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Cis-regulatory Sequences

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 Sequences

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...

Cooperative Binding of Transcription Regulators

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...

What is Natural Selection?

What is Natural Selection?

Natural selection is an evolutionary process in which individuals with survival-promoting traits reproduce at higher rates. These favorable traits become more common within a population or species. Naturally selected traits initially arise via random genetic mutations. In order for selection to occur, there must be variation within a population, the trait controlling the variation must be heritable, and there must be an evolutionary advantage for variation in the trait.The Theory of Natural...

Limits to Natural Selection

Limits to Natural Selection

Organisms that are well-adapted to their environment are more likely to survive and reproduce. However, natural selection does not lead to perfectly adapted organisms. Several factors constrain natural selection.For one, natural selection can only act upon existing genetic variation. Hypothetically, redtusks may enhance elephant survival by deterring ivory-seeking poachers. However, if there are no gene variants—or alleles—for redtusks, natural selection cannot increase the prevalence of...

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Quantitative Comparison of cis-Regulatory Element (CRE) Activities in Transgenic Drosophila melanogaster

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Published on: December 19, 2011

Detecting natural selection on cis-regulatory DNA.

Matthew W Hahn¹

¹Department of Biology and School of Informatics, Indiana University, Bloomington, IN, 47405, USA. mwh@indiana.edu

|September 7, 2006

Summary

Natural selection shapes evolution by altering gene expression through non-coding regulatory DNA. Studies reveal diverse selection forces, including local adaptation and balancing selection, acting beyond protein-coding genes.

Area of Science:

Evolutionary biology
Genetics
Molecular biology

Background:

Transcriptional regulation is crucial for evolutionary genetic changes.
Non-coding regulatory sequences are key drivers of these changes.
Studying selection in non-coding DNA presents unique challenges compared to protein-coding sequences.

Purpose of the Study:

To review the literature on evolutionary forces governing non-coding regulatory sequences.
To assess the applicability of neutrality tests from coding regions to non-coding regions.
To explore emerging patterns of natural selection in gene regulation.

Main Methods:

Review of existing literature on cis-regulatory variation and selection.
Application of neutrality tests to non-coding DNA.

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Using Sniper-Cas9 to Minimize Off-target Effects of CRISPR-Cas9 Without the Loss of On-target Activity Via Directed Evolution

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Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay (EMSA) and DNA-affinity Precipitation Assay (DAPA)

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Analysis of single locus and whole genome studies.

Main Results:

Most neutrality tests used for coding regions are applicable to non-coding regions with caveats.
Cis-regulatory variation exhibits known and novel forms of selection.
Local adaptation and balancing selection are widespread in non-coding DNA.

Conclusions:

Natural selection significantly impacts non-coding regulatory DNA.
The ability to fine-tune gene expression may drive local adaptation and balancing selection.
Evolutionary changes extend beyond protein-coding sequences to regulatory elements.