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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 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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Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
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Gene expression is a dynamic process that is significantly influenced by environmental factors. This interaction underlies the complex nature of biological development and the phenotypic differences observed among individuals, even among those with identical genetic makeups. Factors such as radiation, temperature, behavior, nutrition, and stress play pivotal roles in determining how genes are expressed. The concept of the reaction range is central to understanding this interaction. It posits...
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Related Experiment Video

Updated: Mar 26, 2026

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA
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Exploring structural variants in environmentally sensitive gene families.

Nevin Dale Young1, Peng Zhou2, Kevin At Silverstein3

  • 1Department of Plant Pathology, 495 Borlaug Hall, University of Minnesota, St. Paul, MN 55108, USA; Department of Plant Biology, 220 BioScience Building, University of Minnesota, St. Paul, MN 55108, USA.

Current Opinion in Plant Biology
|February 9, 2016
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Summary

Discovering structural variation in plant gene families is improved by de novo genome assemblies. This approach overcomes reference genome limitations, enabling more accurate insights into gene family evolution and rapid adaptation.

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Area of Science:

  • Genomics
  • Plant Biology
  • Evolutionary Biology

Background:

  • Environmentally sensitive plant gene families exhibit high variability.
  • Existing methods for structural variation discovery in gene families are often incomplete.
  • Reference genome-dependent methods lead to misplacement of paralogous sequences and incomplete results.

Purpose of the Study:

  • To highlight the advantages of de novo genome assemblies for studying gene family variation.
  • To address the limitations of traditional reference-based approaches.
  • To enable more comprehensive and accurate insights into plant gene family evolution.

Main Methods:

  • Utilizing de novo genome assemblies for variant discovery.
  • Comparing de novo assembly approaches with older array-based and read-mapping methods.
  • Leveraging long-read sequencing technologies to minimize artifacts and improve assembly accuracy.

Main Results:

  • De novo assemblies overcome reference genome biases and reduce paralog misplacement.
  • This approach allows for more accurate reconstruction of gene family structures, including tandem clusters.
  • Longer reads in de novo sequencing minimize artifacts and facilitate the study of rapid evolution.

Conclusions:

  • De novo genome assemblies provide a more accurate and comprehensive approach to studying structural variation in plant gene families.
  • This methodology is crucial for understanding gene family evolution and adaptation.
  • Advancements in long-read sequencing will further enhance the power of de novo assemblies for genomic research.