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Related Concept Videos

Gene Duplication and Divergence02:37

Gene Duplication and Divergence

The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
Gene Families01:57

Gene Families

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.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form dimers that...
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...
Regulation of Expression Occurs at Multiple Steps02:24

Regulation of Expression Occurs at Multiple Steps

Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...

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Related Experiment Video

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Standardized Modular Assembly of Polycistronic Operons with Modular Cloning (MoClo) using the In-Cloning toolkit
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Formation of regulatory modules by local sequence duplication.

Armita Nourmohammad1, Michael Lässig

  • 1Institute for Theoretical Physics, University of Cologne, Köln, Germany.

Plos Computational Biology
|October 15, 2011
PubMed
Summary
This summary is machine-generated.

Local DNA duplications rapidly create new transcription factor binding sites in fly genomes. This mechanism, distinct from independent evolution, shapes complex gene regulation in higher eukaryotes.

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Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
11:34

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

Area of Science:

  • Molecular Evolution
  • Genomics
  • Developmental Biology

Background:

  • Regulatory sequence and function turnover is key to molecular evolution.
  • Understanding the mechanisms of rapid regulatory site formation and loss is crucial.

Purpose of the Study:

  • To investigate the modes of sequence evolution leading to the formation and loss of regulatory sites.
  • To analyze the evolutionary origins of neighboring transcription factor binding sites in the fly genome.

Main Methods:

  • Statistical analysis of 346 cis-regulatory modules in Drosophila melanogaster.
  • Comparison with intergenic regulatory sequences in Saccharomyces cerevisiae.
  • Analysis using an evolutionary model with two distinct modes of site formation.

Main Results:

  • A significant fraction of neighboring transcription factor binding sites in the fly genome originate from local duplications.
  • Duplicated sequences can seed new binding sites near existing ones, which then evolve via point mutations.
  • Pairs of binding sites in fly regulatory modules exhibit enhanced sequence similarity up to 50 bp.

Conclusions:

  • Local sequence duplications are a pervasive mechanism for generating new transcription factor binding sites.
  • This duplication-driven evolution contributes to the complex regulatory architecture of higher eukaryotes.
  • The prevalence of local duplications distinguishes eukaryotic regulatory complexity from unicellular organisms.