Quantifying Gene Gain and Loss in Mammals

Michael Eisen, University of California, Berkeley Identifying the genomic regions bound by sequence specific regulatory factors is central both to deciphering the complex DNA cis-regulatory code that controls transcription in metazoans and to determining the range of genes that shape animal morphogenesis. We have used whole-genome tiling arrays to map sequences bound in Drosophila melanogaster embryos by the six maternal and gap transcription factors that initiate anteriorposterior patterning. We find that these sequence-specific DNA binding proteins bind with quantitatively different specificities to an overlapping set of several thousand genomic regions in blastoderm embryos. The more highly-bound regions include all of the over forty well-characterized enhancers known to respond to these factors as well as several hundred putative new cis -regulatory modules clustered near developmental regulators and other genes with patterned expression at this stage of embryogenesis. In addition to these highly-bound regions, there are several thousand regions that are reproducibly bound at lower levels. However, these poorly-bound regions are, collectively, far more distant from genes transcribed in the blastoderm than highly-bound regions and are preferentially found in proteincoding sequences. We have extensively analyzed the evolution of recognition sequences in these bound regions and find little evidence for their preferential conservation. Together these observations suggest that many of these poorly-bound regions are not involved in early-embryonic transcriptional regulation and may be non-functional. I will propose that the pervasive view amongst both experimental and computational biologists that most protein-DNA interactions observed in vivo are functional is wrong. Quantifying Gene Gain and Loss in Mammals Matthew Hahn, Indiana University Newly duplicated genes have one of two eventual fates: loss or maintenance by natural selection. Though loss is considered to be the much more likely outcome, the evolutionary modes by which duplicates are maintained have attracted much more theoretical and empirical attention. In this talk I address both of these outcomes. Using the genomes of multiple mammalian species, we are able quantify the amount of gene gain and loss and ask whether natural selection has played a role in these changes. We have developed a novel method that allows estimation of rate heterogeneity in gain and loss among lineages; using this method we find that the rate of gene turnover in primates is more than 2.5X faster than in other mammals and may be due to both mutational and selective forces. By reconciling the gene trees for all of the gene families included in the analysis, we are able to independently verify the numbers of inferred duplications. We also use two methods based on the genome assembly of rhesus macaque to further verify our results. Our analyses identify several gene families that have expanded or contracted more rapidly than is expected even after accounting for an overall rate acceleration in primates, including brain-related families that have more than doubled in size in humans. Looking only at duplicates specific to the human lineage, we identify genes that have undergone adaptive natural selection since our split with chimpanzees. We also examine the frequency of gene loss in these lineages, both among duplicate genes and single-copy genes. Gene loss occurs at high rates in all species, though we are able to demonstrate selection against the loss of single-copy genes. Multiple Genetic Differences in Sialic Acid Biology Between Humans and Great Apes Ajit Varki, University of California, San Diego As “nothing in biology makes sense, except in the light of evolution” (Dobzhansky 1973), it follows that understanding human evolution will shed much light on the origins, mechanisms and therapy of human disease. One powerful approach to human evolution is the genetic one. When comparing individual protein sequences, humans are remarkably similar to the “great apes”, (chimpanzees, bonobos, gorillas and orangutans), our closest evolutionary relatives. Indeed, studies of these relationships have resulted in a reclassification of the entire clade as “hominids”, a term previously reserved for humans and their fossil ancestors. Despite these similarities, there are remarkable differences between humans and “great apes” in the incidence and severity of many major diseases, and some of these differences should have genetic explanations. We have discovered multiple genetic and biochemical differences between humans and great apes, in relation to cell surface sugars called Sialic acids (Sias) and in a family of receptors called Siglecs (Sia-recognizing Ig superfamily lectins). One major kind of Sia called Neu5Gc is widely expressed in mammals including great apes, but not in humans. This dramatic change in the human “sialome” resulted from an inactivating mutation in the human CMAH gene, mediated by an Alu replacement ~3 million years ago. This apparently set in motion a series of additional human-specific changes in Sia biology have so far been found to affect >10 genes. In particular, we find multiple human-specific differences in a family of molecules called the Siglecs (Sialic Acid-recognizing Immunoglobulin Family Lectins). Since <60 genes are involved overall in synthesis, recognition and turnover of Sias, these changes are likely related to one another in evolutionary history and potentially significant for human evolution, biology and disease. Indeed, there are implications for unique features of the human phenotype, ranging from susceptibility or resistance to some microbial pathogens; effects on the reactivity of the immune system; unusual aspects of human parturition, and the expression of Neu5Gc as a “foreign” antigen in cancers. Neu5Gc can also be metabolically incorporated from animal-derived culture materials and feeder layers into biotherapeutic molecules and cellular preparations and into intact humans from dietary sources, particularly red meat and milk products. Meanwhile, all humans have significant levels of circulating antibodies directed against Neu5Gc-containing epitopes. This has implications for human reactions to biotechnology products, and also for comC O M P A R A T I V E