1. Sackler Medical School
UCSC Genome Browser
Dror Hollander
Gil Ast Lab
Sackler Medical School

2. Understanding the Genome
histone midifications
genes
GC content
promoters
repetitive elements
conservation
SNPs
nucleosome occupancy
miRNA
gene expression
non-coding RNA
secondary structure
alternative splicing
exon-intron structure
How can you examine a genomic segment while
taking all of these factors into account?
DNA
protein
RNA

3. Lecture Overview UCSC Genome Browser Galaxy
Interface & selected tracks
Detecting alternative splicing events
Chromatin organization & epigenetics
BLAT
PCR
Galaxy

4. UCSC Genome Browser (64 eukaryote genome genomes) track track
Basic design: “the Genome Browser stacks annotation tracks beneath genome coordinate positions, allowing rapid visual correlation of different types of information”
(64 eukaryote
genomes)
genome
track
track

5. Genome Browsing…

6. Basic Genome Browser Interface
chromosomal position
genomic coordinates
zoom
start codons in green
mark and drag here to zoom in
stop codons in red
UCSC Genes track
Refseq Genes track
Black - feature has a corresponding entry in the Protein Data Bank (PDB)
Dark blue - transcript has been reviewed or validated by either the RefSeq, SwissProt or CCDS staff
Medium blue - other RefSeq transcripts
Light blue - non-RefSeq transcripts
intron
CDS
UTR
gene direction
(> / <)

7. Basic Genome Browser Interface
Configure track visualization:

8. Basic Genome Browser Interface
“RefSeq track shows known human protein-coding and non-protein-coding genes taken from the NCBI RNA reference sequences collection (RefSeq). The data are updated daily”
“The UCSC track shows gene predictions based on data from RefSeq, Genbank, CCDS and UniProt… includes both protein-coding and putative non-coding transcripts… Compared to RefSeq, this gene set has generally about 10% more protein-coding genes, approximately five times as many putative non-coding genes, and about twice as many splice variants”
Let’s examine a few examples online…
Press on track name for full visualization
Examples:
UCSC: show RefSeq description, GeneCards & GO annotation
RefSeq: show summary and genomic alignment
Show gene with alternative ATG: ?????

9. Basic Genome Browser Interface
A few more tracks worth mentioning:
miRNA (Genes and Gene Prediction Tracks -> sno/miRNA)
conservation (Comparative Genomics -> Conservation)
Expression tracks
Regulation tracks (chromatin structure and modifications, DNA methylation, etc.; includes ENCODE data)
RNA secondary structure (Genes and Gene Prediction Tracks -> EvoFold)
SNPs (Variation and Repeats -> SNPs)
Mention that additional tracks are available for the hg18 genome

10. Basic Genome Browser Interface
Get genomic DNA for the viewed coordinates:
Convert sequence to a different genome assembly or genome:
Convert browser window to an image file:

11. Lecture Overview UCSC Genome Browser Galaxy
Interface & selected tracks
Detecting alternative splicing events
Chromatin organization & epigenetics
BLAT
PCR
Galaxy

12. Detecting Alternative Splicing Events
Via Human mRNAs & Spliced ESTs tracks (mRNA and EST Tracks)
“The mRNA track shows alignments between human mRNAs in GenBank and the genome”
“…alignments between human expressed sequence tags (ESTs) in GenBank and the genome… ESTs are single-read sequences, typically about 500 bases in length”
gene DNA
Mention the different fields in each mRNA / EST
mRNA

13. Detecting Alternative Splicing Events
Via Alt Events track (Genes and Gene Prediction Tracks) – based on UCSC genes
gene DNA
cassetteExon
>

14. Detecting Alternative Splicing Events
Via Burge RNA-seq track (Expression)
Click on the track name to choose tissues
gene DNA
Burge
RNA-seq

15. Different Alternative Splicing Types
Exon skipping
Alternative splice site (3’)
Intron retention
Exon skipping (PTBP1; chr19:804, ,685)
Alternative 3’ splice site; (PTBP1; chr19:804, ,685)
Alternative 5’ splice site; (SLC11A2; chr12:51,401,760-51,402,755)
Intron retention; (CD163; chr12:7,639,792-7,641,193)

16. Lecture Overview UCSC Genome Browser Galaxy
Interface & selected tracks
Detecting alternative splicing events
Chromatin organization & epigenetics
BLAT
PCR
Galaxy

17. Histone Modifications

18. Transcription Factor Binding

19. DNA Methylation

20. Lecture Overview UCSC Genome Browser Galaxy
Interface & selected tracks
Detecting alternative splicing events
Chromatin organization & epigenetics
BLAT
PCR
Galaxy

21. BLAT BLAT = Blast-Like Alignment Tool
BLAT query
BLAT query
BLAT = Blast-Like Alignment Tool
BLAT is designed to find similarity of >95% on DNA and >80% for protein
CACGCCCAGACCTGCCTTCCGGGGACAGCCAGCCCTCGCTGGACCAGACCATGGCCGCGGCCTTCGGTGCACCTGGTATAATCTCAGCCTCTCCGTATGCAGGAGCTGGTTTCCCTC

22. Lecture Overview UCSC Genome Browser Galaxy
Interface & selected tracks
Detecting alternative splicing events
Chromatin organization & epigenetics
BLAT
PCR
Galaxy

23. amplicon in fasta format
PCR
coordinates
strand
primers
amplicon in fasta format
amplicon
Primers:
CREB-ATF2_F: cggccaatgtagctcctcta Tm= 60.37
CREB-ATF2_R: CTCAATGGGTGCGTCAACTA Tm= 59.72
temperatures

24. Lecture Overview UCSC Genome Browser Galaxy
Interface & selected tracks
Detecting alternative splicing events
Chromatin organization & epigenetics
BLAT
PCR
Galaxy

25. Galaxy
“Galaxy allows you to do analyses you cannot do anywhere else without the need to install or download anything. You can analyze multiple alignments, compare genomic annotations, profile metagenomic samples and much much more...”

26. Galaxy – What Is It Good for?
Getting the best out of UCSC
Operating on UCSC data
Supports operations both at the interval level, and at the sequence level
Designed for biologists!

27. Galaxy – Typical Workflow
Extract sets of coordinates
either upload from computer or from UCSC table browser
Operate on different sets of coordinates (intersect, subtract etc.)
Fetch genomic sequences of coordinates