Journal article
Using RNA sequencing for identifying gene imprinting and random monoallelic expression in human placenta
Epigenetics, Vol.9(10), pp.1397-1409
2014
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.
Details
- Title
- Using RNA sequencing for identifying gene imprinting and random monoallelic expression in human placenta
- Authors/Creators
- T. Metsalu (Author/Creator) - Czech Academy of Sciences, Institute of Computer ScienceT. Viltrop (Author/Creator) - University of TartuA. Tiirats (Author/Creator) - University of TartuB. Rajashekar (Author/Creator) - University of TartuE. Reimann (Author/Creator) - University of TartuS. Kõks (Author/Creator) - University of TartuK. Rull (Author/Creator) - Tartu University HospitalL. Milani (Author/Creator) - University of TartuG. Acharya (Author/Creator)P. Basnet (Author/Creator) - UiT The Arctic University of NorwayJ. Vilo (Author/Creator) - University of TartuR. Magi (Author/Creator) - University of TartuA. Metspalu (Author/Creator) - University of TartuM. Peters (Author/Creator) - University of TartuK. Haller-Kikkatalo (Author/Creator) - University of TartuA. Salumets (Author/Creator) - University of Tartu
- Publication Details
- Epigenetics, Vol.9(10), pp.1397-1409
- Publisher
- Taylor & Francis
- Identifiers
- 991005540602907891
- Copyright
- © 2014 Taylor & Francis Group, LLC
- Murdoch Affiliation
- Murdoch University
- Language
- English
- Resource Type
- Journal article
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- Collaboration types
- Domestic collaboration
- International collaboration
- Citation topics
- 1 Clinical & Life Sciences
- 1.186 Chromosome Disorders
- 1.186.1533 Genomic Imprinting
- Web Of Science research areas
- Biochemistry & Molecular Biology
- Genetics & Heredity
- ESI research areas
- Molecular Biology & Genetics