In silico analysis of the X-chromosome epigenetic state in human pre-implantation embryos

• Grant number: 15/03610-0
• Support type: Scholarships in Brazil - Post-Doctorate
• Effective date (Start): October 01, 2015
• Effective date (End): March 31, 2019
• Field of knowledge: Biological Sciences - Genetics
• Principal researcher: Maria Dulcetti Vibranovski
• Grantee: Joana Carvalho Moreira de Mello
• Home Institution: Instituto de Biociências (IB). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• Associated scholarship(s): 17/23243-7 - Unraveling the role of RNF12 and REX1 in the initiation of human X chromosome inactivation., BE.EP.PD

Abstract

X-chromosome inactivation (XCI) is an epigenetic phenomenon observed in female mammals cells to ensure transcriptional dosage compensation of X-linked genes between males (XY) and females (XX). Most processes and steps involved in XCI in mice are well studied, however, in humans our knowledge is still very limited, especially during early embryo development. Advances in single-cell whole transcriptome high throughput sequencing techniques (scRNA-Seq) open a new era to the XCI field. scRNA-Seq results from all stages of human pre-implantation embryo development were published by Xue et cols and Yan et cols in 2013. From those data, using bioinformatics techniques, I have previously found that the XIST gene (closely involved in XCI) is first detected at the 8-cell stage of human development in both female and male embryos. At the blastocyst stage, XIST expression is stabilized and up regulated in females where X-linked genes are beginning to be silenced. The project aim is to verify whether the increased expression of XIST gene in human embryos from 8-cell stage already triggers the transcriptional silencing of X-linked genes and whether the X inactivation process is random or imprinted. For this purpose, we will determine in which phase of human embryo development X-linked genes begin to be silenced; the parental origin of the inactive X and of the genes involved in the XCI process; the extension of the X-linked gene transcriptional silencing in the different pre-implantation stages. X-linked SNPs located in transcribed gene regions will work as tools for biallelic and monoallelic expression pattern detection as well as parental origin identification of the expressed allele. These SNPs will be used to construct haplotypes to identify if the expression of several genes along the X originates from the same homolog (reflecting the presence of an already inactivated X) or not (reflecting the presence of two active X). In addition, to help determine the X inactive state of each independent cell in all developmental phases, transcriptional level of X-linked genes will be analyzed to verify the spreading of the transcriptional silencing signal and the inactivation synchrony of cells within each embryo. Therefore it will be possible to determine the exact moment where XCI begins in humans. For this purpose existing bioinformatics techniques will be adapted for that suit to study scRNA-Seq and employed statistical analysis for data validation resulting in basic knowledge about the beginning of human development.

Scientific publications

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

MOREIRA DE MELLO, JOANA C.; FERNANDES, GUSTAVO R.; VIBRANOVSKI, MARIA D.; PEREIRA, LYGIA V. Early X chromosome inactivation during human preimplantation development revealed by single-cell RNA-sequencing. SCIENTIFIC REPORTS, v. 7, SEP 7 2017. Web of Science Citations: 21.

HE, NANNAN; LIM, SHUJING J.; MOREIRA DE MELLO, JOANA C.; NAVARRO, INJERREAU; BIALECKA, MONIKA; SALVATORI, DANIELA C. F.; VAN DER WESTERLAKEN, LUCETTE A. J.; PEREIRA, LYGIA V.; LOPES, SUSANA M. CHUVA DE SOUSA. At Term, XmO and XpO Mouse Placentas Show Differences in Glucose Metabolism in the Trophectoderm-Derived Outer Zone. FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY, v. 5, 2017. Web of Science Citations: 1.