Allele-specific expression analysis reveals conserved and unique features of preimplantation development in equine ICSI embryos

2021 ◽  
Author(s):  
D E Goszczynski ◽  
P S Tinetti ◽  
Y H Choi ◽  
P J Ross ◽  
K Hinrichs
Keyword(s):  
Gene Expression ◽  
Early Development ◽  
X Chromosome ◽  
Dosage Compensation ◽  
Blastocyst Stage ◽  
X Chromosome Inactivation ◽  
Specific Gene ◽  
Cell Stage ◽  
Specific Gene Expression ◽  
Genome Activation

Abstract Embryonic genome activation and dosage compensation are major genetic events in early development. Combined analysis of single embryo RNA-seq data and parental genome sequencing was used to evaluate parental contributions to early development and investigate X-chromosome dynamics. In addition, we evaluated dimorphism in gene expression between male and female embryos. Evaluation of parent-specific gene expression revealed a minor increase in paternal expression at the 4-cell stage that increased at the 8-cell stage. We also detected eight genes with allelic expression bias that may have an important role in early development, notably NANOGNB. The main actor in X-chromosome inactivation, XIST, was significantly upregulated at the 8-cell, morula, and blastocyst stages in female embryos, with high expression at the latter. Sexual dimorphism in gene expression was identified at all stages, with strong representation of the X-chromosome in females from the 16-cell to the blastocyst stage. Female embryos showed biparental X-chromosome expression at all stages after the 4-cell stage, demonstrating the absence of imprinted X-inactivation at the embryo level. The analysis of gene dosage showed incomplete dosage compensation (0.5 < X:A < 1) in MII oocytes and embryos up to the 4-cell stage, an increase of the X:A ratio at the 16-cell and morula stages after genome activation, and a decrease of the X:A ratio at the blastocyst stage, which might be associated with the beginning of X-chromosome inactivation. This study represents the first critical analysis of parent- and sex-specific gene expression in early equine embryos produced in vitro.

139 SEX-SPECIFIC GENE EXPRESSION IN PORCINE PRE-IMPLANTATION EMBRYOS

2016 ◽  
Vol 28 (2) ◽  
pp. 199
Author(s):  
D. Kradolfer ◽  
J. Knubben ◽  
V. Flöter ◽  
J. Bick ◽  
S. Bauersachs ◽  
...  
Keyword(s):  
Gene Expression ◽  
X Chromosome ◽  
Current Knowledge ◽  
Critical Time ◽  
Blastocyst Stage ◽  
X Chromosome Inactivation ◽  
Chromosome Inactivation ◽  
Specific Gene ◽  
Embryo Survival ◽  
Specific Gene Expression

X-Chromosome inactivation in female mammals starts during early blastocyst stage with expression of the X-inactive specific transcript (XIST), which coats and silences the inactive X chromosome. However, this compensation is not complete in blastocysts, as a large number of X-linked transcripts are more highly expressed in female embryos than in males. Furthermore, the process of X chromosome inactivation is altered in IVF and cloned porcine embryos, possibly explaining problems of embryo survival with these techniques. The aim of this study was to gain more insights into the transcriptional dynamics of the porcine pre-implantation embryo, with a particular focus on sex-specific differences. RNA sequencing (RNA-Seq) was performed for individual blastocysts at 8, 10, and 12 days after ovulation, and the temporal development of sex-specific transcripts was analysed. German Landrace sows were cycle synchronized and inseminated with sperm of the same Pietrain boar. On Days 8, 10, and 12 post-insemination, sows were slaughtered and embryos were removed from the uterus using 10 mL of PBS (pH 7.4) per horn. Single embryos were shock frozen in liquid nitrogen and stored at –80°C until the extraction of RNA and DNA (AllPrep DNA/RNA Micro Kit, Qiagen, Valencia, CA, USA). Using the isolated DNA, the sex of the embryos was determined and 5 female and male embryos, respectively, were analysed per stage. Illumina TruSeq Stranded mRNA libraries (Illumina Inc., San Diego, CA, USA) were sequenced on a HiSEqn 2500 (Illumina Inc.), and 15 to 25 million 100-bp single-end reads were generated per sample. Reads were filtered and processed using Trimmomatic and mapped to the porcine genome assembly Sscrofa10.2 with TopHat2. Mapped reads were counted by the use of QuasR qCount based on the current National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/) GFF3 annotation file. Statistical analysis of count data was performed with the BioConductor R (https://www.bioconductor.org/) package DESEqn 2. At all 3 stages, we found 7 Y-linked transcripts that were highly expressed in male embryos (EIF2S3, EIF1AY, LOC100624590, LOC100625207, LOC100624329, LOC102162178, LOC100624937). On the other hand, 47 X-linked transcripts showed increased expression in female blastocysts, most of them at all 3 time points. However, a small number of genes (DDX3X, LAMP2, and RPS6KA3) were more highly expressed in females at Days 8 and 10 but more highly expressed in males at Day 12. Three X-linked genes (OFD1, KAL1, and LOC100525092) were more highly expressed in male embryos, although only at a low fold change of 1.2 to 1.4. Furthermore, expression of 8 transcripts located on autosomes was higher in females. In conclusion, our study expands the current knowledge of sex-specific gene expression in 8- to 12-day-old porcine blastocysts, a critical time period during pre-implantation embryo development.

scholarly journals Random X Inactivation and Extensive Mosaicism in Human Placenta Revealed by Analysis of Allele-Specific Gene Expression along the X Chromosome

PLoS ONE ◽  
2010 ◽  
Vol 5 (6) ◽  
pp. e10947 ◽  
Author(s):  
Joana Carvalho Moreira de Mello ◽  
Érica Sara Souza de Araújo ◽  
Raquel Stabellini ◽  
Ana Maria Fraga ◽  
Jorge Estefano Santana de Souza ◽  
...  
Keyword(s):  
Gene Expression ◽  
X Chromosome ◽  
Human Placenta ◽  
X Inactivation ◽  
Specific Gene ◽  
Specific Gene Expression ◽  
Allele Specific

scholarly journals Diverse developmental strategies of X chromosome dosage compensation in eutherian mammals

2019 ◽  
Vol 63 (3-4-5) ◽  
pp. 223-233 ◽  
Author(s):  
Alexander I. Shevchenko ◽  
Elena V. Dementyeva ◽  
Irina S. Zakharova ◽  
Suren M. Zakian
Keyword(s):  
Gene Expression ◽  
X Chromosome ◽  
Dosage Compensation ◽  
Mammalian Species ◽  
X Chromosome Inactivation ◽  
Chromosome Inactivation ◽  
Autosomal Gene ◽  
Mammalian Development ◽  
Compensation Mechanisms ◽  
Early Mammalian Development

In eutherian mammals, dosage compensation arose to balance X-linked gene expression between sexes and relatively to autosomal gene expression in the evolution of sex chromosomes. Dosage compensation occurs in early mammalian development and comprises X chromosome upregulation and inactivation that are tightly coordinated epigenetic processes. Despite a uniform principle of dosage compensation, mechanisms of X chromosome inactivation and upregulation demonstrate a significant variability depending on sex, developmental stage, cell type, individual, and mammalian species. The review focuses on relationships between X chromosome inactivation and upregulation in mammalian early development.

127 REGULATION OF H3K27me3 AND H3K4me3 DURING INITIAL PORCINE EMBRYONIC DEVELOPMENT

2010 ◽  
Vol 22 (1) ◽  
pp. 222
Author(s):  
Y. Gao ◽  
V. Hall ◽  
P. Hyttel
Keyword(s):  
Gene Expression ◽  
Embryonic Development ◽  
Histone Methylation ◽  
Blastocyst Stage ◽  
Limb Bud ◽  
High Expression ◽  
Cell Stage ◽  
Stage Of Development ◽  
Low Levels ◽  
Genome Activation

During mammalian development, gene expression is partly regulated by posttranslational modifications of histones. In particular, H3K27me3 and H3K4me3 are involved in transcriptional repression and activation, respectively. In this study, we examined the global levels of H3K27me3 and H3K4me3, as well as the expression levels of their specific methylases and demethylases during porcine pre-implantation embryonic development. Global histone methylation was analyzed by immunocytochemical quantification within in vivo porcine embryos at 1-cell (Day 1), 4-cell (Day 3), morula (Day 5), and late blastocyst (containing the epiblast; Day 9). The numbers of embryos analyzed for H3K27me3 at the 1-cell, 4-cell, morula, and late blastocyst stage were 7, 8, 6, and 5, respectively, and for H3K4me3 at these four stages were 7, 6, 6, and 5, respectively. At the same developmental stages, mRNA expression of methylases (EZH2, EED, and SUZ12, three core components of PRC2) and demethylases (JMJD3 and UTX) of H3K27me3 was performed on pooled embryos (n = 10), as well as expression of methylases (MLL1 and ASH1L) and demethylase (RBP2) of H3K4me3, by comparative RT-PCR. Expression was compared with pooled embryos from the limb bud stage (Day 21). GAPDH was used as the reference gene, and expression was normalized to Day 21 embryos. Our results show that the levels of global histone methylation of H3K27me3 and H3K4me3 decrease gradually from 1-cell to morula, but both were increased in late blastocysts. The levels of H3K27me3 methylase (EZH2, EED, and SUZ12) transcripts increased from 1-cell to late blastocyst stage. Low expression of the H3K27me3 demethylase JMJD3 was found at 1-cell stage and high expression at the 4-cell stage from when it decreased gradually to the late blastocyst. UTX expression was low but peaked at the 4-cell stage. Expression of H3K4me3 methylase MLL1, was low, whereas ASH1L expression was high at the 4-cell stage. RBP2, a demethylase of H3K4me3, was highly expressed at the late blastocyst stage. In conclusion, at the major genome activation (the 4-cell stage), H3K27me3 and H3K4me3 have decreased to moderate levels, which apparently balance each other with respect to gene repression and activation allowing for genome activation. At the 4-cell stage the activation of H3K4me3 is favored as a consequence of low levels of H3K27 methylases and high levels of H3K27 demethylases combined with high levels of H3K4 methylases and low levels of H3K4 demethylases. Interestingly, at the late blastocyst stage of development, high expression of H3K27me3 methylases and the H3K4me3 demethylase, RBP2, are observed, indicating repression of gene expression, which is counterintuitive to accelerating development. We speculate other factors, such as microRNA or other kinds of epigenetic mechanisms, might play a critical role at this developmental stage. Thus, further research is required to explain these phenomena occurred during early porcine development.

scholarly journals Spen links RNA-mediated endogenous retrovirus silencing and X chromosome inactivation

2019 ◽  
Author(s):  
Ava C. Carter ◽  
Jin Xu ◽  
Meagan Y. Nakamoto ◽  
Yuning Wei ◽  
Quanming Shi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Silencing ◽  
X Chromosome ◽  
Dosage Compensation ◽  
Sex Chromosome ◽  
Embryonic Stem ◽  
X Chromosome Inactivation ◽  
Chromosome Inactivation ◽  
Rna Domains ◽  
In Cis

Dosage compensation between the sexes has emerged independently multiple times during evolution, often harnessing long noncoding RNAs (lncRNAs) to alter gene expression on the sex chromosomes. In eutherian mammals, X chromosome inactivation (XCI) in females proceeds via the lncRNA Xist, which coats one of the two X chromosomes and recruits repressive proteins to epigenetically silence gene expression in cis1,2. How Xist evolved new functional RNA domains to recruit ancient, pleiotropic protein partners is of great interest. Here we show that Spen, an Xist-binding repressor protein essential for XCI3-7, binds to ancient retroviral RNA, performing a surveillance role to recruit chromatin silencing machinery to these parasitic loci. Spen inactivation leads to de-repression of a subset of endogenous retroviral (ERV) elements in embryonic stem cells, with gain of chromatin accessibility, active histone modifications, and ERV RNA transcription. Spen binds directly to ERV RNAs that show structural similarity to the A-repeat of Xist, a region critical for Xist-mediated gene silencing8-9. ERV RNA and Xist A-repeat bind the RRM3 domain of Spen in a competitive manner. Insertion of an ERV into an A-repeat deficient Xist rescues binding of Xist RNA to Spen and results in local gene silencing in cis. These results suggest that insertion of an ERV element into proto-Xist may have been a critical evolutionary event, which allowed Xist to coopt transposable element RNA-protein interactions to repurpose powerful antiviral chromatin silencing machinery for sex chromosome dosage compensation.

scholarly journals The absence of a Ca2+ signal during mouse egg activation can affect parthenogenetic preimplantation development, gene expression patterns, and blastocyst quality

Reproduction ◽  
2006 ◽  
Vol 132 (1) ◽  
pp. 45-57 ◽  
Author(s):  
N T Rogers ◽  
G Halet ◽  
Y Piao ◽  
J Carroll ◽  
M S H Ko ◽  
...  
Keyword(s):  
Gene Expression ◽  
Inner Cell Mass ◽  
Expression Patterns ◽  
Cell Mass ◽  
Blastocyst Stage ◽  
Distinct Pattern ◽  
Egg Activation ◽  
Cell Stage ◽  
Embryonic Genome ◽  
Genome Activation

A series of Ca2+ oscillations during mammalian fertilization is necessary and sufficient to stimulate meiotic resumption and pronuclear formation. It is not known how effectively development continues in the absence of the initial Ca2+ signal. We have triggered parthenogenetic egg activation with cycloheximide that causes no Ca2+ increase, with ethanol that causes a single large Ca2+ increase, or with Sr2+ that causes Ca2+ oscillations. Eggs were co-treated with cytochalasin D to make them diploid and they formed pronuclei and two-cell embryos at high rates with each activation treatment. However, far fewer of the embryos that were activated by cycloheximide reached the blastocyst stagecompared tothose activated by Sr2+ orethanol. Any cycloheximide-activated embryos that reached the blastocyst stage had a smaller inner cell mass number and a greater rate of apoptosis than Sr2+-activated embryos. The poor development of cycloheximide-activated embryos was due to the lack of Ca2+ increase because they developed to blastocyst stages at high rates when co-treated with Sr2+ or ethanol. Embryos activated by either Sr2+ or cycloheximide showed similar signs of initial embryonic genome activation (EGA) when measured using a reporter gene. However, microarray analysis of gene expression at the eight-cell stage showed that activation by Sr2+ leads to a distinct pattern of gene expression from that seen with embryos activated by cycloheximide. These data suggest that activation of mouse eggs in the absence of a Ca2+ signal does not affect initial parthenogenetic events, but can influence later gene expression and development.

Sign in / Sign up

Export Citation Format

Share Document