EGAS00001000160-4-sc-20130719 - samples
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ABSTRACT:
PROVIDER: EGAD00001000638 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Insertion of processed pseudogenes is known to occur in the germline but has not previously been observed in somatic cells. Formation of pseudogenes could represent a new class of mutation in cancers and a new source of potential driver events.
| EGAD00001000637 | EGA
Project description:Insertion of processed pseudogenes is known to occur in the germline but has not previously been observed in somatic cells. Formation of pseudogenes could represent a new class of mutation in cancers and a new source of potential driver events.
| EGAD00001000639 | EGA
Project description:Background: Canonical Nonsense Mediated Decay (NMD) is an important splicing-dependent process for mRNA surveillance in mammals. However, processed pseudogenes are not able to trigger NMD due to their lack of introns. It is largely unknown whether they have evolved other surveillance mechanisms. Results: Here, we find that the RNAs of pseudogenes, especially processed pseudogenes, have dramatically higher m6A levels than their cognate protein-coding genes, associated with de novo m6A peaks and motifs in human cells. Furthermore, pseudogenes have rapidly accumulated m6A motifs during evolution. The m6A sites of pseudogenes are evolutionarily younger than neutral sites and their m6A levels are increasing, supporting the idea that m6A on the RNAs of pseudogenes is under positive selection. We then find that the m6A RNA modification of processed, rather than unprocessed, pseudogenes promotes cytosolic RNA degradation and attenuates interference with the RNAs of their cognate protein-coding genes. We experimentally validate the m6A RNA modification of two processed pseudogenes, DSTNP2 and NAP1L4P1, which promotes the RNA degradation of both pseudogenes and their cognate protein-coding genes DSTN and NAP1L4. In addition, the m6A of DSTNP2 regulation of DSTN is partially dependent on the miRNA miR-362-5p. Conclusions: Our discovery reveals a novel evolutionary role of m6A RNA modification in cleaning up the unnecessary processed pseudogene transcripts to attenuate their interfering with the regulatory network of proteincoding genes.
2021-05-27 | GSE172219 | GEO
Project description:We aim to comprehensively characterize the small RNA population in oocytes Pseudogenes populate the mammalian genome as remnants of artifactual incorporation of coding mRNAs into transposon pathways 1. Here, we show that a subset of pseudogenes generates endogenous small interfering RNAs (endo-siRNAs) in mouse oocytes. In these cases, endo-siRNAs are often processed from double-stranded RNAs formed by hybridization of spliced transcripts from protein coding genes to antisense transcripts from homologous pseudogenes. In at least one case, an inverted repeat pseudogene gives rise to abundant small RNAs directly. A second class of endo-siRNAs may enforce repression of mobile genetic elements, acting in concert with piwi-interacting RNAs (piRNAs). Loss of Dicer increases expression of endo-siRNA targets, demonstrating the regulatory activity of these small RNAs. Our findings provide a function for pseudogenes in regulating gene expression via the RNAi pathway and may, in part, explain the evolutionary pressure to conserve Argonaute-mediated catalysis in mammals. Keywords: small RNAs profile
2008-03-28 | GSE10364 | GEO
Project description:Positive natural selection of N6-methyladenosine on the RNAs of processed pseudogenes
| PRJNA722485 | ENA
Project description:This dataset contains data from two acute myeloid leukaemia (AML) specimens processed with the Illumina CytoSNP-12 SNP array platform. SNP array data showed evidence of chromothripsis in these two specimens. Each deletion in the mosaic specimen was present in the same proportion of cells, which supports the view that the many breaks occur as a single event. Complementary FISH studies highlighted the inclusion of centromeres from different chromosomes during the formation of the new chromosomes.
2013-08-04 | GSE43522 | GEO
Project description:We developed SCAN-seq2, a high-throughput and highly sensitive single-cell RNA sequencing method based on the TGS platform. Our study demonstrated that SCAN-seq2 improves upon the previous method, SCAN-seq, in terms of sensitivity and throughput. By using reference-guided assembly of single-cell data, we were able to identify thousands of novel full-length RNA isoforms, including cell type-specific expression patterns of pseudogenes. We also accurately determined V(D)J rearrangement events in T and B cells. Lastly, we found that treatment of HepG2 and Hela cells with the spliceosome inhibitor Isoginkgetin (IGG) resulted in a subpopulation of cells with distinct apoptosis features. Our study provides a promising new tool for single-cell transcriptome research. The source code for SCAN-seq2 data analysis pipelines is available at https://github.com/liuzhenyu-yyy/SCAN-seq2 .
2022-11-15 | GSE203561 | GEO
Project description:Insertions occur when a segment of one chromosome is translocated and inserted into a new region of the same chromosome or a non-homologous chromosome. We report 69 cases with unbalanced insertions identified using array CGH and FISH, representing 1.25% of 5,683 cases referred to our laboratory for array CGH and found to have copy-number abnormalities. Although the majority of insertions were non-recurrent, several recurrent unbalanced insertions were detected, including three der(Y)ins(Y;18)(q?11.2;p11.32p11.32)pat inherited from parents carrying an unbalanced insertion. The clinical significance of these recurrent rearrangements is unclear, although the small size, limited gene content, and inheritance pattern of each suggests the phenotypic consequences may be benign. Moreover, cryptic, submicroscopic duplications were observed at or near the insertion sites in two patients, further confounding the clinical interpretation of these insertions. Using FISH, linear amplification and array CGH we identified a 126-kb duplicated region from 19p13.3 inserted into MECP2 at Xq28 in a patient with symptoms of Rett syndrome. Our results demonstrate that although the interpretation of most non-recurrent insertions is unclear without high-resolution insertion site characterization, the potential for an otherwise benign duplication to result in a clinically relevant outcome through the disruption of a gene necessitates the use of FISH to determine whether copy-number gains detected by array CGH represent tandem duplications or unbalanced insertions. Further follow-up testing using techniques such as linear amplification coupled with array CGH or sequencing should be used to determine gene involvement at the insertion site after FISH has identified the presence of an insertion. 88 total samples analyzed. No replicates included. Each sample run against a standard sex-matched control.
2011-02-28 | E-GEOD-27080 | biostudies-arrayexpress
Project description:Class switch recombination generates antibody distinct isotypes critical to a robust adaptive immune system and defects are associated with auto-immune disorders and lymphomagenesis. Transcription is required during class switch to recruit the cytidine deaminase AID—an essential step for the formation of DNA doublestrand breaks—and strongly induces the formation of R loops within the immunoglobulin heavy chain locus. However, the impact of R loops on double-strand break formation and repair during class switch recombination remains unclear. Here we report that cells lacking two enzymes involved in R loop removal— Senataxin and RNase H2—exhibit increased R loop formation and genome instability at the immunoglobulin heavy chain locus without impacting class switch recombination efficiency, transcriptional activity, or AID recruitment. Senataxin and RNase H2-deficient cells also exhibit increased insertion mutations at switch junctions, a hallmark of alternative end joining. Importantly, these phenotypes were not observed in cells lacking Senataxin or RNase H2B alone. We propose that Senataxin acts redundantly with RNase H2 to mediate timely R loop removal, promoting efficient repair while suppressing AID-dependent genome instability and insertional mutagenesis.
2022-12-14 | GSE201210 | GEO
Project description:The Plasmodium falciparum human malaria parasite genome is incompletely annotated and does not accurately represent the transcriptomic diversity of this species. To address this need, we performed long-read transcriptomic sequencing. To increase representation of mRNA isoforms expressed during intraerythrocytic stages, RNA was extracted from samples taken at time-points from synchronized cultures. 5 capped mRNA was enriched and converted to cDNA library. The cDNA libraries were sequenced on Nanopore and PacBio long-read platforms. Candidate non-redundant isoforms were annotated from each library dataset for creating a new transcript annotation catalog. Isoforms with alternative 5 ends represented the largest class of novel isoforms, although the majority of these do not seem to represent the products of alternative transcription initiation events. We suggest that most isoforms do not encode protein isoforms and instead represent RNA decay products.
2022-10-26 | GSE186109 | GEO