LINE-1 elements are derepressed in senescent cells and elicit a chronic Type-I Interferon response
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE109700 | GEO | 2018/10/26
REPOSITORIES: GEO
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Project description:LINE-1 elements are derepressed in senescent cells and elicit a chronic Type-I Interferon response
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Project description:Functional abnormality of TAR DNA-binding protein 43 (TDP-43), an aggregation-prone RNA and DNA binding protein, is observed in the vast majority of both familial and sporadic ALS cases and in ~40% of FTLD cases, but the cascade of events leading to cell death are not understood. We have expressed human TDP-43 (hTDP-43) in Drosophila neurons and glia, a model that recapitulates many of the characteristics of TDP-43-linked human disease including protein aggregation pathology, locomotor impairment, and premature death. We report that such expression of hTDP-43 impairs small interfering RNA (siRNA) silencing, which is the major post-transcriptional mechanism of retrotransposable element (RTE) control in somatic tissue. This is accompanied by de-repression of a panel of both LINE and LTR families of RTEs, with somewhat different elements being active in glia vs neurons. hTDP-43 expression in glia causes an early and severe loss of control of a specific RTE, the endogenous retrovirus (ERV) gypsy. We demonstrate that gypsy causes the degenerative phenotypes in these flies because we are able to rescue the toxicity of glial hTDP-43 either by genetically blocking expression of this RTE or by pharmacologically inhibiting RTE reverse transcriptase activity. Moreover, we provide evidence that activation of DNA damage-mediated programmed cell death underlies both neuronal and glial hTDP-43 toxicity, consistent with RTE-mediated effects in both cell types. Our findings suggest a novel mechanism in which RTE activity contributes to neurodegeneration in TDP-43-mediated diseases such as ALS and FTLD.
2017-02-15 | GSE85398 | GEO
Project description:Here, we profiled N6-methyladenosine (m6A) deposition on nascent RNAs in human cells by a new method MINT-Seq, which revealed that many classes of RTE RNAs, particularly intronic LINE-1s (L1s), are strongly methylated. These m6A-marked intronic L1s (MILs) are evolutionarily young, sense-oriented to hosting genes and nucleate a dozen RNA binding proteins (RBPs) that are putative novel m6A readers, including a nuclear matrix protein SAFB. Notably, m6A positively controls the expression of both autonomous L1s and co-transcribed L1 relics, promoting L1 retrotransposition. We showed that MILs preferentially reside in long genes, where they act as transcriptional ‘roadblock’ to impede the hosting gene expression, revealing a novel host-weakening strategy by the L1s. In counteraction, the host uses the SAFB reader complex to bind m6A-L1s to reduce their levels, and to safeguard hosting gene transcription.
2021-05-14 | GSE137752 | GEO
Project description:DNA methylation is an important epigenetic modification that is thought to contribute to the maintenance of genomic integrity in somatic cells, in part through the silencing of transposable elements (TEs). In this study we used CRISPR/Cas9 mediated gene editing to disrupt DNMT1, the key maintenance methyltransferase in somatic human cells. Surprisingly, and in contrast to findings in mouse, inactivation of DNMT1 in human neural progenitor cells (hNPCs) resulted in viable proliferating cells that maintained the expression of appropriate marker genes. Removal of DNA methylation in hNPCs resulted in a specific activation of hominid-specific LINE-1 elements (L1s), while other classes of TEs remained silent. We also found that the transcriptionally activated L1s acted as alternative promoters for many protein-coding genes involved in neuronal functions, uncovering an L1-based transcriptional network influencing neuronal protein-coding genes. Our results prove novel mechanistic insight into the role of DNA methylation in somatic human cells.
2019-05-30 | PXD008648 | Pride
Project description:Defective silencing of retroviral elements has been linked to inflamm-aging, cancer and auto-immune diseases. However, the underlying mechanisms are only partially understood. Here, we implicate the histone H3.3 chaperone Daxx, a retrotransposable element (RTE) repressor inactivated in myeloid leukemia and other neoplasms, in protection from inflammatory disease. Loss of Daxx has profound effects on chromatin landscapes and histone marks of hematopoietic progenitors, leading to engagement of a Pu.1-dependent transcriptional program for myelopoiesis at the expense of B-cell differentiation. This causes neutrophilia and inflammation, predisposing mice to development of an autoinflammatory skin disease. These molecular and phenotypic perturbations are in part reverted in animals lacking both Pu.1 and Daxx. However, hematopoietic progenitors in these mice also show unique chromatin and transcriptome alterations, suggesting synergistic interaction between the two pathways. Overall, our findings implicate RTE silencing in hematopoiesis and reveal a potential functional relationship between the H3.3 loading machinery and the pioneer transcription factor Pu.1.
2021-08-31 | GSE168367 | GEO
Project description:DNA methylation is thought to contribute to the maintenance of genomic integrity in somatic cells, in part through the silencing of transposable elements (TEs). In this study, we used CRISPR/Cas9 technology to delete DNMT1, the key maintenance DNA methyltransferase in human neural progenitor cells (hNPCs). Surprisingly, and in contrast to previous findings in mouse somatic cells, inactivation of DNMT1 in hNPCs resulted in viable proliferating cells despite the global loss of DNA CpG-methylation. DNA demethylation led to specific transcriptional activation and chromatin remodeling of evolutionarily young, hominoid-specific LINE-1 elements (L1s), while older L1s and other classes of TEs remained silent. The activated L1s acted as alternative promoters for many protein-coding genes involved in neuronal functions, revealing a hominoidspecific L1-based transcriptional network controlled by DNA methylation that influences neuronal protein-coding genes. Our results give a novel mechanistic insight into the role of DNA methylation in silencing TEs in somatic human cells, as well as further implicating L1s in human brain development and disease.
2019-05-29 | GSE107580 | GEO
Project description:TET-dependent regulation of retrotransposable elements in mouse embryonic stem cells
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Project description:High and moderate intensity endurance exercise alters gene expression in human white blood cells (WBCs), but the understanding of how this effect occurs is limited. To increase our knowledge of the nature of this process, we investigated the effects of passing the anaerobic threshold (AnT) on the gene expression profile in WBCs of athletes. Nineteen highly trained skiers participated in a treadmill test with an incremental step protocol until exhaustion (ramp test to exhaustion; RTE). The average total time to exhaustion was 14:40 min and time after AnT was 4:50 min. Two weeks later, seven of these skiers participated in a moderate treadmill test (MT) at 80% peak O2 uptake for 30 min, which was slightly below their AnTs. Blood samples were obtained before and immediately after both tests. RTE was associated with substantially greater leukocytosis and acidosis than MT. Gene expression in WBCs was measured using whole genome microarray expression analysis before and immediately after each test. A total of 310 upregulated genes were found after RTE, and 69 genes after MT, of which 64 were identical to RTE. Both tests influenced a variety of known gene pathways related to inflammation, stress response, signal transduction and apoptosis. A large group of differentially expressed, and previously unknown, small nucleolar RNA and small Cajal body RNA was found. In conclusion, a 15 min test to exhaustion was associated with substantially greater changes of gene expression than a 30 min test just below the AnT. After a general medical checkup, the subjects performed a ramp-type progressive exercise test on a treadmill. Blood samples were taken from the antecubital vein using indwelling catheter before (T0) and immediately after ramp test to exaustion (T1), and before (T2) and immediately after moderate treadmill test (T3).
2011-04-09 | E-GEOD-28498 | biostudies-arrayexpress
Project description:Limited data exists regarding changes of microRNA (miRNA) expression during senescence in human cells and no reports correlate telomerase expression with regulation of senescence-related miRNAs. We used miRNA microarrays to provide a detailed account of miRNA profiles for early passage and senescent human foreskin (BJ) fibroblasts as well as early and late passage immortalized fibroblasts (BJ-hTERT) that stably express the human telomerase reverse transcriptase subunit hTERT. The revelation that miRNA expression changes with extended passaging in BJ-hTERT cells will contribute to a comprehensive understanding of the connections between telomerase expression, senescence and processes of cellular aging.
2010-06-05 | GSE22134 | GEO
Project description:The underlying mechanisms of atherosclerosis, the second leading cause of death among Werner syndrome (WS) patients, is not fully understood. Here, we established an in vitro co-culture system using macrophages (iMφs), vascular endothelial cells (iVECs), and vascular smooth muscle cells (iVSMCs) derived from induced pluripotent stem cells. In co-culture, WS-iMφs induced endothelial dysfunction in WS-iVECs and characteristics of the synthetic phenotype in WS-iVSMCs. RNA-seq and ATAC-seq revealed accelerated activation of type I interferon signaling and reduced chromatin accessibility of several transcriptional binding sites required for cellular homeostasis in WS-iMφs. Furthermore, the reduced H3K9me3 levels showed inverse correlation with retrotransposable elements, and retrotransposable element-derived dsRNA activated the DHX58-dependent cytoplasmic RNA sensing pathway in WS-iMφs. Conversely, silencing type I interferon signaling in WS-iMφs rescued cell proliferation and suppressed cellular senescence and inflammation. These findings suggest that Mφ-specific inhibition of type I interferon signaling could be targeted to treat atherosclerosis in WS patients.
2024-03-20 | GSE247721 | GEO