title: Using RNA sequencing for identifying gene imprinting and random monoallelic expression in human placenta.
abstract: Given the possible critical importance of placental gene imprinting and random monoallelic expression on fetal and infant health, most of those genes must be identified, in order to understand the risks that the baby might meet during pregnancy and after birth. Therefore, the aim of the current study was to introduce a workflow and tools for analyzing imprinted and random monoallelic gene expression in human placenta, by applying whole-transcriptome (WT) RNA sequencing of placental tissue and genotyping of coding DNA variants in family trios. Ten family trios, each with a healthy spontaneous single-term pregnancy, were recruited. Total RNA was extracted for WT analysis, providing the full sequence information for the placental transcriptome. Parental and child blood DNA genotypes were analyzed by exome SNP genotyping microarrays, mapping the inheritance and estimating the abundance of parental expressed alleles. Imprinted genes showed consistent expression from either parental allele, as demonstrated by the SNP content of sequenced transcripts, while monoallelically expressed genes had random activity of parental alleles. We revealed 4 novel possible imprinted genes (LGALS8, LGALS14, PAPPA2 and SPTLC3) and confirmed the imprinting of 4 genes (AIM1, PEG10, RHOBTB3 and ZFAT-AS1) in human placenta. The major finding was the identification of 4 genes (ABP1, BCLAF1, IFI30 and ZFAT) with random allelic bias, expressing one of the parental alleles preferentially. The main functions of the imprinted and monoallelically expressed genes included: i) mediating cellular apoptosis and tissue development; ii) regulating inflammation and immune system; iii) facilitating metabolic processes; and iv) regulating cell cycle.
authors.affiliation: a Institute of Computer Science ; University of Tartu ; Tartu , Estonia.
authors.forename: Tauno
authors.initials: T
authors.lastname: Metsalu
authors.forename: Triin
authors.initials: T
authors.lastname: Viltrop
authors.forename: Airi
authors.initials: A
authors.lastname: Tiirats
authors.forename: Balaji
authors.initials: B
authors.lastname: Rajashekar
authors.forename: Ene
authors.initials: E
authors.lastname: Reimann
authors.forename: Sulev
authors.initials: S
authors.lastname: Kõks
authors.forename: Kristiina
authors.initials: K
authors.lastname: Rull
authors.forename: Lili
authors.initials: L
authors.lastname: Milani
authors.forename: Ganesh
authors.initials: G
authors.lastname: Acharya
authors.forename: Purusotam
authors.initials: P
authors.lastname: Basnet
authors.forename: Jaak
authors.initials: J
authors.lastname: Vilo
authors.forename: Reedik
authors.initials: R
authors.lastname: Mägi
authors.forename: Andres
authors.initials: A
authors.lastname: Metspalu
authors.forename: Maire
authors.initials: M
authors.lastname: Peters
authors.forename: Kadri
authors.initials: K
authors.lastname: Haller-Kikkatalo
authors.forename: Andres
authors.initials: A
authors.lastname: Salumets
mesh_terms: D000328:Adult; D000483:Alleles; D005260:Female; D015870:Gene Expression; D020869:Gene Expression Profiling; D018392:Genomic Imprinting; D005838:Genotype; D006801:Humans; D008297:Male; D010920:Placenta / Q000378:metabolism*; D020641:Polymorphism, Single Nucleotide; D011247:Pregnancy; D017423:Sequence Analysis, RNA; D055815:Young Adult
keywords: ASE, allele-specific expression; FDR, false discovery rate; GEO, Gene Expression Omnibus; IUGR, intrauterine growth restriction; MAF, minor allele frequency; MHC, major histocompatibility complex; NK cells, natural killer cells; RNA sequencing; RNA-Seq, RNA-sequencing; RPKM, reads per kilobase per million; UCSC, University of California Santa Cruz; WT, whole-transcriptome; allele-specific expression; imprinting; placenta; random monoallelic expression; short read mapping