Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

Detecting non-coding selective pressure in coding regions.

Hui Chen1, Mathieu Blanchette

  • 1McGill Centre for Bioinformatics, McGill University, Montreal, QC, Canada H3A 2B4. hui@mcb.mcgill.ca

BMC Evolutionary Biology
|February 10, 2007
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

[Prevalence of germinal center B-cell-like and non-germinal center B-cell-like types of diffuse large B-cell lymphoma in Shanghai, China].

Zhonghua bing li xue za zhi = Chinese journal of pathology·2010
Same author

[Pathological characteristics and clinical significance of macrochilia secondary to venular malformation].

Zhonghua kou qiang yi xue za zhi = Zhonghua kouqiang yixue zazhi = Chinese journal of stomatology·2010
Same author

Enhancement of exo-polysaccharide production and antioxidant activity in submerged cultures of Inonotus obliquus by lignocellulose decomposition.

Journal of industrial microbiology & biotechnology·2010
Same author

Two new dihydrobenzofuran lignans from Rabdosia lophanthoides (Buch.-Ham.ex D.Don) Hara.

Journal of Asian natural products research·2010
Same author

Biogenic silica in intertidal marsh plants and associated sediments of the Yangtze Estuary.

Journal of environmental sciences (China)·2010
Same author

Analysis of oral microbiota in children with dental caries by PCR-DGGE and barcoded pyrosequencing.

Microbial ecology·2010
Same journal

Globins in the marine annelid Platynereis dumerilii shed new light on hemoglobin evolution in bilaterians.

BMC evolutionary biology·2020
Same journal

Is there any intron sliding in mammals?

BMC evolutionary biology·2020
Same journal

The evolution of the huntingtin-associated protein 40 (HAP40) in conjunction with huntingtin.

BMC evolutionary biology·2020
Same journal

You don't have the guts: a diverse set of fungi survive passage through Macrotermes bellicosus termite guts.

BMC evolutionary biology·2020
Same journal

Mitochondrial DNAs provide insight into trypanosome phylogeny and molecular evolution.

BMC evolutionary biology·2020
Same journal

Stress-related changes in leukocyte profiles and telomere shortening in the shortest-lived tetrapod, Furcifer labordi.

BMC evolutionary biology·2020
See all related articles

This study introduces a novel comparative genomics method to identify non-coding functional elements within coding regions. The approach successfully detected known elements and revealed new regions under selective pressure, highlighting the prevalence of these regulatory elements.

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Comparative genomics excels at identifying non-coding regulatory regions in intergenic/intronic DNA.
  • Non-coding functional elements within coding regions (e.g., exonic splicing enhancers) are often missed by standard comparative genomics.
  • These elements are challenging to detect due to the high conservation of coding sequences.

Purpose of the Study:

  • To develop a comparative genomics approach for detecting non-coding functional elements within coding regions.
  • To model codon evolution under various selective pressures to distinguish functional elements.
  • To identify novel non-coding functional elements in coding sequences.

Main Methods:

  • Developed a comparative genomics approach using mixture models for codon evolution.

Related Experiment Videos

  • Modeled codon evolution under specific types of coding selective pressure.
  • Computed posterior distributions of entropy and parsimony scores.

    • Main Results:

    • Successfully detected a known exonic splicing enhancer in growth hormone 1 mRNA sequences.
    • Identified a novel region of several hundred base pairs under strong non-coding selective pressure in CORTBP2 genes.
    • Demonstrated the method's capability to find functional elements within coding regions.

    Conclusions:

    • Non-coding functional elements, especially those in post-transcriptional regulation, are likely more common than previously thought.
    • The proposed comparative genomics approach is powerful for detecting these elements.
    • Ongoing genome sequencing projects will enhance the utility of such methods.