BioForum - California Academy of Sciences What makes us human? Katherine S. Pollard Gladstone Institutes, Institute for Human Genetics and Division of Biostatistics - UCSF http://docpollard.com BioForum - California Academy of Sciences October 3, 2009

Chimpanzee: Pan troglodytes Our closest living relative (MRCA ~6 million years ago) Similar Different Disease HIV-1/SIV AIDS, Alzheimer's, heart disease Anatomy Thumbs Hair, brain size Behavior Culture, tools Agriculture Language Numeracy Spoken language I was part of the international consortium that published the initial sequence and analysis of the chimp genome. This is a question that will help us understand human-specific biology and health gets at a more general question of how closely related species diverge

Leading Causes of Death Comparative Medicine Humans Chimps Dogs Heart disease Infectious disease Cancer Predation Heart failure Stroke Assault Kidney failure Leading Causes of Death Comparisons across many species will shed insight into human disease. Naturally occurring variation in disease susceptibility likely has some genetic basis. What DNA changes are responsible?

Human genome 2001 Mouse genome 2002 Chimp genome 2005

Comparison to Human Genome Chimp Mouse Overall identity 95% 28% Aligned bases 97% 40% Identity at aligned bases 99% 69% Identity in genes 85%

The Chimp Genome Project How different are our genes? ~30% of proteins are identical Average protein has 2 amino acid changes (1 per lineage) 15 genes where human disease variant is the only version in the chimp population  are we evolving away from ancestral version?

Evolution of Human Digestion Our diet has changed a lot … Cooking: tubers, other hard foods Agriculture: grains, gluten Animal husbandry: dairy, eggs, more meat Some genes have adapted Lactose tolerance (LCT gene) High starch food sources (AMY gene)  Vary between worldwide human populations Tubers, AMY1 = Nathaniel Dominy (UCSC)

Non-coding ≠ “junk DNA” ~5% of the human genome is functionally constrained and highly conserved in the mouse genome. But only ~1% codes for proteins.  Most constrained sequences are non-coding Siepel et al. 2005

Comparative Genomics 2009 Human Chimp Gorilla Old World Monkeys New World Monkeys Mouse Chicken Fish 6mya 8mya 44 vertebrates 20 genome projects 24 2x mammals 25mya 35mya 75mya ~300mya Unbiased and non-coding ~400mya

Substitution Rates Much of the DNA in eukaryotic genomes is evolving at a background (neutral) rate: Negative selection on functional elements decreases the number of substitutions: Other forces increase substitutions... Positive selection Mutation rate increase

Human Accelerated Regions HAR1: novel RNA gene Human-Chimp Differences Likelihood Ratio Test 202 Human Accelerated Regions (HARs) Altered regulation of developmental genes Human Mouse Guillemot Lab Median length 140 bp, mostly non-coding HAR1 is transcribed - did 5’ RACE and identified two transcripts on opposite strands, overlapping in 5’ ends in HAR1 RNA structure Expressed in fetal brain, low levels in adult brain, HAR1R in adult testes (no other tissues) HAR2 drives limb expression in mouse embryos - hg version has a different pattern in the forearm and hand Highly Conserved Elements HAR2: limb enhancer Rubin Lab Pollard et al. (2006) Nature, Pollard et al. (2006) PLoS Genetics

Location of HARs Mostly non-coding elements 66% intergenic 32% intronic 1.5% protein coding 0.5% UTR Nearby genes involved in transcriptional regulation, development, and disease. 11 predicted RNA genes 38 change a known TF binding site ITPR1, SPRY4, hypothetical protein NGN2 (3’ UTR) HAR170 Intron of the “speech gene” FOXP2 RNA structure Many human changes

What have we learned? Being human is not all about the brain. Proteins are nearly identical to chimp’s. We need to decipher the effects of non-coding changes, e.g. gene regulation. 99% vs. 99.9% identity  human genomes Pollard (2009) Scientific American

Collaborators University of California, Santa Cruz Gladstone Institutes, UCSF David Haussler Dennis Kostka Sofie Salama Genevieve Erwin Tim Dreszer Alisha Holloway Adam Siepel (Cornell) Joshua Ladau Jakob Pedersen (Copenhagen) Samantha Riesenfeld Thomas Sharpton University of Brussels (ULB), Belgium Alex Zambon (UCSD) Pierre Vanderhaeghen Nelle Lambert Uppsala University Marie-Alexandra Lambot Matthew Webster Sandra Coppens Jonus Berglund National Institute for Medical Research Indiana University (MRC), England Matthew Hahn Francois Guillemot Laura Galinanes-Garcia