1. Speaker: Xudong Zou Time: 17 th April, 2014 Peking University ShenZhen Graduate School 1

2. Outline  Background  Molecular mechanisms  Exon shuffling  Gene duplication  Lateral gene transfer  Gene fusion/fission  De novo gene origination  Summary 2

3. Outline  Background  Molecular mechanisms  Exon shuffling  Gene duplication  Lateral gene transfer  Gene fusion/fission  De novo gene origination  Summary 3

4. In an ancient Chinese legend, the first Chinese emperor Yande (3,000 BC) brother to the Yellow- Emperor, had a pretty princess named Jingwei. Like other legendary southern Chinese goddesses, Jingwei liked to swim. Unfortunately, she drowned in the East China Sea. She was reincarnated into a beautiful bird, who, to save others from possible tragedy, carried soil and stones in an attempt to fill in the ocean. The legend of Jingwei 4

5. Manyuan Long and the Jingwei gene Manyuan Long Department of Ecology & Evolution Biological Sciences Collegiate Division University of Chicago Jingwei The first young gene described in the early 1990s. It is a very young gene that if we set 1 million years as an age unit, the common old genes are often 1000~3000 years old, while Jingwei is 2 years old. 5

6. 1950s-- In 1953, DNA double helix In 1966, Richard Lewontin and Huby found that natural selection can’t explain molecular evolution In 1968, Motoo Kimura introducing neutral theory of molecular evolution 1990s-- In 1993, Manyuan Long described the Jingwei gene, open a new field to study the origination and evolution of new genes 6

7. CHARLES H. LANGLEY In 1990, Manyuan Long joined Langley’s lab and investigated degree of fitness of neutral theory on DNA. Michael Ashburner told that gene Adh of D. melanogaster was a pseudogene. Long found that almost all of the mutation occur at the third site of a codon. Means it may be a real gene rather than a pseudogene. Long confirmed the complex processes of the origination of this gene and named it Jingwei. 7

8. Outline  Background  Molecular mechanisms  Exon shuffling  Gene duplication  Lateral gene transfer  Gene fusion/fission  De novo gene origination  Summary 8

9. Exon shuffling Two or more exons from different genes can be brought together ectopically, often mediated by transposons, or the same exons can be duplicated to create new exon- intron structure.  Long interspersed element(LINE)  Helitron  Long-terminal repeat retrotransposons Examples: fucosyltransferase, jingwei, Tre2 Transposon: 9 Long MY, et al. Nat Rev Gent. 2003

10. Exon shuffling  Yellow-emperor  Adh: a pseudogene Origination of jingwei from the following two genes: Sphinx structure 10 Long MY, Science. 1993 Long MY, et al. Nat Rev Gent. 2003

11. Gene duplication This classical model creates a duplicate gene that can evolve new functions, whereas the ancestral copy maintain its original functions. Examples: CGβ, Cid, RNASE1B New duplicated genes under positive selection and evolve new functions Gene duplication may be three variable tpyes: Complete gene duplication, partial gene duplication and dispersed gene duplication. 11 Long MY, et al. Nat Rev Gent. 2003 Cardoso-Moreira M and Long MY. 2004

12. Gene duplication  RNASE1 and RNASE1B were generated by recent duplication from other old world monkey.  RNASE1 has not changed since duplication, while RNASE1B accumulated many substitutions.  The ability to digesting double-strand RNA of RNASE1, lost in RNASE1B 12 Zhang J, et al. Nature Genet. 2002

13. Lateral gene transfer Examples: acytylneuraminate lysase, Escherichia coli, mutU and mutS Lateral gene transfer is the gene tranferred between different organisms. Often in Prokaryotes, rare in eukaryotes. 13 Long MY, et al. Nat Rev Gent. 2003 Cardoso-Moreira M and Long MY. 2004

14. Gene fusion/fission Examples: Fatty-acid synthesis enzymes, Kua-UEV, Sdic Two adjacent genes can fuse into a single gene or a single gene can split into two single genes by mutations on stop codon or initial codon. 14 Long MY, et al. Nat Rev Gent. 2003

15. De novo origination Examples: AFGPs, BC1RNA, BC200RNA De novo genes refer to events, where a coding region originates from a previously non-coding region. 15 Long MY, et al. Nat Rev Gent. 2003 Cardoso-Moreira M and Long MY. 2004

16. Outline  Background  Molecular mechanisms  Exon shuffling  Gene duplication  Lateral gene transfer  Gene fusion/fission  De novo gene origination  Summary 16

17. 17 Long MY, et al. Nat Rev Gent. 2003