Primate-specific evolution of noncoding element insertion into PLA2G4C and human preterm birth The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Plunkett, Jevon et al. “Primate-specific Evolution of Noncoding Element Insertion into PLA2G4C and Human Preterm Birth.” BMC Medical Genomics 3.1 (2010): 62. Web. 1 Mar. 2012. As Published http://dx.doi.org/10.1186/1755-8794-3-62 Publisher Springer (Biomed Central Ltd.) Version Final published version Citable link http://hdl.handle.net/1721.1/69548 Terms of Use Creative Commons Attribution Detailed Terms http://creativecommons.org/licenses/by/2.0 Plunkett et al. BMC Medical Genomics 2010, 3:62 http://www.biomedcentral.com/1755-8794/3/62 RESEARCH ARTICLE Open Access Primate-specific evolution of noncoding element insertion into PLA2G4C and human preterm birth Jevon Plunkett1,2, Scott Doniger3, Thomas Morgan1,4, Ritva Haataja5, Mikko Hallman5, Hilkka Puttonen6, Ramkumar Menon7,8, Edward Kuczynski9, Errol Norwitz9, Victoria Snegovskikh9, Aarno Palotie10,11,12,13, Leena Peltonen10,11,12, Vineta Fellman14,15, Emily A DeFranco16, Bimal P Chaudhari17, John Oates18, Olivier Boutaud18, Tracy L McGregor1, Jude J McElroy1, Kari Teramo6, Ingrid Borecki19, Justin C Fay20, Louis J Muglia1,21* Abstract Background: The onset of birth in humans, like other apes, differs from non-primate mammals in its endocrine physiology. We hypothesize that higher primate-specific gene evolution may lead to these differences and target genes involved in human preterm birth, an area of global health significance. Methods: We performed a comparative genomics screen of highly conserved noncoding elements and identified PLA2G4C, a phospholipase A isoform involved in prostaglandin biosynthesis as human accelerated. To examine whether this gene demonstrating primate-specific evolution was associated with birth timing, we genotyped and analyzed 8 common single nucleotide polymorphisms (SNPs) in PLA2G4C in US Hispanic (n = 73 preterm, 292 control), US White (n = 147 preterm, 157 control) and US Black (n = 79 preterm, 166 control) mothers. Results: Detailed structural and phylogenic analysis of PLA2G4C suggested a short genomic element within the gene duplicated from a paralogous highly conserved element on chromosome 1 specifically in primates. SNPs rs8110925 and rs2307276 in US Hispanics and rs11564620 in US Whites were significant after correcting for multiple tests (p < 0.006). Additionally, rs11564620 (Thr360Pro) was associated with increased metabolite levels of the prostaglandin thromboxane in healthy individuals (p = 0.02), suggesting this variant may affect PLA2G4C activity. Conclusions: Our findings suggest that variation in PLA2G4C may influence preterm birth risk by increasing levels of prostaglandins, which are known to regulate labor. Background signal does not seem to precede human labor [3]. Other A growing body of evidence supports genetic influences parturition-related traits, such as placental morphology on preterm birth risk; however, few genes have been and source of progesterone, also differ importantly in consistently associated with the disorder [1,2]. Investiga- humans compared to model organisms typically studied tors have typically focused on candidate genes selected and may limit what generalizations can be made [3]. based on predicted parturition physiology; however, this Differences in parturition physiology between apes, approach may be limited by the divergence in physiolo- including humans, and other mammals may have devel- gical mechanisms between humans and model organ- oped in response to uniquely human adaptations includ- isms that have been typically studied. For example, ing relatively large human head size and narrow birth while a rapid decline in progesterone plays a prominent canal cross-sectional area [4]. Genes involved in parturi- role in initiating parturition in rodents and sheep, this tion likely have evolved differentially along the human and/or higher primate phylogenetic lineages to decrease the length of gestation and alleviate the complications * Correspondence: [email protected] 1Department of Pediatrics, Vanderbilt University School of Medicine, arising from such cephalopelvic constraints. As a result, Nashville, TN 37232, USA the set of genes rapidly evolving on the human and/or Full list of author information is available at the end of the article © 2010 Plunkett et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Plunkett et al. BMC Medical Genomics 2010, 3:62 Page 2 of 9 http://www.biomedcentral.com/1755-8794/3/62 higher primate lineage likely includes genes that play conserved noncoding element in intron 14 of PLA2G4C, important roles in regulating parturition and potentially located on chromosome 19q13.3, which strongly sug- influence preterm birth risk. Consistent with our gested the gene’s designation as rapidly evolving along hypothesis, we identified FSHR as having rapidly evolved the human lineage, in comparison to other mammalian by nucleotide substitution and as being associated with and primate genomes. From such comparisons, we preterm birth risk across independent populations ([5] determined that this 130 bp element on human chromo- and (Plunkett J, Doniger S, Orabona G, Morgan T, some 19 was highly similar to a highly conserved non- Haataja R, Hallman M, Puttonen H, Menon R, coding element on human chromosome 1 (BLASTN Kuczynski E, Norwitz E et al: Evolutionary history of 114/130 bp identical (87%), BLAST Expect value (i.e. FSHR in human predicts role in birth time, submitted)). number of matches of this similarity likely to occur by In addition to nucleotide substitution, genomic rear- chance alone) = 5x10-38; Figure 1B). Subsequent analysis rangements account for a substantial portion of genomic showed that the MultiZ alignments that we used in our divergence among species. For example, Frazer et al. [6] comparative genomics screen had misaligned the human and Wetterbom et al. [7] observed insertions and dele- chromosome 19 element with sequences in other mam- tions frequently when comparing genome sequences mals which were orthologous to human chromosome 1. among humans, chimpanzees and other primate species. When appropriate alignments were examined, we Moreover, such rearrangements may account for a lar- observed that the human chromosome 19 element was ger fraction of genomic divergence than nucleotide sub- nearly identical in higher primate species (chimpanzee, stitutions [7]. Rearrangements can lead to loss or gorilla, orangutan, macaque) examined, but absent in acquisition of exons, splice sites and promoters, facilitat- syntenic sequences in lower primates (lemur, bushbaby, ing differences in expression patterns, such as those tarsier) and other mammalian species. Chromosome 1 observed for transcript variants of CHRM3 and SFTPB elements from higher primates are more similar to with differing transposable element insertion events lower primates and other mammalian species than chro- [8,9]. Hence, genomic rearrangement may contribute to mosome 19 elements (Figure 2). The chromosome 1 ele- rapid evolution along the human and/or higher primate ment occurs in the 5’ untranslated region of RNF11,a lineages in response to unique physiological constraints. gene involved in inflammatory signaling (UniProt KB) in We hypothesized that genes with genomic rearrange- mouse. Thus, a duplication of chromosome 1 noncoding ments departing from the ancestral state and occurring on element to chromosome 19 likely occurred before the the human and/or higher primate lineages may play last common ancestor between apes and macaque. A important roles in birth timing and preterm delivery. phylogenetic tree of coding sequences for PLA2G4C fol- Thus, we investigated association with preterm birth for lows the expected mammalian phylogeny (Figure 3), common variants in a gene, PLA2G4C, which is expressed suggesting that the duplication did not include coding in the uterus [10] and involved in prostaglandin synthesis, sequences. Together these results suggest that neither suggesting a potential role in parturition, and in which we element would qualify as rapidly evolving along the have identified a primate-specific insertion. human lineage due to nucleotide substitution, but the chromosome 19 element may represent a primate-speci- Results fic change meriting further study. Evolutionary history of a primate-specific PLA2G4C noncoding element Association with preterm birth We identified genes showing evidence of rapid evolution Having identified PLA2G4C as a candidate gene for regu- along the human lineage, based on evidence from a lation of parturition timing, we tested variants in this comparative genomic screen of highly conserved non- gene for association with preterm birth in a case-control coding elements as previously described [5]. Among the study involving diverse clinical populations. Because of rapidly evolving genes emerging from our noncoding recent data suggesting that heritability of preterm birth screen, PLA2G4C was identified as the most statistically risk acts largely or exclusively through the maternal gen- significant human-lineage accelerated gene (p = 2.2 × ome [14-16], we genotyped US Hispanic (73 preterm,