1. BioSci D145 lecture 1 page 1 © copyright Bruce Blumberg 2014. All rights reserved BioSci D145 Lecture #1 Bruce Blumberg (blumberg@uci.edu) –4103 Nat Sci 2 - office hours Tu, Th 3:30-5:00 (or by appointment) –phone 824-8573 TA – Bassem Shoucri (bshoucri@uci.edu) –4351 Nat Sci 2, 824-6873 – office hours TBA check e-mail and noteboard daily for announcements, etc.. –Please use the course noteboard for discussions of the material lectures will be posted on web pages after lecture –http://blumberg.bio.uci.edu/biod145-w2015http://blumberg.bio.uci.edu/biod145-w2015 –http://blumberg-lab.bio.uci.edu/biod145-w2015http://blumberg-lab.bio.uci.edu/biod145-w2015

2. BioSci D145 lecture 1 page 2 © copyright Bruce Blumberg 2014. All rights reserved Introductions and Goals Let’s introduce each other - –Name –Major –Favorite thing about UCI –Least favorite thing about UCI On a 3 x 5 card write –a sentence or two describing what you want (or expect) to get out of this class.

3. BioSci D145 lecture 1 page 3 © copyright Bruce Blumberg 2014. All rights reserved Class requirements Grading Midterm35% Final exam35% Presentation10% Term paper10% Participation10% (attendance, class discussion) How are grades determined? 20 minute presentation and discussion of a journal article is required These will be randomly assigned – Bassem will schedule yours Presentations will be done as teams for most papers (depending on class size) Volunteers for 1/15 and 1/22? Attendance and participation is important Please come to class having read assigned material Final examination will not be cumulative, however, understanding of concepts and techniques from first part of course is required.

4. BioSci D145 lecture 1 page 4 © copyright Bruce Blumberg 2014. All rights reserved General comments Overall philosophy –This class is about understanding genomic and proteomic (i.e. whole genome) approaches to problems of biological interest Focus will be on research problems –Intended to be informative and cutting edge but also interesting and relevant, even fun. –Office hours are after class but I am always around –Questions are welcome Please stop me and ask questions if something is unclear –I am going to ask you questions Answers get participation credit Memorizing vs. understanding –I am not concerned with your memory –This course is about problem solving – how to address interesting biological problems using modern, whole-genome approaches

5. BioSci D145 lecture 1 page 5 © copyright Bruce Blumberg 2014. All rights reserved General comments Letters of recommendation –If you want a letter from me, I need to know you as more than a student number and grade come to office hours participate in class discussions make your interest in the subject apparent

6. BioSci D145 lecture 1 page 6 © copyright Bruce Blumberg 2014. All rights reserved About the texts Bookstore vs. online? Neither text book is absolutely required –Copies are on reserve at the library –Brown is a very basic text with lots of introductory material that will help to fill in background between BioSci 99 and this class Reading noted in text books are intended to supplement lecture material Main source of material for this class will be lectures and assigned papers.

7. BioSci D145 lecture 1 page 7 © copyright Bruce Blumberg 2014. All rights reserved Requirements for the term paper Goals –Analytical thinking –Improved writing Select a topic related of interest to you and then propose a whole genome approach to address the problem (not necessarily your 199 research!) –Talk with me about your topic (so that I can help you focus it on something do-able and rewarding to you) Write a short paper (5 pages) in the style of a research grant describing how you will attack this problem (examples posted). –Specific aims (1/2 page) Hypotheses to be tested How will you test hypotheses? –Background and significance (1-2 pages) What is known, what remains to be learned why should someone give you money to study this problem? –Research plan (~3 pages) specific experiments to answer the questions posed in specific aims How will you handle expected vs. unexpected results

8. BioSci D145 lecture 1 page 8 © copyright Bruce Blumberg 2014. All rights reserved Requirements for the term paper (contd) Outline (due Thursday January 22) –Title and topic –Introductory paragraph telling why the problem is important –What is the hypothesis that your proposed research will address? –Enumerate 1-3 specific aims in the form of questions that will test aspects of your hypothesis Topic can be changed later, if necessary What is a hypothesis? What is a theory ?

9. BioSci D145 lecture 1 page 9 © copyright Bruce Blumberg 2014. All rights reserved Requirements for the oral presentation Goal – again to get you to think more analytically –Exposure to literature (classic and current) –Learn critical reading –Discuss practical applications of what we are learning Powerpoint (“journal club”) presentation – as a presenter –15-20 minutes with time allowed for discussion (max of 15 – 20 slides) –Frame the problem – what is the big picture question? What was known before they started? What was unknown? Present background (not more than 5 slides) –What are specific questions asked or hypotheses tested Discuss figures –What is the question being asked in each figure or panel? –What experiments did the authors do to answer questions? –Do the data support the conclusions drawn? What did they conclude overall? What could have been improved? –Point out a few papers for further reading (reviews, follow-ups, etc) –Summarize main points and key techniques used at the end

10. BioSci D145 lecture 1 page 10 © copyright Bruce Blumberg 2014. All rights reserved Requirements for the oral presentation (contd) Powerpoint presentation – as a listener –READ THE PAPERS – you are responsible for the material covered –Study the figures What points don’t you understand? –Make notations, ask the speaker to clarify these –Listen to the speaker If presentation is unclear, ask the speaker to elaborate Always feel free to ask questions – we want an open discussion Papers are posted on the web sites listed Logistics –Prepare presentation and either e-mail to me or bring it on a USB drive

11. BioSci D145 lecture 1 page 11 © copyright Bruce Blumberg 2014. All rights reserved Presentation schedule Week 1 papers – Dear and Cook, 1993, Rana et al., 2006 (Bassem) Week 2 papers – (1) Geisler et al., 1999 (2) Redon et al., 2006 (3) Osoegawa et al., 2000 Week 3 papers – (4) Myers et al., 2000 (5) Venter et al., 2004, (6) Margulies et al., 2005 Week 4 papers – (7) Lindblad-Toh et al., 2011 (8) Chen et al., 2012 (9) Iyer et al., 1999 Week 5 – Midterm, no presentations Week 6 papers – (10) RIKEN, 2005 (11) Kapranov et al., 2007 (12) t'Hoen, 2008 Week 7 papers – (13) Thurman et al, 2012 (14) Filon et al., 2010 (15) Seisenberger et al, 2012 Week 8 papers – (16) Boutros et al., 2004 (17) Gilbert et al., 2013 (18) Luo et al., 2009 Week 9 papers – (19) Ito et al., 2001 (20) Dejardin and Kingston, 2009 (21) Gavin et al., 2002 Week 10 papers - (22) Halama et al., 2011 (23) Illig et al., 2010 (24) Scheer et al., 2008

12. BioSci D145 lecture 1 page 12 © copyright Bruce Blumberg 2014. All rights reserved Lecture Outline – Organization and Structure of Genomes Today’s topics –Genome complexity –Implications of split genes for protein diversity –Repetitive elements and gene evolution The big picture for the next 2 lectures –How are genomes similar and different? –How do we find out this information? –Why do we care? What is genomics? Proteomics?

13. BioSci D145 lecture 1 page 13 © copyright Bruce Blumberg 2014 All rights reserved The rise of -omics The -omics revolution of science –http://www.genomicglossaries.com/content/omes.asphttp://www.genomicglossaries.com/content/omes.asp What does it all mean? –Transcriptomics – –Proteomics – –Functional genomics – –Structural genomics – –Pharmacogenomics – –Toxicogenomics – –Metabolomics – –Interactomics – –Bibliomics –

14. BioSci D145 lecture 1 page 14 © copyright Bruce Blumberg 2014. All rights reserved Organization and Structure of Genomes (contd) Genome size –i.e. total number of DNA bp –Varies widely - WHY? –i.e., what is the source of the differences? Do the number of genes required vary so much? —(how many “phyla” are represented at the right?)

15. BioSci D145 lecture 1 page 15 © copyright Bruce Blumberg 2014. All rights reserved Organization and Structure of Genomes (contd) How to measure genome complexity? –Hybridization kinetics –Shear and melt DNA –Allow to hybridize and measure double- stranded vs. single-stranded by spectrophotometry C o t ½ - measures genome size and complexity –What does a large value (longer to hybridize) mean?

16. BioSci D145 lecture 1 page 16 © copyright Bruce Blumberg 2014. All rights reserved Organization and Structure of Genomes (contd) Assumptions –C o t ½ measures rate of association of sequences –Simple curves at right suggest simple composition No repetitive sequences What would a more complex genome look like? –Would it be just shifted further to the right? –Or ?

17. BioSci D145 lecture 1 page 17 © copyright Bruce Blumberg 2014. All rights reserved Organization and Structure of Genomes (contd) Measure eukaryotic DNA –Multiple components –Can calculate more than 1 C o t ½ value –Either means starting material is not pure (i.e., multiple types of DNA) –Or means different frequency classes of DNA Highly repetitive Moderately repetitive Unique –Very big surprise

18. BioSci D145 lecture 1 page 18 © copyright Bruce Blumberg 2014. All rights reserved Organization and Structure of Genomes (contd) What can we conclude from great variation in genome size ?

19. BioSci D145 lecture 1 page 19 © copyright Bruce Blumberg 2014. All rights reserved Organization and Structure of Genomes (contd) What can we learn by hybridizing RNA back to the genomic DNA? –Label RNA and hybridize with excess DNA – measure formation of hybrids over time –R o t ½ analysis shows that RNA does not hybridize with highly repetitive DNA –What does this mean?

20. BioSci D145 lecture 1 page 20 © copyright Bruce Blumberg 2014. All rights reserved Organization and Structure of Genomes (contd) Gene content is proportional to single copy DNA –Amount of non-repetitive DNA has a maximum,total genome size does not –What is all the extra DNA, i.e., what is it good for? –Where did all this junk come from and why is it still around?

21. BioSci D145 lecture 1 page 21 © copyright Bruce Blumberg 2014. All rights reserved Organization and Structure of Genomes (contd) What is this highly repetitive DNA? Selfish DNA? –Parasitic sequences that exist solely to replicate themselves? Or evolutionary relics? –Produced by recombination, duplication, unequal crossing over

22. BioSci D145 lecture 1 page 22 © copyright Bruce Blumberg 2014. All rights reserved Transcription of Prokaryotic vs Eukaryotic genomes Prokaryotic genes are expressed in linear order on chromosome –mRNA corresponds directly to gDNA Most eukaryotic genes are interrupted by non-coding sequences –Introns (Gilbert 1978) –These are spliced out after transcription and prior to transport out of nucleus –Post-transcriptional processing in an important feature of eukaryotic gene regulation Why do eukaryotes have introns, i.e., what are they good for?

23. BioSci D145 lecture 1 page 23 © copyright Bruce Blumberg 2014. All rights reserved Introns and splicing Alternative splicing can generate protein diversity –Many forms of alternative splicing seen –Some genes have numerous alternatively spliced forms Dozens are not uncommon, e.g., cytochrome P450s

24. BioSci D145 lecture 1 page 24 © copyright Bruce Blumberg 2014. All rights reserved Introns and splicing Alternative splicing can generate protein diversity (contd) –Others show sexual dimorphisms Sex-determining genes Classic chicken/egg paradox –how do you determine sex if sex determines which splicing occurs and spliced form determines sex?

25. BioSci D145 lecture 1 page 25 © copyright Bruce Blumberg 2014. All rights reserved Origins of intron/exon organization Introns and exons tend to be short but can vary considerably –“Higher” organisms tend to have longer lengths in both –First introns tend to be much larger than others – WHY?

26. BioSci D145 lecture 1 page 26 © copyright Bruce Blumberg 2014. All rights reserved Origins of intron/exon organization Exon number tends to increase with increasing organismal complexity –Possible reasons?

27. BioSci D145 lecture 1 page 27 © copyright Bruce Blumberg 2014. All rights reserved Origins of intron/exon organization When did introns arise –Introns early – Walter Gilbert There from the beginning, lost in bacteria and many simpler organisms –Introns late – Cavalier-Smith, Ford Doolittle, Russell Doolittle Introns acquired over time as a result of transposable elements, aberrant splicing, etc If introns benefit protein evolution – why would they be lost? –Which is it? What is common factor among animals that share intron locations?