The placenta goes viral: Retroviruses control gene expression in pregnancy

Chuong, Edward B.

doi:10.1371/journal.pbio.3000028

Cited by 68 publications

(41 citation statements)

References 37 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…However, there are also numerous examples of TE sequences being co-opted for use by the host. In mammals, syncytin genes are ERV-derived envelope protein genes which are expressed by cells of the placenta during embryonic development and are involved in placental cell-cell fusion to form the characteristic placental structure (Chuong, 2018). Other placental genes such as corticotropinreleasing hormone have been shown to be regulated by ERV sequence enhancers, showing that ERV sequences are important for placental development and mammalian evolution (Chuong, 2018).…”

Section: Introductionmentioning

confidence: 99%

“…In mammals, syncytin genes are ERV-derived envelope protein genes which are expressed by cells of the placenta during embryonic development and are involved in placental cell-cell fusion to form the characteristic placental structure (Chuong, 2018). Other placental genes such as corticotropinreleasing hormone have been shown to be regulated by ERV sequence enhancers, showing that ERV sequences are important for placental development and mammalian evolution (Chuong, 2018). Another recent study showed that subsets of ERV and LINE DNA sequences participate in a gene regulatory network that controls innate immune response genes downstream of interferon γ signaling (Chuong et al, 2016), suggesting important roles in host innate immunity.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Virus-induced transposable element expression up-regulation in human and mouse host cells

2020

View full text Add to dashboard Cite

Virus–host cell interactions initiate a host cell–defensive response during virus infection. How transposable elements in the host cell respond to viral stress at the molecular level remains largely unclear. By reanalyzing next generation sequencing data sets from dozens of virus infection studies from the Gene Expression Omnibus database, we found that genome-wide transposon expression up-regulation in host cells occurs near antiviral response genes and exists in all studies regardless of virus, species, and host cell tissue types. Some transposons were found to be up-regulated almost immediately upon infection and before increases in virus replication and significant increases in interferon β expression. These findings indicate that transposon up-regulation is a common phenomenon during virus infection in human and mouse and that early up-regulated transposons are part of the first wave response during virus infection.

show abstract

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Virus-induced transposable element expression up-regulation in human and mouse host cells

2020

View full text Add to dashboard Cite

show abstract

“…A recent study reported that, in trophoblast stem cells, RlllLTR13D5s, which comprise a mouse-specific ERVK family, have enhancer functions to establish a trophoblast stem cell-specific regulatory network, and the same study predicted the existence of enhancer-like ERVs in testes and embryonic stem cells 35 . Curiously, placenta is known to be a fast-evolving organ in which many ERVs have been co-opted 54,55 . Thus, it is intriguing to speculate that ERVs are drivers of species-specific transcriptomes in rapidly evolving organs such as the testis and placenta, although mechanisms underlying intrinsic ERV activity in testes and placenta remain undetermined.…”

Section: Discussionmentioning

confidence: 99%

Endogenous retroviruses drive species-specific germline transcriptomes in mammals

Sakashita

Maezawa

Alavattam

et al. 2020

Preprint

View full text Add to dashboard Cite

24Gene regulation in the germline ensures the production of high-quality gametes, long-term 25 maintenance of the species, and speciation. Germline transcriptomes undergo dynamic 26 changes after the mitosis-to-meiosis transition in males and have been subject to evolutionary 27 divergence among mammals. However, the mechanism that underlies germline regulatory 28 divergence remains undetermined. Here, we show that endogenous retroviruses influence 29 species-specific germline transcriptomes in mammals. We show that the expression of 30 endogenous retroviruses, particularly the evolutionarily young K family (ERVK), is 31 associated with gene activation after the mitosis-to-meiosis transition in male mice. We 32 demonstrate that accessible chromatin and H3K27ac, a marker of active enhancers, are 33 tightly associated with ERVK loci as well as with the activation of neighboring evolutionarily 34 young germline genes. Thus, ERVKs serve as evolutionarily novel enhancers in mouse 35 spermatogenesis. These ERVK loci bear binding motifs for critical regulators of 36 spermatogenesis such as A-MYB. The genome-wide transposition of ERVKs might have 37 rewired germline gene expression in a species-specific manner. Notably, these features are 38 present in human spermatogenesis, but independently evolved ERVs are associated with 39 expression of germline genes, demonstrating the prevalence of ERV-driven mechanisms in 40 mammals. Together, we propose a model whereby species-specific transcriptomes are fine-41 tuned by endogenous retroviruses in the mammalian germline.42 43 84for germline genes 25,26 . These enhancers drive expression of evolutionarily novel germline genes 85 after the mitosis-to-meiosis transition, thereby defining the species-specificity of germline 86 transcriptomes in mammals. Notably, we demonstrate the prevalence of ERV-driven germline 87 genes in humans. We propose a model whereby ERVs fine-tune species-specific transcriptomes in 88 the mammalian germline. 90 Results 91A large group of endogenous retroviruses are differentially expressed at the mitosis-to-92 meiosis transition in spermatogenesis.To determine the expression dynamics of repetitive elements interspersed throughout the 94 genome in spermatogenesis, we analyzed previously published RNA-seq datasets for representative 95 stages of spermatogenesis 5,6,27 using RepBase, a database of consensus sequences for repetitive 96 DNA elements 28 . We included in the analysis the transcriptomes of THY1 + undifferentiated 97 spermatogonia from postnatal day 7 (P7) testes, which contain spermatogonial stem cells and 98 progenitor cells; KIT + differentiating spermatogonia from P7 testes; purified pachytene 99 spermatocytes (PS) in the midst of meiosis; postmeiotic round spermatids (RS) from adult testes; 100 and mature sperm ( Fig. 1a). Among the 1,195 consensus repetitive DNA elements of Mus musculus 101 in RepBase, we detected 307 differentially expressed types of repetitive elements between at least 102 two stages of spermatogenesis ( Fig. 1b, Supplemen...

show abstract

“…One important finding was the identification of Syncytin and L1-retrotransposons genes in the venom gland of B. jararaca. Syncytin genes are associated with placental evolution in mammals and viviparous anim als [ 73 ]. Up to now, these coding sequences were never described in transcriptomes of viviparous snakes, mainly B. jararaca .…”

Section: Discussionmentioning

confidence: 99%

In-depth transcriptome reveals the potential biotechnological application of Bothrops jararaca venom gland

Pereira

Messias

Sorroche

et al. 2020

J. Venom. Anim. Toxins incl. Trop. Dis

View full text Add to dashboard Cite

Background: Lack of complete genomic data of Bothrops jararaca impedes molecular biology research focusing on biotechnological applications of venom gland components. Identification of full-length coding regions of genes is crucial for the correct molecular cloning design. Methods: RNA was extracted from the venom gland of one adult female specimen of Bothrops jararaca . Deep sequencing of the mRNA library was performed using Illumina NextSeq 500 platform. De novo assembly of B. jararaca transcriptome was done using Trinity. Annotation was performed using Blast2GO. All predicted proteins after clustering step were blasted against non-redundant protein database of NCBI using BLASTP. Metabolic pathways present in the transcriptome were annotated using the KAAS-KEGG Automatic Annotation Server. Toxins were identified in the B. jararaca predicted proteome using BLASTP against all protein sequences obtained from Animal Toxin Annotation Project from Uniprot KB/Swiss-Pro database. Figures and data visualization were performed using ggplot2 package in R language environment. Results: We described the in-depth transcriptome analysis of B. jararaca venom gland, in which 76,765 de novo assembled isoforms, 96,044 transcribed genes and 41,196 unique proteins were identified. The most abundant transcript was the zinc metalloproteinase-disintegrin-like jararhagin. Moreover, we identified 78 distinct functional classes of proteins, including toxins, inhibitors and tumor suppressors. Other venom proteins identified were the hemolytic lethal factors stonustoxin and verrucotoxin. Conclusion: It is believed that the application of deep sequencing to the analysis of snake venom transcriptomes may represent invaluable insight on their biotechnological potential focusing on candidate molecules.

show abstract

The placenta goes viral: Retroviruses control gene expression in pregnancy

Cited by 68 publications

References 37 publications

Virus-induced transposable element expression up-regulation in human and mouse host cells

Virus-induced transposable element expression up-regulation in human and mouse host cells

Endogenous retroviruses drive species-specific germline transcriptomes in mammals

In-depth transcriptome reveals the potential biotechnological application of Bothrops jararaca venom gland

Contact Info

Product

Resources

About