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.
| EGAD00001000639 | 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.
| EGAD00001000637 | EGA
Project description:The human genome harbors 15,000 pseudogenes, except very few can transcribe non-coding RNAs or encode truncated proteins, a large number of which without transcriptional capacity are functionally unknown. Here, we proposed and verified that pseudogene DNA sequences can form chromatin contacts that act as anchors of chromatin loops and boundaries of topologically associating domains (TADs). More amazing, due to the sequence-specificity of pseudogenes, TAD boundaries containing them in the human genome were primarily species-specific, including human-specific and primate-specific ones. We found that during primate evolution, by inheritance from parent genes, certain pseudogenes can introduce additional transcription factor-binding sequences, especially CTCF, at their insertion sites to generate species-specific TAD boundaries, and due to the participation in TAD evolution, CTCF binding motifs on pseudogenes were subjected to significantly heightened selection pressure. Deleting these pseudogenes in human embryonic stem cells (hESCs) disrupted the structure of species-specific TADs, whereas inserting them in mouse embryonic stem cells (mESCs) mediated new TADs formation, and pseudogenes involved in three-dimensional (3D) genome formation were critical for maintaining hESCs self-renewal. The structural necessity and biological function of these pseudogenes demonstrated the broad significance of pseudogenes in 3D genome construction and evolution.
2025-10-01 | GSE297131 | GEO
Project description:The human genome harbors 15,000 pseudogenes, except very few can transcribe non-coding RNAs or encode truncated proteins, a large number of which without transcriptional capacity are functionally unknown. Here, we proposed and verified that pseudogene DNA sequences can form chromatin contacts that act as anchors of chromatin loops and boundaries of topologically associating domains (TADs). More amazing, due to the sequence-specificity of pseudogenes, TAD boundaries containing them in the human genome were primarily species-specific, including human-specific and primate-specific ones. We found that during primate evolution, by inheritance from parent genes, certain pseudogenes can introduce additional transcription factor-binding sequences, especially CTCF, at their insertion sites to generate species-specific TAD boundaries, and due to the participation in TAD evolution, CTCF binding motifs on pseudogenes were subjected to significantly heightened selection pressure. Deleting these pseudogenes in human embryonic stem cells (hESCs) disrupted the structure of species-specific TADs, whereas inserting them in mouse embryonic stem cells (mESCs) mediated new TADs formation, and pseudogenes involved in three-dimensional (3D) genome formation were critical for maintaining hESCs self-renewal. The structural necessity and biological function of these pseudogenes demonstrated the broad significance of pseudogenes in 3D genome construction and evolution.
2025-10-01 | GSE297130 | GEO
Project description:The human genome harbors 15,000 pseudogenes, except very few can transcribe non-coding RNAs or encode truncated proteins, a large number of which without transcriptional capacity are functionally unknown. Here, we proposed and verified that pseudogene DNA sequences can form chromatin contacts that act as anchors of chromatin loops and boundaries of topologically associating domains (TADs). More amazing, due to the sequence-specificity of pseudogenes, TAD boundaries containing them in the human genome were primarily species-specific, including human-specific and primate-specific ones. We found that during primate evolution, by inheritance from parent genes, certain pseudogenes can introduce additional transcription factor-binding sequences, especially CTCF, at their insertion sites to generate species-specific TAD boundaries, and due to the participation in TAD evolution, CTCF binding motifs on pseudogenes were subjected to significantly heightened selection pressure. Deleting these pseudogenes in human embryonic stem cells (hESCs) disrupted the structure of species-specific TADs, whereas inserting them in mouse embryonic stem cells (mESCs) mediated new TADs formation, and pseudogenes involved in three-dimensional (3D) genome formation were critical for maintaining hESCs self-renewal. The structural necessity and biological function of these pseudogenes demonstrated the broad significance of pseudogenes in 3D genome construction and evolution.
2025-10-01 | GSE297129 | GEO
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:The human genome harbors 15,000 pseudogenes, except very few can transcribe non-coding RNAs or encode truncated proteins, a large number of which without transcriptional capacity are functional unknown. Here, we found that DNA sequence of pseudogenes can form chromatin contacts, acting as anchors of chromatin loops and boundaries of topological associated domains (TADs), many of them are proved to be structural important and essential for human embryonic stem cells (hESCs) survival. Incorporating genetic data, we defined a hominoidea-specific pseudogene, TUBBP2, which acted as a TAD boundary by enriching CTCF, to maintain the 3D genome and self-renewal of hESCs. Evolutionally, TUBBP2 was generated in 18.8 million years ago through retroposition and inherited the CTCF binding motif from its parent gene-TUBB, thus enhance the strength of TADs at the insertion site in great apes genome. More amazing, by inheritance from parent genes or sequence variation, a part of pseudogenes can introduce additional CTCF binding sequence at their insertion sites to generate species-specific topological domains, which may contribute to species evolution. Overall, we not only demonstrate the essentiality of pseudogenes in the formation and maintenance of 3D chromatin structure, but provide insights on their functions of driving species evolution.
2025-10-01 | GSE246286 | GEO
Project description:The human genome harbors 15,000 pseudogenes, except very few can transcribe non-coding RNAs or encode truncated proteins, a large number of which without transcriptional capacity are functional unknown. Here, we found that DNA sequence of pseudogenes can form chromatin contacts, acting as anchors of chromatin loops and boundaries of topological associated domains (TADs), many of them are proved to be structural important and essential for human embryonic stem cells (hESCs) survival. Incorporating genetic data, we defined a hominoidea-specific pseudogene, TUBBP2, which acted as a TAD boundary by enriching CTCF, to maintain the 3D genome and self-renewal of hESCs. Evolutionally, TUBBP2 was generated in 18.8 million years ago through retroposition and inherited the CTCF binding motif from its parent gene-TUBB, thus enhance the strength of TADs at the insertion site in great apes genome. More amazing, by inheritance from parent genes or sequence variation, a part of pseudogenes can introduce additional CTCF binding sequence at their insertion sites to generate species-specific topological domains, which may contribute to species evolution. Overall, we not only demonstrate the essentiality of pseudogenes in the formation and maintenance of 3D chromatin structure, but provide insights on their functions of driving species evolution.
2025-10-01 | GSE246285 | GEO
Project description:The human genome harbors 15,000 pseudogenes, except very few can transcribe non-coding RNAs or encode truncated proteins, a large number of which without transcriptional capacity are functional unknown. Here, we found that DNA sequence of pseudogenes can form chromatin contacts, acting as anchors of chromatin loops and boundaries of topological associated domains (TADs), many of them are proved to be structural important and essential for human embryonic stem cells (hESCs) survival. Incorporating genetic data, we defined a hominoidea-specific pseudogene, TUBBP2, which acted as a TAD boundary by enriching CTCF, to maintain the 3D genome and self-renewal of hESCs. Evolutionally, TUBBP2 was generated in 18.8 million years ago through retroposition and inherited the CTCF binding motif from its parent gene-TUBB, thus enhance the strength of TADs at the insertion site in great apes genome. More amazing, by inheritance from parent genes or sequence variation, a part of pseudogenes can introduce additional CTCF binding sequence at their insertion sites to generate species-specific topological domains, which may contribute to species evolution. Overall, we not only demonstrate the essentiality of pseudogenes in the formation and maintenance of 3D chromatin structure, but provide insights on their functions of driving species evolution.
2025-10-01 | GSE246661 | 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