cis-Decoder: A Tool for Discovering Conserved DNA Sequences in Enhancers
Author Information
Author(s): Brody Thomas, Rasband Wayne, Baler Kevin, Kuzin Alexander, Kundu Mukta, Odenwald Ward F
Primary Institution: Neural Cell-Fate Determinants Section, NINDS, NIH, Bethesda, MD, USA
Hypothesis
The use of cis-Decoder suggests that enhancers use overlapping repertoires of highly conserved core elements.
Conclusion
The study reveals that enhancers employ overlapping repertoires of highly conserved core elements, identified through the analysis of conserved sequence blocks.
Supporting Evidence
- cis-Decoder identifies conserved sequence blocks that have remained unchanged for over 160 million years.
- The analysis included 2,086 conserved sequence blocks from 135 characterized enhancers.
- Most conserved sequence blocks consist of shorter overlapping elements that are either enhancer type-specific or common to enhancers with divergent regulatory behaviors.
Takeaway
This study shows how scientists can find important DNA sequences that help control gene activity in different tissues by using a special tool called cis-Decoder.
Methodology
A systematic approach for analysis of evolutionarily conserved cis-regulatory DNA using cis-Decoder, which identifies conserved sequence elements shared between similarly regulated enhancers.
Limitations
The study does not address the functional roles of over half of the identified conserved sequences, which currently have no assigned functions.
Digital Object Identifier (DOI)
Want to read the original?
Access the complete publication on the publisher's website