elements (CREs) that have undergone accelerated evolution or are active in the human brain.
  • To compare CREs showing signs of positive selection with those exhibiting differential activity between humans and chimpanzees.
  • To identify CREs associated with neuropsychiatric diseases.

Main Methods:

  • Experimentally combined human and chimpanzee CREs exhibiting accelerated evolution or brain activity.
  • Utilized massively parallel reporter assays (MPRA) to test CRE transcriptional activity in human neural progenitor cells and neurons.
  • Analyzed CREs for signs of positive selection and differential expression.

Main Results:

  • Identified 179 CREs with differential activity between human and chimpanzee neural cells.
  • Detected 722 CREs with evidence of positive selection in the human lineage.
  • Found that selected and differentially expressed CREs vary in expression levels, size, and genomic location.
  • Discovered 69 CREs in loci linked to genetic variants associated with neuropsychiatric diseases.

Conclusions:

  • Regulatory element evolution plays a crucial role in human neural phenotype divergence.
  • The study provides a novel framework for examining noncoding element evolution contributing to human-specific neural traits.
  • Identified CREs highlight the importance of regulatory activity in neural development and disease susceptibility.