Current Topics in

Evolutionary Genomics

Wen-Hsiung Li and Justin Borevitz

Potential Topics:

 I. Evolution of Gene Expression

  II. Evolution of transcriptional regulatory code

 III. Evolution of regulatory networks

 IV. Evolution of new and duplicate genes

  V. Protein Protein interactions

 VI. Genetic variation within and between species

VII. Effects of recombination and gene conversion

on GC content and substitution rate

 I. Evolution of Gene Expression

Examine how gene expression has diverged between species (or between duplicate genes). A study may examine only changes in expression but not changes in regulatory sequences.

There have been many studies on this topic.

 

 II. Evolution of transcriptional regulatory code

Regulatory code of a gene:

(1) Regulatory sequences of the gene, especially the cis elements.

(2) Combinatorial rules of the cis elements.

 

MFA2TFTFTF

Ndd1/Fkh1 Mcm1 Swi5

2( )MFAY t

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MFA2

RealEst.

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MFA2

)(1 tg )(2 tg )(3 tg

)(2,1 tg)(3,2 tg

)(3,1 tg

)(:)(

)(:)()(:)(

)(:)()(:)(

)(:)()(:)(

5,13,2

5,1,1/13,2,15,1/13,1

1,1/12,112

531/11

tgtg

tgtgtgtg

tgtgtgtg

tgtgtgtg

SwiMcm

SwiMcmFkhNddSwiFkhNdd

McmFkhNddMcm

SwiFkhNdd

)(3,2,1 tg

CisCis-regulatory circuit of -regulatory circuit of MFA2MFA2

a cell cycle genea cell cycle gene

 II. Evolution of transcriptional regulatory code

• This topic may include evolution of regulatory sequences and also methods for inferring transcription factor binding sites (TFBSs).

• It is a fairly new topic but is receiving a great deal of attention.

 

 III. Evolution of regulatory networks

A regulatory or gene network (module):

What are the genes in a regulatory pathway?

Which are the upstream genes and which are the downstream genes?

Under what conditions is the regulatory network on? 

 III. Evolution of regulatory networks

• This is a new topic and, to my knowledge, not much progress has been made yet because few regulatory modules are known for certain.

• It has a great future because it is new and because it is complex.

 

Other Potential Topics:

IV. Evolution of duplicate genes

  V. Emergence of new genes

 VI. Genetic variation within and between

species

VII. Effects of recombination and gene

conversion on GC content and

substitution rate

How the class should be organized and conducted?

• Meet once a week for 2 to 2 1/2 hours?

• Select papers for each class: Open to suggestions. Look for new developments.

• In each class two persons present materials on two related topics for discussion (not much detail).

• Every participant should read the papers and participate in discussion.

How the class should be organized and conducted?

• 

Assignments of Topics:

 I. Evolution of Gene Expression

 JJ, Megan

II. Evolution of transcriptional regulatory code

Geoff, Shinhan

 III. Evolution of regulatory networks

 Josh, Elliot

IV. Evolution of duplicate and new genes

 Sidi, Jun

Assignments of Topics:

V. Protein Protein Interactions

 Josh, Ying

VI. Genetic variation within and between species

David, Julie

VII. Effects of recombination and gene conversion

on GC content and substitution rate

Loic, Roman

 I. Evolution of Gene Expression

Brem, R.B., Yvert, G., Clinton, R. & Kruglyak, L. Science 296, 752-755 (2002). Genetic dissection of transcriptional regulation in budding yeast. Science 296(5568):752-5.

Yvert G, Brem RB, Whittle J, Akey JM, Foss E, Smith EN, Mackelprang R, Kruglyak L.

Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors. Nat Genet. 2003 Sep;35(1):57-64.

Rifkin SA, Kim J, White KP. Evolution of gene expression in the Drosophila melanogaster subgroup. Nat. Genet. 33, 138-144 (2003).

Meiklejohn CD, Parsch J, Ranz JM, Hartl DL. Rapid evolution of male-biased gene expression in Drosophila. Proc Natl Acad Sci U S A. 100:9894-9 (2003).

Ranz JM, Castillo-Davis CI, Meiklejohn CD, Hartl DL. Sex-dependent gene expression and evolution of the Drosophila transcriptome. Science. 2003 Jun 13;300(5626):1742-5.