1. Detection of genome regulation sequences
Roi Rodríguez González

2. Introduction Regulation of gene expression
Essential for development, cell differentiation, physiological and stress responses.
Regulatory elements:
Cis-regulatory elements
Trans-regulatory elements
Promoters,
Enhancers,
Silencers, etc.
Transcription Factors

3. Detection of reg-seq Ideally using raw DNA sequence
Actual understanding too low
Functional analyses in laboratory
DNase I hypersensive assays
In vivo and In vitro
ChIP-chip and ChIP-seq
Deduce function

4. DNase I hypersensive assays
Promoters, Enhancers, Silencers, Insulators…

5. ChIP-chip and ChIP-seq
Comparable data between species

6. Detection of reg-seq Ideally using raw gen sequence
Current understanding too low
Functional analyses in laboratory
Requires large known about function and transcription
Slow, expensive and low-predictive

7. Detection of reg-seq Current capacity to massive sequencing
Large amount of sequences
Laboratory approaches can’t analyse all
Comparative computational methods
Require functional validation
Fast, available and high-predictive

8. Computational methods
Comparison among species
Closer enough for functional homologies
Enough divergence for identified noise similarities
Substitutions per site:
Intragenic Intergenic
Nucleotide changes, Insertions, Deletions, Duplications…

9. Computational methods
Algorithms find regulatory sequences
Locating genes
Positional localization of conserved motifs
Transcription start points promoter boxes, TFBS…
TATA box
Transcription start point localization (Eponine algorithm)

10. Computational methods
Algorithms find regulatory sequences
Locating genes
Positional localization of conserved motifs
Transcription start points promoter boxes, TFBS…
Physical features of DNA in regulatory sequences
Bendability for TFBS (DragonGSF algorithm)

11. Computational methods
Using data bases and de novo sequencing
Develop and combination of algorithms
Identify regulatory sequences and their Transcription Factor binding sites (TFBS)
Predict locations, function
Still being necessary functional studies to assure results

12. Thanks for your attention