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Long terminal repeat THE1B is a candidate enhancer for placenta-specific gene regulation

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE118289 | GEO | 2018/08/09

REPOSITORIES: GEO

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Long terminal repeat THE1B is a candidate enhancer for placenta-specific gene regulation [ChIP-Seq]

Project description:The purpose of the study was to examine histone marks H3K27ac and H3K4me1 at THE1B elements in human placenta.

2018-08-09 | GSE118286 | GEO

Long terminal repeat THE1B is a candidate enhancer for placenta-specific gene regulation [RNA-Seq]

Project description:The purpose of the study was to identify mRNA transcripts in human placenta that contained a THE1B element.

2018-08-09 | GSE118285 | GEO

Long terminal repeat THE1B is a candidate enhancer for placenta-specific gene regulation

Project description:Long terminal repeat THE1B is a candidate enhancer for placenta-specific gene regulation

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Long terminal repeat THE1B is a candidate enhancer for placenta-specific gene regulation [RNA-Seq]

Project description:Long terminal repeat THE1B is a candidate enhancer for placenta-specific gene regulation [RNA-Seq]

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Long terminal repeat THE1B is a candidate enhancer for placenta-specific gene regulation [ChIP-Seq]

Project description:Long terminal repeat THE1B is a candidate enhancer for placenta-specific gene regulation [ChIP-Seq]

| PRJNA485083 | ENA

Specific suppression of long terminal repeat retrotransposon mobilization in plants.

Project description:The tissue culture passage necessary for the generation of transgenic plants induces genome instability. This instability predominantly involves the uncontrolled mobilization of LTR retrotransposons (LTR-TEs), which are the most abundant class of mobile genetic elements in plant genomes. Here, we demonstrate that in conditions inductive for high LTR-TE mobilization, like abiotic stress in Arabidopsis (Arabidopsis thaliana) and callus culture in rice (Oryza sativa), application of the reverse transcriptase (RT) inhibitor known as Tenofovir substantially affects LTR-TE RT activity without interfering with plant development. We observed that Tenofovir reduces extrachromosomal DNA accumulation and prevents new genomic integrations of the active LTR-TE ONSEN in heat-stressed Arabidopsis seedlings, and transposons of O. sativa 17 and 19 (Tos17 and Tos19) in rice calli. In addition, Tenofovir allows the recovery of plants free from new LTR-TE insertions. We propose the use of Tenofovir as a tool for studies of LTR-TE transposition and for limiting genetic instabilities of plants derived from tissue culture.

| S-EPMC10069891 | biostudies-literature

Global Long Terminal Repeat activation participates in establishing the unique gene expression program of classical Hodgkin Lymphoma

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-12-13 | GSE120331 | GEO

Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-11-08 | E-GEOD-51312 | biostudies-arrayexpress

Cell Compartment-Specific Folding of Ty1 Long Terminal Repeat Retrotransposon RNA Genome.

Project description:The structural transitions RNAs undergo during trafficking are not well understood. Here, we used the well-developed yeast Ty1 retrotransposon to provide the first structural model of genome (g) RNA in the nucleus from a retrovirus-like transposon. Through a detailed comparison of nuclear Ty1 gRNA structure with those established in the cytoplasm, virus-like particles (VLPs), and those synthesized in vitro, we detected Ty1 gRNA structural alterations that occur during retrotransposition. Full-length Ty1 gRNA serves as the mRNA for Gag and Gag-Pol proteins and as the genome that is reverse transcribed within VLPs. We show that about 60% of base pairs predicted for the nuclear Ty1 gRNA appear in the cytoplasm, and active translation does not account for such structural differences. Most of the shared base pairs are represented by short-range interactions, whereas the long-distance pairings seem unique for each compartment. Highly structured motifs tend to be preserved after nuclear export of Ty1 gRNA. In addition, our study highlights the important role of Ty1 Gag in mediating critical RNA-RNA interactions required for retrotransposition.

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A unique C-terminal repeat domain maintains the cytosolic localization of the placenta-specific tristetraprolin family member ZFP36L3.

Project description:Members of the tristetraprolin family of CCCH tandem zinc finger proteins bind to AU-rich elements in certain cellular mRNAs, leading to their deadenylation and destabilization. Studies in knock-out mice demonstrated roles for three of the family members, tristetraprolin, ZFP36L1, and ZFP36L2, in inflammation, chorioallantoic fusion, and early embryonic development, respectively. However, little is known about a recently discovered placenta-specific tristetraprolin family member, ZFP36L3. Tristetraprolin, ZFP36L1, and ZFP36L2 have been shown to shuttle between the nucleus and cytoplasm, using typical hydrophobic amino acid-rich nuclear export sequences, and nuclear localization sequences located within the tandem zinc finger domain. In contrast, we previously showed that green fluorescent protein-labeled ZFP36L3, expressed in HEK 293 cells, remained cytosolic, even in the presence of the nuclear export blocker leptomycin B. We show here that the conserved tandem zinc finger domain contains an active nuclear localization signal. However, the sequence corresponding to the nuclear export signal in the other family members was nonfunctional, and thus did not contribute to the cytosolic localization. The unique C-terminal repeat domain could override the activity of the nuclear localization sequence, preventing the import of ZFP36L3 into the nucleus. Immunostaining of mouse placenta demonstrated that ZFP36L3 was located only in the cytoplasm of trophoblast cells. Thus, in contrast to the other mammalian members of this protein family, ZFP36L3 is a "full-time" cytosolic protein, rather than a nucleocytoplasmic shuttling protein. The significance of this difference in subcellular localization to the physiology of placental trophoblast cells, where ZFP36L3 is selectively expressed, remains to be determined.

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