scholarly journals Exploratory analysis of transposable elements expression in the C. elegans early embryo

2019 ◽  
Vol 20 (S9) ◽  
Author(s):  
Federico Ansaloni ◽  
Margherita Scarpato ◽  
Elia Di Schiavi ◽  
Stefano Gustincich ◽  
Remo Sanges
Keyword(s):  
Nervous System ◽  
Transposable Elements ◽  
Embryo Development ◽  
Cell Types ◽  
Early Embryo ◽  
Bioinformatics Pipeline ◽  
Early Embryo Development ◽  
C Elegans ◽  
Differentiated Cells ◽  
Different Cell Types

Abstract Background Transposable Elements (TE) are mobile sequences that make up large portions of eukaryote genomes. The functions they play within the complex cellular architecture are still not clearly understood, but it is becoming evident that TE have a role in several physiological and pathological processes. In particular, it has been shown that TE transcription is necessary for the correct development of mice embryos and that their expression is able to finely modulate transcription of coding and non-coding genes. Moreover, their activity in the central nervous system (CNS) and other tissues has been correlated with the creation of somatic mosaicisms and with pathologies such as neurodevelopmental and neurodegenerative diseases as well as cancers. Results We analyzed TE expression among different cell types of the Caenorhabditis elegans (C. elegans) early embryo asking if, where and when TE are expressed and whether their expression is correlated with genes playing a role in early embryo development. To answer these questions, we took advantage of a public C. elegans embryonic single-cell RNA-seq (sc-RNAseq) dataset and developed a bioinformatics pipeline able to quantify reads mapping specifically against TE, avoiding counting reads mapping on TE fragments embedded in coding/non-coding transcripts. Our results suggest that i) canonical TE expression analysis tools, which do not discard reads mapping on TE fragments embedded in annotated transcripts, may over-estimate TE expression levels, ii) Long Terminal Repeats (LTR) elements are mostly expressed in undifferentiated cells and might play a role in pluripotency maintenance and activation of the innate immune response, iii) non-LTR are expressed in differentiated cells, in particular in neurons and nervous system-associated tissues, and iv) DNA TE are homogenously expressed throughout the C. elegans early embryo development. Conclusions TE expression appears finely modulated in the C. elegans early embryo and different TE classes are expressed in different cell types and stages, suggesting that TE might play diverse functions during early embryo development.

scholarly journals The Specification and Global Reprogramming of Histone Epigenetic Marks during Gamete Formation and Early Embryo Development in C. elegans

PLoS Genetics ◽  
2014 ◽  
Vol 10 (10) ◽  
pp. e1004588 ◽  
Author(s):  
Mark Samson ◽  
Margaret M. Jow ◽  
Catherine C. L. Wong ◽  
Colin Fitzpatrick ◽  
Aaron Aslanian ◽  
...  
Keyword(s):  
Embryo Development ◽  
Early Embryo ◽  
Early Embryo Development ◽  
Epigenetic Marks ◽  
C Elegans ◽  
Gamete Formation

Minor Splicing Factors Zrsr1 and Zrsr2 Essential for Gametogenesis, Early Embryo Development and Conversion of Stem Cells into 2C-Like

2019 ◽  
Author(s):  
Isabel Gómez-Redondo ◽  
Priscila Ramos-Ibeas ◽  
Eva Pericuesta ◽  
Benjamín Planells ◽  
Raul Fernández-González ◽  
...  
Keyword(s):  
Stem Cells ◽  
Embryo Development ◽  
Early Embryo ◽  
Splicing Factors ◽  
Early Embryo Development

scholarly journals Large organized chromatin lysine domains help distinguish primitive from differentiated cell populations

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Seyed Ali Madani Tonekaboni ◽  
Benjamin Haibe-Kains ◽  
Mathieu Lupien
Keyword(s):  
Transposable Elements ◽  
Histone Modifications ◽  
Cell Types ◽  
Regulatory Elements ◽  
Cell Populations ◽  
Genomic Features ◽  
Differentiated Cells ◽  
Chromatin Interactions ◽  
Topologically Associating Domains ◽  
Highly Expressed Genes

AbstractThe human genome is partitioned into a collection of genomic features, inclusive of genes, transposable elements, lamina interacting regions, early replicating control elements and cis-regulatory elements, such as promoters, enhancers, and anchors of chromatin interactions. Uneven distribution of these features within chromosomes gives rise to clusters, such as topologically associating domains (TADs), lamina-associated domains, clusters of cis-regulatory elements or large organized chromatin lysine (K) domains (LOCKs). Here we show that LOCKs from diverse histone modifications discriminate primitive from differentiated cell types. Active LOCKs (H3K4me1, H3K4me3 and H3K27ac) cover a higher fraction of the genome in primitive compared to differentiated cell types while repressive LOCKs (H3K9me3, H3K27me3 and H3K36me3) do not. Active LOCKs in differentiated cells lie proximal to highly expressed genes while active LOCKs in primitive cells tend to be bivalent. Genes proximal to bivalent LOCKs are minimally expressed in primitive cells. Furthermore, bivalent LOCKs populate TAD boundaries and are preferentially bound by regulators of chromatin interactions, including CTCF, RAD21 and ZNF143. Together, our results argue that LOCKs discriminate primitive from differentiated cell populations.

scholarly journals LIN28 coordinately promotes nucleolar/ribosomal functions and represses the 2C-like transcriptional program in pluripotent stem cells

2021 ◽  
Author(s):  
Zhen Sun ◽  
Hua Yu ◽  
Jing Zhao ◽  
Tianyu Tan ◽  
Hongru Pan ◽  
...  
Keyword(s):  
Stem Cells ◽  
Embryo Development ◽  
Pluripotent Stem Cells ◽  
Rna Binding ◽  
Stem Cell Differentiation ◽  
Early Embryo ◽  
Transcriptional Program ◽  
Cell Stage ◽  
Early Embryo Development ◽  
Nucleolar Stress

AbstractLIN28 is an RNA binding protein with important roles in early embryo development, stem cell differentiation/reprogramming, tumorigenesis and metabolism. Previous studies have focused mainly on its role in the cytosol where it interacts with Let-7 microRNA precursors or mRNAs, and few have addressed LIN28’s role within the nucleus. Here, we show that LIN28 displays dynamic temporal and spatial expression during murine embryo development. Maternal LIN28 expression drops upon exit from the 2-cell stage, and zygotic LIN28 protein is induced at the forming nucleolus during 4-cell to blastocyst stage development, to become dominantly expressed in the cytosol after implantation. In cultured pluripotent stem cells (PSCs), loss of LIN28 led to nucleolar stress and activation of a 2-cell/4-cell-like transcriptional program characterized by the expression of endogenous retrovirus genes. Mechanistically, LIN28 binds to small nucleolar RNAs and rRNA to maintain nucleolar integrity, and its loss leads to nucleolar phase separation defects, ribosomal stress and activation of P53 which in turn binds to and activates 2C transcription factor Dux. LIN28 also resides in a complex containing the nucleolar factor Nucleolin (NCL) and the transcriptional repressor TRIM28, and LIN28 loss leads to reduced occupancy of the NCL/TRIM28 complex on the Dux and rDNA loci, and thus de-repressed Dux and reduced rRNA expression. Lin28 knockout cells with nucleolar stress are more likely to assume a slowly cycling, translationally inert and anabolically inactive state, which is a part of previously unappreciated 2C-like transcriptional program. These findings elucidate novel roles for nucleolar LIN28 in PSCs, and a new mechanism linking 2C program and nucleolar functions in PSCs and early embryo development.

scholarly journals Geminin deletion in mouse oocytes results in impaired embryo development and reduced fertility

2016 ◽  
Vol 27 (5) ◽  
pp. 768-775 ◽  
Author(s):  
Xue-Shan Ma ◽  
Fei Lin ◽  
Zhong-Wei Wang ◽  
Meng-Wen Hu ◽  
Lin Huang ◽  
...  
Keyword(s):  
Embryo Development ◽  
Primordial Follicle ◽  
Early Embryo ◽  
Cell Cycle Checkpoint ◽  
Low Fertility ◽  
Early Embryo Development ◽  
Damage Repair ◽  
Cycle Checkpoint ◽  
Oocyte Meiotic Maturation ◽  
Zygote Stage

Geminin controls proper centrosome duplication, cell division, and differentiation. We investigated the function of geminin in oogenesis, fertilization, and early embryo development by deleting the geminin gene in oocytes from the primordial follicle stage. Oocyte-specific disruption of geminin results in low fertility in mice. Even though there was no evident anomaly of oogenesis, oocyte meiotic maturation, natural ovulation, or fertilization, early embryo development and implantation were impaired. The fertilized eggs derived from mutant mice showed developmental delay, and many were blocked at the late zygote stage. Cdt1 protein was decreased, whereas Chk1 and H2AX phosphorylation was increased, in fertilized eggs after geminin depletion. Our results suggest that disruption of maternal geminin may decrease Cdt1 expression and cause DNA rereplication, which then activates the cell cycle checkpoint and DNA damage repair and thus impairs early embryo development.

scholarly journals The Potential Roles of the G1LEA and G3LEA Proteins in Early Embryo Development and in Response to Low Temperature and High Salinity in Artemia sinica

PLoS ONE ◽  
2016 ◽  
Vol 11 (9) ◽  
pp. e0162272 ◽  
Author(s):  
Wei Zhao ◽  
Feng Yao ◽  
Mengchen Zhang ◽  
Ting Jing ◽  
Shuang Zhang ◽  
...  
Keyword(s):  
Low Temperature ◽  
Embryo Development ◽  
High Salinity ◽  
Early Embryo ◽  
Artemia Sinica ◽  
Early Embryo Development

Early embryo development anomalies identified by time-lapse system: prevalence and impacting factors

2021 ◽  
Author(s):  
Xavier Ferraretto ◽  
Karima Hammas ◽  
Marie-Astrid Llabador ◽  
Solenne Gricourt ◽  
Julie Labrosse ◽  
...  
Keyword(s):  
Embryo Development ◽  
Time Lapse ◽  
Early Embryo ◽  
Early Embryo Development ◽  
Impacting Factors

Nutritional Status Impacts Epigenetic Regulation in Early Embryo Development: A Scoping Review

2021 ◽  
Author(s):  
Shuang Cai ◽  
Shuang Quan ◽  
Guangxin Yang ◽  
Meixia Chen ◽  
Qianhong Ye ◽  
...  
Keyword(s):  
Embryonic Development ◽  
Embryo Development ◽  
Epigenetic Regulation ◽  
Scoping Review ◽  
Epigenetic Modification ◽  
Reproductive Technologies ◽  
Early Embryo ◽  
Epigenetic Modifications ◽  
Nutrition Status ◽  
Early Embryo Development

ABSTRACTWith the increasing maternal age and the use of assisted reproductive technology in various countries worldwide, the influence of epigenetic modification on embryonic development is increasingly notable and prominent. Epigenetic modification disorders caused by various nutritional imbalance would cause embryonic development abnormalities and even have an indelible impact on health in adulthood. In this scoping review, we summarize the main epigenetic modifications in mammals and the synergies among different epigenetic modifications, especially DNA methylation, histone acetylation, and histone methylation. We performed an in-depth analysis of the regulation of various epigenetic modifications on mammals from zygote formation to cleavage stage and blastocyst stage, and reviewed the modifications of key sites and their potential molecular mechanisms. In addition, we discuss the effects of nutrition (protein, lipids, and one-carbon metabolism) on epigenetic modification in embryos and emphasize the importance of various nutrients in embryonic development and epigenetics during pregnancy. Failures in epigenetic regulation have been implicated in mammalian and human early embryo loss and disease. With the use of reproductive technologies, it is becoming even more important to establish developmentally competent embryos. Therefore, it is essential to evaluate the extent to which embryos are sensitive to these epigenetic modifications and nutrition status. Understanding the epigenetic regulation of early embryo development will help us make better use of reproductive technologies and nutrition regulation to improve reproductive health in mammals.

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