Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA168638 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR514012.fastq.gz | Fastqsanger.gz | |||
| SRR514013.fastq.gz | Fastqsanger.gz | |||
| SRR514014.fastq.gz | Fastqsanger.gz | |||
| SRR514015_1.fastq.gz | Fastqsanger.gz | |||
| SRR514015_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 9 |
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Project description:Nearly half the human genome is comprised of repetitive DNA, including short interspersed nuclear elements (SINEs) such as Alu. SINEs spread by retrotransposition, which requires their transcripts to be copied into DNA and then inserted into new chromosomal sites. This can lead to genetic damage through insertional mutagenesis and through chromosomal rearrangements between nonallelic SINEs at distinct loci. SINE DNA is heavily methylated and this is thought to suppress its accessibility and transcription, thereby protecting against retrotransposition. However, we provide several lines of evidence that methylated SINE DNA is occupied genome-wide by RNA polymerase III, including the use of high-throughput bisulphite sequencing of ChIP DNA (ChIP-BS-Seq). Loss of DNA methylation has little effect on expression of SINEs or their accessibility to transcription machinery. We present evidence that methylation of histones rather than DNA plays a dominant role in suppressing SINE expression.
2015-03-23 | GSE38794 | GEO
Project description:Short interspersed nuclear elements (SINEs) are retrotransposons evolutionarily derived from endogenous RNA Polymerase III RNAs. Though SINE elements have undergone exaptation into gene regulatory elements, how transcribed SINE RNA impacts transcriptional and post-transcriptional regulation is largely unknown. This is partly due to a lack of information regarding which of the loci have transcriptional potential. Here, we present an approach (short interspersed nuclear element sequencing, SINE-seq), which selectively profiles RNA Polymerase III-derived SINE RNA, thereby identifying transcriptionally active SINE loci. Applying SINE-seq to monitor murine B2 SINE expression during a gammaherpesvirus infection revealed transcription from 28,270 SINE loci, with ~50% of active SINE elements residing within annotated RNA Polymerase II loci. Furthermore, B2 RNA can form intermolecular RNA-RNA interactions with complementary mRNAs, leading to nuclear retention of the targeted mRNA via a mechanism involving p54nrb. These findings illuminate a pathway for the selective regulation of mRNA export during stress via retrotransposon activation.
2016-10-31 | GSE85518 | GEO
Project description:In plants, the maintenance of DNA methylation is controlled by several self-reinforcing loops involving histone methylation and non-coding RNAs. However, how methylation is initially patterned at specific genomic loci is largely unknown. Here, we describe four Arabidopsis REM transcription factors, VDD, VAL, REM12 and REM13, that recognize specific sequence regions, and together with the protein GENETICS DETERMINES EPIGENETICS1 (GDE1), recruit RNA polymerase IV transcription complexes. This targeted recruitment leads to the production of 24-nucleotide small interfering RNAs (24nt-siRNAs) that guide DNA methylation to specific genomic sites in plant female reproductive tissues. In the absence of GDE1, Pol IV transcription complexes are directed to loci bound by an alternative transcription factor, REM8, highlighting the role of REM transcription factors and GDE1 proteins as positional cues for epigenetic modulation. These findings establish a direct connection between sequence-specific transcription factors and the spatial regulation of siRNAs production and DNA methylation, offering refreshed insights into the genetic control of epigenetic patterning.
2025-04-14 | MSV000097625 | MassIVE
Project description:The cellular accumulation of short non-coding RNAs (ncRNAs) transcribed by RNA Polymerase III (Pol III) is a hallmark of various cellular stressors and inflammatory-associated diseases. Yet, the mechanisms driving the accumulation of these RNAs are largely undefined. Infection with several DNA viruses is known to significantly alter the cellular Pol III transcriptome, leading to the induction of a class of non-coding retrotransposons known as short interspersed nuclear elements (SINE) and tRNA genes. Here, we sought to define the mechanisms driving Pol III transcribed ncRNA abundance during viral infection, using the murine herpesvirus MHV68 as a model. Our findings reveal that while the expression of Pol III transcripts, such as the murine-specific family of B2 SINE ncRNAs and pre-tRNAs, significantly increase during MHV68 infection, Pol III genomic occupancy is enhanced at a much fewer subset of B2 SINE and tRNA genes. Using DNA motif analyses and a convolutional neural network (CNN) based model, we identified non-promoter sequence elements within B2 SINE genes that distinguish infection-induced loci. We found that infection-induced B2 SINE genes are enriched for signal sequences that confer polyadenylation, and endogenous B2 SINE ncRNA polyadenylation depends on mRNA cleavage and polyadenylation (CPSF) machinery. We discovered that mRNA CPSF components are recruited to sites of Pol III transcription in response to MHV68 infection in a manner dependent on Pol III occupancy. Chromatin-associated B2 SINE ncRNAs are also bound by the CPSF complex, suggesting an RNA-dependent, co-transcriptional polyadenylation of B2 SINE ncRNAs. This uncovers an inducible, coupled relationship between Pol III transcription and mRNA-like polyadenylation of ncRNAs. Also, CPSF recruitment to Pol III genes is not restricted to murine genomes but also occurs at human SINE and tRNA genes, suggesting that this previously unknown coupled relationship may be a widespread feature of Pol III transcription.
2025-03-10 | GSE288677 | GEO
Project description:Lifecycle progression of the malaria parasite Plasmodium falciparum requires a finely tuned regulation of gene expression including histone methylation. The histone methyltransferase PfSET10 was previously identified as a histone H3 lysine K4 methyltransferase involved in var gene regulation, making it a prominent antimalarial target. We here investigated the role of PfSET10 in the P. falciparum blood stages in more detail, using tagged PfSET10-knockout (KO) and -knockdown (KD) lines. We demonstrated a nuclear localization of PfSET10 in the P. falciparum blood stages with peak protein levels in schizonts. PfSET10 deficiency resulted in reduced intraerythrocytic growth, but had no effect on gametocyte formation. When the PfSET10-KO line was screened for histone methylation variations, lack of PfSET10 rendered the parasites unable to mark H3K18me1, while no significant changes in the H3K4 methylation status were observed. Comparative transcriptomic profiling of PfSET10-KO schizonts demonstrated the up-regulation of transcripts particularly encoding proteins of erythrocyte invasion and multi gene family proteins, suggesting a suppressive function of the histone methylation mark. TurboID coupled with mass spectrometry further revealed an extensive nuclear PfSET10 interaction network with roles in transcriptional regulation, DNA replication and repair, chromatin remodeling and mRNA processing. Main interactors of PfSET10 included ApiAP2 transcription factors, epigenetic regulators, mediators of RNA polymerase II and DNA replication licensing factors. The combined data pinpoint PfSET10 as a histone H3 lysine K18 methyltransferase regulating DNA and RNA metabolic processes important for intraerythrocytic development of P. falciparum.
2024-09-24 | PXD052931 | JPOST Repository
Project description:B2-SINEs are noncoding RNAs which are transcribed by RNA polymerase III (Pol III) from short interspersed nuclear elements (SINEs), which are high copy number transposable elements in the mouse genome. Unexpectedly have observed significant induction of non-coding RNAs from the B2-SINE subclass of repeat element RNAs in DRG neurons following sciatic nerve injury. We next sought to identify intracellular targets of GI-SINEs, by protein pull-down from sciatic nerve axoplasm using biotinylated B2-SINE RNA as bait. We generated two constructs from the B2 consensus sequence, comprising 5’ (1-75nt) and 3’ (75-166nt) sequences, both predicted to retain their respective structures, and used the constructs to pull down axoplasm proteins for mass spectrometry analysis
2025-09-29 | PXD041633 | Pride
Project description:B2-SINEs are noncoding RNAs which are transcribed by RNA polymerase III (Pol III) from short interspersed nuclear elements (SINEs), which are high copy number transposable elements in the mouse genome. Unexpectedly have observed significant induction of non-coding RNAs from the B2-SINE subclass of repeat element RNAs in DRG neurons following sciatic nerve injury. We next sought to identify intracellular targets of GI-SINEs, by protein pull-down from sciatic nerve axoplasm using biotinylated B2-SINE RNA as bait. We generated two constructs from the B2 consensus sequence, comprising 5’ (1-75nt) and 3’ (75-166nt) sequences, both predicted to retain their respective structures, and used the constructs to pull down axoplasm proteins for mass spectrometry analysis. Further confirmatory experiments were performed using the mentioned -175nt sequence vs a control U1 SL3+4 RNA
2025-05-05 | PXD060976 | Pride
Project description:H3K36me3 is a hallmark of actively and recently transcribed genes and contributes to cellular memory and identity. The deposition of H3K36me3 occurs co-transcriptionally when the methyltransferase SETD2 associates with RNA polymerase II. Using electron microscopy assisted by protein-protein crosslinking mass spectrometry, we solved three cryo-EM structures of SETD2 bound to Pol II elongation complexes at different states of nucleosome passage. Together with functional probing, our results suggest a 3-step mechanism of transcription-coupled H3K36me3 deposition. First, binding to the elongation factor SPT6 tethers the catalytic SET domain in proximity to the upstream DNA. Second, Pol II nucleosome passage leads to the transfer of a hexasome from downstream to upstream, poised for methylation. Finally, continued transcription leads to upstream nucleosome reassembly, partial dissociation of the histone chaperone FACT and sequential methylation of both H3 tails, completing H3K36me3 deposition of an upstream nucleosome after RNA polymerase II passage.
2025-09-18 | PXD067197 | Pride
Project description:Small interspersed elements (SINEs) is transcribed by RNA polymerase III (Pol III) to produce RNAs of typically 100 to 500 nucleotides in length. Although the abundance of SINE RNAs can be analyzed by Northern blotting and primer extension, the nature (sequence, exact length, and genomic origin) of these RNAs cannot be revealed by these methods. Moreover, mRNA sequencing (mRNA-seq) is not able to distinguish bona fide SINE RNAs and SINE sequences present in longer transcripts. To elucidate the abundance, source loci, and sequence nature of SINE RNAs, we have established a deep sequencing method, designated as melRNA-seq (medium length RNA-seq), which can determine whole-length sequences of RNAs. The total RNA samples were treated with 5' Pyrophosphohydrolase (RppH), which allowed ligation of an RNA adaptor to the 5’ end of intact SINE RNAs. Another adaptor was ligated to the 3’ end, followed by reverse transcription, PCR amplification, size selection, and single-end deep sequencing. Analysis of two biological replicates of RNAs from mouse spermatogonia showed high reproducibility of the SINE expression data both at family level and locus level. Therefore, this new method can be used for the quantification and detailed sequence analysis of medium length non-coding RNAs, such as rRNA, snRNA, tRNAs, and SINE RNAs. The dynamic range is much wider than Northern blotting and primer extension.
2021-07-01 | GSE171593 | GEO
Project description:Genome-wide MAF1-dependent regulation of RNA polymerase III transcription [RNA-Seq]
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