1 / 35

Lecture 15: HW2 Feedback Ultraconservation

Lecture 15: HW2 Feedback Ultraconservation. Ultraconserved Elements in the Human Genome: The Hip & The Hype. GGTGCCAGGGAAAGGGCAGGAGGTGAGTGCTGGGAGGCAGCTGAGGTCAACTTCTTTTGAACTTCCACGTGGTATTTACTCAGAGCAATTGGTGCCAGAG

cybele
Download Presentation

Lecture 15: HW2 Feedback Ultraconservation

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript


  1. http://cs273a.stanford.edu [Bejerano Fall10/11]

  2. Lecture 15: HW2 Feedback Ultraconservation http://cs273a.stanford.edu [Bejerano Fall10/11]

  3. Ultraconserved Elements in theHuman Genome: The Hip & The Hype GGTGCCAGGGAAAGGGCAGGAGGTGAGTGCTGGGAGGCAGCTGAGGTCAACTTCTTTTGAACTTCCACGTGGTATTTACTCAGAGCAATTGGTGCCAGAG GCTCAGGGCCCTGGAGTATAAAGCAGAATGTCTGCTCTCTGTGCCCAGACGTGAGCAGGTGAGCAGCTGGGGCGAAAGACCTGTTGGAGGCTATGAATGC AATCAAGGTGACAGACAACTGGTGCAATGATGGTAGTGGAAATGGAGGAGAGGGGATTGATTCAAGATGCATTTAGGACCAAGAATCGGGAGCTTGTGAA CGTGTGTATGAGTACTGTAGACGGAGTGGGTGTGTCATCAGAGAAGATCTGAGCATTTGGGCTTGCTCTCCTCAGAGGCCCTGCGAGTGGAGTTCAGCTT TTCCTCATGGGGCAAATCTCACTTTCGCTCCAGTTCCTGGGGCTCAGAGTCCCTGGCCCAGATGCCTCTTGCCATCTCATCTTCACCCTGCCTGGCTTCC CTTGCTTGTTCCAGGATTGTTTCATAAAGAGGGATGTGGTTGGTCTTTAACCCTATGAATGCTGGCTGAGGATGCCTGCGGAACCTGTAGTGAAGCTTTC AGGGGCTGCTCGGGTTCTGGCTGGTAGGTGAACACTGTCCATCTTGCCGGCTGGGACACAGTGACTCTGGGTAGTTGTGTAAGAGAGGGGCCCTTGGCAG ACAAACAGGTTCTTCTCTGTTGGTGGGCCAGCCAGCAGGTCAGTGGGAAGGTTAAAGGTCATGGGGTTTGGGAGAACTGGGTGAGGAGTTCAGCCCCATC CCCCGTAAAGCTCCTGGGAAGCACTTCTCTACTGGGGCAGCCCCTGATACCAGGGCACTCATTAACCCTCTGGGTGCCAGGGAAAGGGCAGGAGGTGAGT GCTGGGAGGCAGCTGAGGTCAACTTCTTTTGAACTTCCACGTGGTATTTACTCAGAGCAATTGGTGCCAGAGGCTCAGGGCCCTGGAGTATAAAGCAGAA TGTCTGCTCTCTGTGCCCAGACGTGAGCAGGTGAGCAGCTGGGGCTGTCTGCTCTCTGTGCCCAGACGTGAGCAGGTGAGCAGCTGGGGCTGTCTGCTCT CTGTGCCCAGACGTGAGCAGGTGAGCAGCTGGGGCTGTCTGCTCTCTGTGCCCAGACGTGAGCAGGTGAGCAGCTGGGGCTGTCTGCTCTCTGTGCCCAG GAAAGACCTGTTGGAGGCTATGAATGCAATCAAGGTGACAGACAACTGGTGCAATGATGGTAGTGGAAATGGAGGAGAGGGGATTGATTCAAGATGCATT TAGGACCAAGAATCGGGAGCTTGTGAACGTGTGTATGAGTACTGTAGACGGAGTGGGTGTGTCATCAGAGAAGATCTGAGCATTTGGGCTTGCTCTCCTC AGAGGCCCTGCGAGTGGAGTTCAGCTTTTCCTCATGGGGCAAATCTCACTTTCGCTCCAGTTCCTGGGGCTCAGAGTCCCTGGCCCAGATGCCTCTTGCC ATCTCATCTTCACCCTGCCTGGCTTCCCTTGCTTGTTCCAGGATTGTTTCATAAAGAGGGATGTGGTTGGTCTTTAACCCTATGAATGCTGGCTGAGGAT GCCTGCGGAACCTGTAGTGAAGCTTTCAGGGGCTGCTCGGGTTCTGGCTGGTAGGTGAACACTGTCCATCTTGCCGGCTGGGACACAGTGACTCTGGGTA GTTGTGTAAGAGAGGGGCCCTTGGCAGACAAACAGGTTCTTCTCTGTTGGTGGGCCAGCCAGCAGGTCAGTGGGAAGGTTAAAGGTCATGGGGTTTGGGA GAAACTGGGTGAGGAGTTCAGCCCCATCCCCCGTAAAGCTCCTGGGAAGCACTTCTCTACTGGGGCAGCCCCTGATACCAGGGCACTCATTAACCCTCTG GGTGCCAGGGAAAGGGCAGGAGGTGAGTGCTGGGAGGCAGCTGAGGTCAACTTCTTTTGAACTTCCACGTGGTATTTACTCAGAGCAATTGGTGCCAGAG GCTCAGGGCCCTGGAGTATAAAGCAGAATGTCTGCTCTCTGTGCCCAGACGTGAGCAGGTGAGCAGCTGGGGCGAAAGACCTGTTGGAGGCTATGAATGC AATCAAGGTGACAGACAACTGGTGCAATGATGGTAGTGGAAATGGAGGAGAGGGGATTGATTCAAGATGCATTTAGGACCAAGAATCGGGAGCTTGTGAA CGTGTGTATGAGTACTGTAGACGGAGTGGGTGTGTCATCAGAGAAGATCTGAGCATTTGGGCTTGCTCTCCTCAGAGGCCCTGCGAGTGGAGTTCAGCTT TTCCTCATGGGGCAAATCTCACTTTCGCTCCAGTTCCTGGGGCTCAGAGTCCCTGGCCCAGATGCCTCTTGCCATCTCATCTTCACCCTGCCTGGCTTCC CTTGCTTGTTCCAGGATTGTTTCATAAAGAGGGATGTGGTTGGTCTTTAACCCTATGAATGCTGGCTGAGGATGCCTGCGGAACCTGTAGTGAAGCTTTC AGGGGCTGCTCGGGTTCTGGCTGGTAGGTGAACACTGTCCATCTTGCCGGCTGGGACACAGTGACTCTGGGTAGTTGTGTAAGAGAGGGGCCCTTGGCAG ACAAACAGGTTCTTCTCTGTTGGTGGGCCAGCCAGCAGGTCAGTGGGAAGGTTAAAGGTCATGGGGTTTGGGAGAACTGGGTGAGGAGTTCAGCCCCATC CCCCGTAAAGCTCCTGGGAAGCACTTCTCTACTGGGGCAGCCCCTGATACCAGGGCACTCATTAACCCTCTGGGTGCCAGGGAAAGGGCAGGAGGTGAGT GCTGGGAGGCAGCTGAGGTCAACTTCTTTTGAACTTCCACGTGGTATTTACTCAGAGCAATTGGTGCCAGAGGCTCAGGGCCCTGGAGTATAAAGCAGAA TGTCTGCTCTCTGTGCCCAGACGTGAGCAGGTGAGCAGCTGGGGCTGTCTGCTCTCTGTGCCCAGACGTGAGCAGGTGAGCAGCTGGGGCTGTCTGCTCT CTGTGCCCAGACGTGAGCAGGTGAGCAGCTGGGGCTGTCTGCTCTCTGTGCCCAGACGTGAGCAGGTGAGCAGCTGGGGCTGTCTGCTCTCTGTGCCCAG Gill Bejerano Dept. of Developmental Biology Dept. of Computer Science Stanford University http://cs273a.stanford.edu [Bejerano Fall10/11] 3

  4. Sequence Conservation implies Function • (but which function/s?...) Comparative Genomics of related species highlights: functional region! ...CTTTGCGA-TGAGTAGCATCTACTATTT... human mammalian ancestor ...ACGTGGGACTGACTA-CATCGACTACGA... mouse http://cs273a.stanford.edu [Bejerano Fall10/11]

  5. Human Genome full of Conserved Non-Coding Elements Human Genome: 3*109 letters 1.5% known function compare to other species >50% junk >5% human genome functional 3x more functional DNA than known! ~106 genomic loci do not code for protein What do they do then? http://cs273a.stanford.edu [Bejerano Fall10/11]

  6. Conserved elements in the Human Genome all human-mouse alignments human-mouse ancestral repeats alignment human-mouse ancestral repeats alignment election Difference: 5% of Human Genome 85%id on average [Mouse consortium, Nature 2002] http://cs273a.stanford.edu [Bejerano Fall10/11]

  7. Conserved elements in the Human Genome all human-mouse alignments human-mouse ancestral repeats alignment human-mouse ancestral repeats alignment election Difference: 5% of Human Genome Ultraconservation 85%id on average http://cs273a.stanford.edu [Bejerano Fall10/11]

  8. Typical DNA Conservation levels (dot = base identical to human) Conserved elements between human and mouse are on average 85% identical. [mouse consortium, 2002] http://cs273a.stanford.edu [Bejerano Fall10/11]

  9. Ultraconserved Elements fish using2 vs. 3species 481 elements perfectly conserved (100%id) over 200bp or more between human, mouse and rat. http://cs273a.stanford.edu [Bejerano Fall10/11] [Bejerano et al., Science 2004]

  10. Contamination http://cs273a.stanford.edu [Bejerano Fall10/11]

  11. What exactly is an Ultraconserved Element? using3 vs. 43species Aha!! http://cs273a.stanford.edu [Bejerano Fall10/11]

  12. Ultraconservation as a Phenomenon More and more species Few species Hmmm…. http://cs273a.stanford.edu [Bejerano Fall10/11]

  13. * * * * * Ultraconserved Elements: Why? Hundreds of long genomic regions identical between amniotes they must have rejected many different changes. But... all functions we understand in our genome are encoded using redundant codes. CDS ncRNA TFBS seq. http://cs273a.stanford.edu [Bejerano Fall10/11]

  14. Conserved elements in the Human Genome all human-mouse alignments human-mouse ancestral repeats alignment human-mouse ancestral repeats alignment Why did I look at the tail? election Difference: 5% of Human Genome Ultraconservation 85%id on average http://cs273a.stanford.edu [Bejerano Fall10/11]

  15. DNA Replication is Imperfect • It’s imperfect on all scales: small, medium and large. • In particular it begets novel functional entities: junk functional ...ACGTACGACTGACTAGCATCGACTACGA... regional duplication functional functional ...ACGTACGACTGACTAGCATCGACTACGA........TCTGACTAGCATCGACTACGA... functional divergence functional’ functional’’ ...ACGTACGACTGACTAGCATCGACTACGA........TCTGACTAGCATCGACTACGA... Protein & RNA gene families come to life this way. What else does? http://cs273a.stanford.edu [Bejerano Fall10/11]

  16. Computational Approach I ~400bp • Group them into paralogfamilies of human functional regions of common origins: • Annotated members induce function on all. • Examine core, substitutions in family. • Test for “guilt by association”. human DNA .....ACGTGCATGACTGACTAGCATCAGACGACTAC..GATAATACGCTACGACTAGCTAC..... T AC ...TGACTAGCATCGACTAC..GATAATACGAC... ...CATCGACTAC..GATAATACGACGGTTGGT... [Bejerano et al., ISMB 2004] http://cs273a.stanford.edu [Bejerano Fall10/11]

  17. Functional Annotation by Families After removing from top 5% Human all annotated regions, and more: 700,000 elements, covering 3.5% Human Genome Puzzling News: 96% of the 700,000 appear unique(!) Good News: We still find 12,027 families novel putative ncRNAs, cis-regulatory elements, etc. [Bejerano et al., ISMB 2004] http://cs273a.stanford.edu [Bejerano Fall10/11]

  18. Computational Approach II related elements (75%id over 200bp) related genes human mouse rat same element 95%id over 200bp same element 96%id over 200bp Classical Biological approach: experiment to understand these regions Computational approach: how many regions like this or “better” are there? http://cs273a.stanford.edu [Bejerano Fall10/11]

  19. Out popped the Ultraconserved Elements Puzzling News: 96% of the 700,000 conserved non-coding elements appear unique(!) Same with Ultras http://cs273a.stanford.edu [Bejerano Fall10/11]

  20. What could ultras be doing? • exonic • non • possibly http://cs273a.stanford.edu [Bejerano Fall10/11]

  21. Associating distal peaks in a gene-based context is statistically inappropriate Gene transcription start site Ultraconserved Element Ontology term (e.g. ‘development’) Evolved into http://great.stanford.edu/ π π π π N = 8 genes in genome K = 3 genes annotated with n = 3 genes selected by proximal peaks k = 2 selected gene annotated with Set gene regulatory domain. Associate Ultras with genes. Per ontology term, count annotated genes selected. Rank terms by enrichment hypergeometric p-value. π π P = Pr(k ≥1 | n=2, K =3, N=8) http://cs273a.stanford.edu [Bejerano Fall10/11]

  22. Enrichment Association of Ultraconserved Elements Exonic Ultras Non-exonic Ultras http://cs273a.stanford.edu [Bejerano Fall10/11]

  23. Ultras are Functional Back in 2004 we hypothesized: 481 ultraconserved elements “nonexonic” subset – transcriptional regulators exonic subset – post transcriptional regulation [Pennacchio et al., Nature, 2006] [Ni et al., Genes Dev.; Lareau et al., Nature, 2007] http://cs273a.stanford.edu [Bejerano Fall10/11]

  24. Ultraconserved Non-coding RNA About 1/3 of all ultras are expressed. Some are predicted to provide microRNA targets. A few are anti-correlated with miRNAexpression levels. A few even act as oncogenes. miRNA complementarity [Calin et al, Cancer Cell, 2007] http://cs273a.stanford.edu [Bejerano Fall10/11]

  25. Ultras are Under Strong Human Selection Mutational cold spots? NO. Rare (new) mutations are introduced to the population. Fierce purifying selection? YES. Very few of these get anywhere near fixation. A A G A A humans chimp NonSyn DAF Ultra DAF [Katzman et al, Science ,2007] http://cs273a.stanford.edu [Bejerano Fall10/11]

  26. No Apparent Phenotype Touch an Ultra And You - DIY [Ahituv et al., PLoS Biology, 2007] http://cs273a.stanford.edu [Bejerano Fall10/11]

  27. What can’t we measure in the lab? Ne is population size, s selective dis/advantage. Both of which are VERY wrong in the lab. http://cs273a.stanford.edu [Bejerano Fall10/11]

  28. So it can happen – but does it FIX? DNA element t mouse http://cs273a.stanford.edu [Bejerano Fall10/11]

  29. Count Fraction Lost, Binned by %id bin by %id count_all t human macaque dog mouse rat count_hole 100bp sliding window dog rat mouse human macaque http://cs273a.stanford.edu [Bejerano Fall10/11]

  30. Quite Some Time Later [McLean & Bejerano, Genome Res., 2008] http://cs273a.stanford.edu [Bejerano Fall10/11]

  31. Ultras are Fiercely Retained through Evolution No Apparent Phenotype 100%id primates-dog: 1,691,090bp rodents deleted: 1,447bp (0.086%) Ultras are >300 fold more persistent than neutral DNA But Doomed ... the genomic deletion is (25% deleted) http://cs273a.stanford.edu [Bejerano Fall10/11]

  32. How special are the Ultras? election Ultraconservation http://cs273a.stanford.edu [Bejerano Fall10/11]

  33. Ultraconservation as a Phenomenon We do not see a bump in the curve More and more species Few species Hmmm…. http://cs273a.stanford.edu [Bejerano Fall10/11]

  34. Ultraconserved Elements: What do we know? • Excessive sequence conservation exists. • Set is heterogeneous from a functional perspective. • Four can be KO-ed with no clear phenotype. • Yet, the set is under extreme selection in natural populations, both for mutations and deletions. • Most ultras have deep orthology, and no paralogy. • One ultra comes from a mobile element co-option events. • Others may have come from similar events. • Ultras appear the tip of a continuum, not a unique peak. http://cs273a.stanford.edu [Bejerano Fall10/11]

  35. * * * * * Ultraconserved Elements: What we don’t • What maintains so much conservation? http://cs273a.stanford.edu [Bejerano Fall10/11]

More Related