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An AT-hook transcription factor promotes transcription of histone, spliced-leader, and piRNA clusters [mRNA-Seq]

ABSTRACT: An AT-hook transcription factor promotes transcription of histone, spliced-leader, and piRNA clusters [mRNA-Seq]

PROVIDER: PRJNA1163267 | ENA |

REPOSITORIES: ENA

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An AT-hook transcription factor promotes transcription of histone, spliced-leader, and piRNA clusters [mRNA-Seq]

Project description:In all three domains of life, genes with related functions can be organized into specific genomic regions known as gene clusters. In eukaryotes, histone, piRNA, and rDNA (ribosomal DNA) clusters are among the most notable clusters which play fundamental roles in chromatin formation, genome integrity, and translation, respectively. These clusters have long been thought to be regulated by distinct transcriptional mechanisms. In this study, using C. elegans as a model system we identify ATTF-6, a member of the AT-hook family, as a key factor for the expression of histone, piRNA, and 5S rDNA-SL1 (spliced leader 1) clusters. ATTF-6 forms distinct nuclear foci at both piRNA and 5S rDNA-SL1 clusters. Loss of ATTF-6 leads to a depletion of histone mRNAs and SL1 transcripts. Additionally, we demonstrate that ATTF-6 is required for the recruitment of USTC (Upstream Sequence Transcription Complex) to piRNA clusters, which is necessary for piRNA production. Collectively, our findings reveal a unifying role for an AT-hook transcription factor in promoting the expression of fundamental gene clusters.

2025-01-28 | GSE277642 | GEO

An AT-hook transcription factor promotes transcription of histone, spliced-leader, and piRNA clusters [ChIP-Seq]

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An AT-hook transcription factor promotes transcription of histone, spliced-leader, and piRNA clusters [smllRNA-seq]

2025-01-28 | GSE277643 | GEO

An AT-hook transcription factor promotes transcription of histone, spliced-leader, and piRNA clusters [smllRNA-seq]

Project description:An AT-hook transcription factor promotes transcription of histone, spliced-leader, and piRNA clusters [smllRNA-seq]

| PRJNA1163269 | ENA

An AT-hook transcription factor promotes transcription of histone, spliced-leader, and piRNA clusters [ChIP-Seq]

Project description:An AT-hook transcription factor promotes transcription of histone, spliced-leader, and piRNA clusters [ChIP-Seq]

| PRJNA1163259 | ENA

Genome-wide map of spliced-leader-led trans-splice sites in Oikopleura dioica

Project description:Polycistronic mRNAs transcribed from operons are resolved via the trans-splicing of a spliced leader (SL) RNA. The SL is also frequently trans-spliced to monocistronic transcripts. Using a modified cap analysis of gene expression (CAGE) protocol we mapped sites of SL trans-splicing genome-wide in the marine chordate Oikopleura dioica and find evidence for proposed functions of SL-trans-splicing. A recent hypothesis postulates that operons facilitate recovery from growth arrested states in metazoans. We examined the expression dynamics of operons across the life-cycle of the animal and during growth arrest recovery. We show that operons do not facilitate recovery from growth arrest in O. dioica. We find that operons are enriched in the germline and that trans-spliced transcripts are predominantly maternal., Interestingly, there is a TOP-like motif in the SL sequence, and trans-splicing in TOP mRNAs, indicating that trans-spliced mRNAs are targets for nutrient-dependent translational control in O. dioica. Total RNA from a number of stages across development were pooled and used in a modified DeepCAGE protocol. A custom designed spliced-leader primer (using the SL exon) was used in the 2nd strand synthesis step.

2015-01-26 | E-GEOD-50849 | biostudies-arrayexpress

Genome-wide map of spliced-leader-led trans-splice sites in Oikopleura dioica

2015-01-26 | GSE50849 | GEO

Functional characterisation of nematode spliced leader 1 trans-splicing factors SUT-1, SNA-2, SNA-3 and SNR-2 by immunoprecipitation and LC-MS/MS.

Project description:Spliced leader trans-splicing is an essential RNA processing step that is required for the formation of mRNA in many eukaryotes, including C. elegans. However, the role of factors involved in this reaction is not well known. Here we further characterise the function of SNA-2, SNA-3, SUT-1 and SNR-2 involved in spliced leader 1 trans-splicing through identification of interacting proteins by immunoprecipitation followed by LC-MS/MS and label-free quantification.

2024-04-23 | PXD040352 | Pride

Identification of RNAs associated with the Caenorhabditis elegans spliced-leader trans-splicing proteins SNA-2, SNA-3, SNR-2 and SUT-1 proteins by RIP-Seq.

Project description:This study aimed to identify RNAs bound to the C. elegans SNA-2, SNA-3, SUT-1 and SNR-2 proteins involved in spliced leader 1 trans-splicing through use of RNA immunoprecipitation sequencing (RIP-Seq). Four IP sample replicates and four control sample replicates were sequenced for each protein.

2024-04-24 | E-MTAB-13193 | biostudies-arrayexpress

Advancing Trypanosoma brucei genome annotation through ribosome profiling and spliced leader mapping

Project description:Since the initial publication of the trypanosomatid genomes, curation has been ongoing. Here we apply the technique of ribosome profiling to Trypanosoma brucei, identifying 223 new coding regions by virtue of ribosome occupancy in the corresponding transcripts. A small number of these putative genes correspond to extra copies of previously annotated genes but 85% are novel. The median size of these novels CDSs is small (74 aa) indicating that past annotation work has excelled at detecting large CDSs. Of the unique CDSs discovered here, over half have candidate orthologues in other trypanosomatid genomes, most of which were not yet annotated as genes. Still, approximately one-third of the new CDSs were found only in T. brucei subspecies. When combined with RNA-seq and spliced leader mapping, we were able to definitively revise the start sites for 430 CDSs as compared to the current gene models. Such data also allowed us to use a structured approach to eliminate 701 putative genes as protein-coding. Finally, the data pointed to several regions of the genome that had sequence errors that altered coding region boundaries.

2015-12-22 | GSE72463 | GEO

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