AbstractThe placenta is formed after the first few weeks of pregnancy and is the genotype of the fetus. It acts as an immune modulator in the uterine environment to sustain a successful pregnancy. One of the X chromosomes in XX females is silenced by a process called X-inactivation. Prior research suggests that incorrect dosage on the X chromosome could lead to poor development of the placenta and ultimately result in complications in pregnancy. Previous studies of X- inactivation in the placenta were either in non-human placentas, or were limited to only a few SNPs and genes in human placentas. Thus, it is not clear whether within human placenta, X- inactivation is completely homogeneous, patchy, or mosaic. Further, X-inactivation is not complete in humans; as many as one-third of the genes on the X chromosome escape X- inactivation, but variability in genes that escape X-inactivation in the placenta has not been investigated. We sequenced RNA from 60 placenta samples from 30 full-term, uncomplicated pregnancies with female offspring. We can confidently rule out X-inactivation being completely mosaic in the human placenta. Rather, we find strong evidence that X-inactivation in the human placenta is patchy, with large potential clonal expansions of either silenced maternal or paternal X-chromosomes, with provocative suggestions of bias towards silencing the paternal X. We also find variation in the degree of silencing, where a high portion of variants (between 26.8-75.3% in any sample) are silenced incompletely. Finally, we find evidence for variability in genes that escape X-inactivation within and among placenta samples.SignificanceThe placenta is formed early during development, is essential for healthy pregnancy, and is largely composed of DNA from the offspring, and thus can be XX or XY. One of the X chromosomes in XX females is silenced by a process called X-inactivation. We studied patterns of X-inactivation in two regions of the placenta across 30 placentas, and find strong evidence for large patches of either maternally or paternally silenced X-chromosomes in the human placenta. We also found that the genes that escape X-inactivation vary both across individuals, and within the placenta of a single individual, suggesting mechanisms for variability in placenta function, and implications for prenatal testing that samples only a single region of the placenta.