Biphasic expression of thyroid hormone receptor TRb1 in mammalian retina and anterior ocular tissues
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE224863 | GEO | 2023/04/18
REPOSITORIES: GEO
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Project description:ChIP-seq data from mouse liver over-expressing GFP and fed a PTU diet and treated with saline, or overexpressing biotinylated TRb1 and GFP and fed a PTU diet, treated with either saline or T3 Mouse liver was infected with adenovirus that either expressed only GFP or GFP and biotinylated TRb1 and were fed a PTU diet, followed by injections with only saline (GFP-only livers) or with saline or T3 (Biotinylated-TRb1 and GFP livers). ChIP assays were performed using streptavidin agarose to capture biotinylated TRb1 followed by library construction and sequencing.
2013-12-18 | E-GEOD-52613 | biostudies-arrayexpress
Project description:Background: Recently we characterised TRB1, a protein from a single-myb-histone family, as a structural and functional component of telomeres in Arabidopsis thaliana. TRB proteins, besides their ability to bind specifically telomeric DNA using their N-terminally positioned myb-like domain of the same type as in human TRF1 or TRF2 shelterin proteins, possess also histone-like domain which is involved in protein-protein interactions e.g., with POT1b. We set to investigate the genome-wide localization pattern of TRB1 to reveal its preferential mode of binding to chromatin in vivo and its potential functional roles in the genome-wide context. Results: Our results demonstrate that in addition to its roles at telomeres, TRB1 is preferentially associated with promoter regions of genes involved in ribosome biogenesis. This preference coincides with a frequent occurrence of telobox motifs in the upstream regions of genes in this category, but is not restricted to the telobox presence. Conclusions: We conclude that TRB1, in addition to its preferential telomeric localization, shows a specific genome-wide distribution pattern suggesting its role in regulation of genes involved in biogenesis of translational machinery. TRB1 DNA-binding activity investigated in 2 biological replicates (2 immunoprecipitation approaches) with controls; with technical replicates.
2015-12-21 | E-GEOD-69431 | biostudies-arrayexpress
Project description:ChIP-seq data from mouse liver over-expressing GFP and fed a PTU diet and treated with saline, or overexpressing biotinylated TRb1 and GFP and fed a PTU diet, treated with either saline or T3
2013-12-18 | GSE52613 | GEO
Project description:We over-expressed biotinylated-thyroid hormone receptor beta 1 (TRb1) in mouse liver using an adenovirus in order to perform ChIP-seq experiments. These microarrays were performed to determine gene expression changes in response to tri-iodothyronine (thyroid hormone; T3) stimulation. A control GFP adenovirus was used and gene expression from these livers was also done as a comparison. We performed microarrays from Ad-GFP-infected propylthiouracil (PTU)-fed livers injected with either saline or T3 and Ad-TRb1-GFP infected livers injected with either saline or T3. RNA was extracted from livers of biotin ligase (BirA)-expressing mice that had been infected with either Ad-GFP or Ad-TRb1, fed with PTU for 3 weeks followed by saline or T3 injections for 4 consecutive days.
2013-12-18 | E-GEOD-52433 | biostudies-arrayexpress
Project description:Background: Recently we characterised TRB1, a protein from a single-myb-histone family, as a structural and functional component of telomeres in Arabidopsis thaliana. TRB proteins, besides their ability to bind specifically telomeric DNA using their N-terminally positioned myb-like domain of the same type as in human TRF1 or TRF2 shelterin proteins, possess also histone-like domain which is involved in protein-protein interactions e.g., with POT1b. We set to investigate the genome-wide localization pattern of TRB1 to reveal its preferential mode of binding to chromatin in vivo and its potential functional roles in the genome-wide context. Results: Our results demonstrate that in addition to its roles at telomeres, TRB1 is preferentially associated with promoter regions of genes involved in ribosome biogenesis. This preference coincides with a frequent occurrence of telobox motifs in the upstream regions of genes in this category, but is not restricted to the telobox presence. Conclusions: We conclude that TRB1, in addition to its preferential telomeric localization, shows a specific genome-wide distribution pattern suggesting its role in regulation of genes involved in biogenesis of translational machinery.
2015-12-21 | GSE69431 | GEO
Project description:The loss of cone photoreceptor cells, which are critical for optimal daylight vision, have the great impact on vision during retinal degenerations. Retinal differentiation of human induced pluripotent stem cell (hiPSC) sources could provide a renewable source of cone photoreceptors towards developing a cone cell replacement therapy to treat blindness. Demonstration of comparable gene expression profiles between human foetal and stem cell-derived cones at equivalent stages is required to progress the cell transplantation approach into the patient, as it is hypothesised stem cell-derived cones are required to show high levels of developmental recapitulation of the in vivo generated cones. In this study, the AAV2/9.pR2.1.GFP reporter was used to specifically label L/M-opsin cone photoreceptors in human foetal retinal samples, obtained from the MRC-Wellcome Trust Human Developmental Biology Resource, at a range of developmental stages. The L/M-opsin cone population represent the majority cone cell types in the adult human retina and are the only photoreceptors present within the fovea. Using fluorescence activated cell sorting, L/M-opsin GFP+ cones and GFP- retinal populations, alongside total foetal retinal samples containing all retinal cell tytpes, were isolated and processed for bulk RNA sequencing and downstream comparative analysis. Using DESeq2 differential gene expression analyses, statistically significant genes enriched within the GFP+ human foetal LM-opsin cone populations were determined which led to the identification of a cone enriched gene signature of human L/M-opsin cone photoreceptors. The AAV2/9.pR2.1.GFP reporter was applied to hiPSC-derived retinal cultures to isolate and process cone-like cell populations for RNA sequencing using the same strategy developed within the human foetal retina. Applying the cone enriched gene signature to the transcriptome of hiPSC-derived GFP+ samples at equivalent developmental stages revealed some expression similarities in genes found to be enriched within the late foetal L/M-opsin cone photoreceptors. This analysis overall revealed an intermediate stage of cone differentiation was achieved within the hiPSC-derived samples and the comparison to human foetal L/M-opsin gene express profiles suggesting further differentiation of hiPSC-derived sample is required.
2018-04-20 | E-MTAB-6057 | biostudies-arrayexpress
Project description:We over-expressed biotinylated-thyroid hormone receptor beta 1 (TRb1) in mouse liver using an adenovirus in order to perform ChIP-seq experiments. These microarrays were performed to determine gene expression changes in response to tri-iodothyronine (thyroid hormone; T3) stimulation. A control GFP adenovirus was used and gene expression from these livers was also done as a comparison. We performed microarrays from Ad-GFP-infected propylthiouracil (PTU)-fed livers injected with either saline or T3 and Ad-TRb1-GFP infected livers injected with either saline or T3.
2013-12-18 | GSE52433 | GEO
Project description:TELOMERE REPEAT BINDING proteins (TRBs) are plant specific transcriptional regulators that combine two DNA binding domains: the GH1 domain shared with H1 linker histones and the Myb/SANT domain that specifically recognize AAACCCT, the telomeric motif, present at telomeres, centromere-proximal Interstitial Telomeric Repeats (ITRs) and at promoters of numerous protein-coding genes. TRB1, TRB2 and TRB3 (TRB1-3) proteins collaborate with PRC2 and JMJ14 for deposition of H3K27me3 and removal of H3K4me3 to induce transcriptional repression in a functionally redundant manner. Here we report that TRB4 and TRB5, which belong to a separate TRB clade conserved among spermatophytes, fulfill chromatin roles distinct from TRB1-3. We show that TRB4 and TRB5 are involved in the transcriptional control of several hundred genes involved in developmental responses to environmental cues and in consequence TRB4 and TRB5 loss of function plants present developmental growth defects including delayed flowering. Most of the trb4 trb5 transcriptomic defects differ from those of trb1 trb2 trb3, suggesting a distinct mode of action at the chromatin level. Indeed, TRB4 binds to several thousand sites in the genome, mainly to TSS and promoter regions of transcriptionally active and H3K4me3-marked genes, but it does not affect global H3K4me3 levels. In contrast to TRB1-3, TRB4 is not enriched at H3K27me3-marked gene bodies, and combined loss of TRB4 and TRB5 affects H3K27me3 only at a small subset of genes. Yet, TRB4 physically interacts with the catalytically active subunit of somatic PRC2 complexes CURLY LEAF (CLF). Unexpectedly, loss of TRB4 and TRB5 partially suppresses developmental defects of clf mutant plants, likely through their role as positive transcriptional regulators of the key flowering genes SOC1 and FT. We further show that TRB4 and TRB1 share multiple target genes and reveal physical and genetic interactions between TRBs of the two distinct clades, altogether unveiling that TRB proteins engage in both positive and negative interplay with other members of the family to regulate plant development through PRC2-dependent and independent mechanisms.
2024-02-12 | GSE253005 | GEO
Project description:TELOMERE REPEAT BINDING proteins (TRBs) are plant specific transcriptional regulators that combine two DNA binding domains: the GH1 domain shared with H1 linker histones and the Myb/SANT domain that specifically recognize AAACCCT, the telomeric motif, present at telomeres, centromere-proximal Interstitial Telomeric Repeats (ITRs) and at promoters of numerous protein-coding genes. TRB1, TRB2 and TRB3 (TRB1-3) proteins collaborate with PRC2 and JMJ14 for deposition of H3K27me3 and removal of H3K4me3 to induce transcriptional repression in a functionally redundant manner. Here we report that TRB4 and TRB5, which belong to a separate TRB clade conserved among spermatophytes, fulfill chromatin roles distinct from TRB1-3. We show that TRB4 and TRB5 are involved in the transcriptional control of several hundred genes involved in developmental responses to environmental cues and in consequence TRB4 and TRB5 loss of function plants present developmental growth defects including delayed flowering. Most of the trb4 trb5 transcriptomic defects differ from those of trb1 trb2 trb3, suggesting a distinct mode of action at the chromatin level. Indeed, TRB4 binds to several thousand sites in the genome, mainly to TSS and promoter regions of transcriptionally active and H3K4me3-marked genes, but it does not affect global H3K4me3 levels. In contrast to TRB1-3, TRB4 is not enriched at H3K27me3-marked gene bodies, and combined loss of TRB4 and TRB5 affects H3K27me3 only at a small subset of genes. Yet, TRB4 physically interacts with the catalytically active subunit of somatic PRC2 complexes CURLY LEAF (CLF). Unexpectedly, loss of TRB4 and TRB5 partially suppresses developmental defects of clf mutant plants, likely through their role as positive transcriptional regulators of the key flowering genes SOC1 and FT. We further show that TRB4 and TRB1 share multiple target genes and reveal physical and genetic interactions between TRBs of the two distinct clades, altogether unveiling that TRB proteins engage in both positive and negative interplay with other members of the family to regulate plant development through PRC2-dependent and independent mechanisms.
2024-02-12 | GSE236267 | GEO
Project description:TELOMERE REPEAT BINDING proteins (TRBs) are plant specific transcriptional regulators that combine two DNA binding domains: the GH1 domain shared with H1 linker histones and the Myb/SANT domain that specifically recognize AAACCCT, the telomeric motif, present at telomeres, centromere-proximal Interstitial Telomeric Repeats (ITRs) and at promoters of numerous protein-coding genes. TRB1, TRB2 and TRB3 (TRB1-3) proteins collaborate with PRC2 and JMJ14 for deposition of H3K27me3 and removal of H3K4me3 to induce transcriptional repression in a functionally redundant manner. Here we report that TRB4 and TRB5, which belong to a separate TRB clade conserved among spermatophytes, fulfill chromatin roles distinct from TRB1-3. We show that TRB4 and TRB5 are involved in the transcriptional control of several hundred genes involved in developmental responses to environmental cues and in consequence TRB4 and TRB5 loss of function plants present developmental growth defects including delayed flowering. Most of the trb4 trb5 transcriptomic defects differ from those of trb1 trb2 trb3, suggesting a distinct mode of action at the chromatin level. Indeed, TRB4 binds to several thousand sites in the genome, mainly to TSS and promoter regions of transcriptionally active and H3K4me3-marked genes, but it does not affect global H3K4me3 levels. In contrast to TRB1-3, TRB4 is not enriched at H3K27me3-marked gene bodies, and combined loss of TRB4 and TRB5 affects H3K27me3 only at a small subset of genes. Yet, TRB4 physically interacts with the catalytically active subunit of somatic PRC2 complexes CURLY LEAF (CLF). Unexpectedly, loss of TRB4 and TRB5 partially suppresses developmental defects of clf mutant plants, likely through their role as positive transcriptional regulators of the key flowering genes SOC1 and FT. We further show that TRB4 and TRB1 share multiple target genes and reveal physical and genetic interactions between TRBs of the two distinct clades, altogether unveiling that TRB proteins engage in both positive and negative interplay with other members of the family to regulate plant development through PRC2-dependent and independent mechanisms.
2024-02-12 | GSE237185 | GEO