Expression Of Repetitive Elements Research Articles

Repetitive element transcripts are elevated in the brain of C9orf72 ALS/FTLD patients.

Significant transcriptome alterations are detected in the brain of patients with amyotrophic lateral sclerosis (ALS), including carriers of the C9orf72 repeat expansion and C9orf72-negative sporadic cases. Recently, the expression of repetitive element transcripts has been associated with toxicity and, while increased repetitive element expression has been observed in several neurodegenerative diseases, little is known about their contribution to ALS. To assess whether aberrant expression of repetitive element sequences are observed in ALS, we analysed RNA sequencing data from C9orf72-positive and sporadic ALS cases, as well as healthy controls. Transcripts from multiple classes and subclasses of repetitive elements (LINEs, endogenous retroviruses, DNA transposons, simple repeats, etc.) were significantly increased in the frontal cortex of C9orf72 ALS patients. A large collection of patient samples, representing both C9orf72 positive and negative ALS, ALS/FTLD, and FTLD cases, was used to validate the levels of several repetitive element transcripts. These analyses confirmed that repetitive element expression was significantly increased in C9orf72-positive compared to C9orf72-negative or control cases. While previous studies suggest an important link between TDP-43 and repetitive element biology, our data indicate that TDP-43 pathology alone is insufficient to account for the observed changes in repetitive elements in ALS/FTLD. Instead, we found that repetitive element expression positively correlated with RNA polymerase II activity in postmortem brain, and pharmacologic modulation of RNA polymerase II activity altered repetitive element expression in vitro. We conclude that increased RNA polymerase II activity in ALS/FTLD may lead to increased repetitive element transcript expression, a novel pathological feature of ALS/FTLD.

Radiation-induced changes in DNA methylation of repetitive elements in the mouse heart

DNA methylation is a key epigenetic mechanism, needed for proper control over the expression of genetic information and silencing of repetitive elements. Exposure to ionizing radiation, aside from its strong genotoxic potential, may also affect the methylation of DNA, within the repetitive elements, in particular. In this study, we exposed C57BL/6J male mice to low absorbed mean doses of two types of space radiation—proton (0.1Gy, 150MeV, dose rate 0.53±0.08Gy/min), and heavy iron ions (56Fe) (0.5Gy, 600MeV/n, dose rate 0.38±0.06Gy/min). Radiation-induced changes in cardiac DNA methylation associated with repetitive elements were detected. Specifically, modest hypomethylation of retrotransposon LINE-1 was observed at day 7 after irradiation with either protons or 56Fe. This was followed by LINE-1, and other retrotransposons, ERV2 and SINE B1, as well as major satellite DNA hypermethylation at day 90 after irradiation with 56Fe. These changes in DNA methylation were accompanied by alterations in the expression of DNA methylation machinery and affected the one-carbon metabolism pathway. Furthermore, loss of transposable elements expression was detected in the cardiac tissue at the 90-day time-point, paralleled by substantial accumulation of mRNA transcripts, associated with major satellites. Given that the one-carbon metabolism pathway can be modulated by dietary modifications, these findings suggest a potential strategy for the mitigation and, possibly, prevention of the negative effects exerted by ionizing radiation on the cardiovascular system. Additionally, we show that the methylation status and expression of repetitive elements may serve as early biomarkers of exposure to space radiation.

Exposure to low-dose (56)Fe-ion radiation induces long-term epigenetic alterations in mouse bone marrow hematopoietic progenitor and stem cells.

There is an increasing need to better understand the long-term health effects of high-linear energy transfer (LET) radiation due to exposure during space missions, as well as its increasing use in clinical treatments. Previous studies have indicated that exposure to (56)Fe heavy ions increases the incidence of acute myeloid leukemia (AML) in mice but the underlying molecular mechanisms remain elusive. Epigenetic alterations play a role in radiation-induced genomic instability and the initiation and progression of AML. In this study, we assessed the effects of low-dose (56)Fe-ion irradiation on epigenetic alterations in bone marrow mononuclear cells (BM-MNCs) and hematopoietic progenitor and stem cells (HPSCs). Exposure to (56)Fe ions (600 MeV, 0.1, 0.2 and 0.4 Gy) resulted in significant epigenetic alterations involving methylation of DNA, the DNA methylation machinery and expression of repetitive elements. Four weeks after irradiation, these changes were primarily confined to HPSCs and were exhibited as dose-dependent hypermethylation of LINE1 and SINE B1 repetitive elements [4.2-fold increase in LINE1 (P < 0.001) and 7.6-fold increase in SINE B1 (P < 0.01) after exposure to 0.4 Gy; n = 5]. Epigenetic alterations were persistent and detectable for at least 22 weeks after exposure, when significant loss of global DNA hypomethylation (1.9-fold, P < 0.05), decreased expression of Dnmt1 (1.9-fold, P < 0.01), and increased expression of LINE1 and SINE B1 repetitive elements (2.8-fold, P < 0.001 for LINE1 and 1.9-fold, P < 0.05 for SINE B1; n = 5) were observed after exposure to 0.4 Gy. In contrast, exposure to (56)Fe ions did not result in accumulation of increased production of reactive oxygen species (ROS) and DNA damage, exhibited as DNA strand breaks. Furthermore, no significant alterations in cellular senescence and apoptosis were detected in HPSCs after exposure to (56)Fe-ion radiation. These findings suggest that epigenetic reprogramming is possibly involved in the development of radiation-induced genomic instability and thus, may have a causative role in the development of AML.

Silencing of LINE-1 retrotransposons contributes to variation in small noncoding RNA expression in human cancer cells.

Noncoding RNAs are key players in the maintenance of genomic integrity, particularly in silencing the expression of repetitive elements, some of which are retrotransposable and capable of causing genomic instability. Recent computational studies suggest an association between L1 expression and the generation of small RNAs. However, whether L1 expression has a role in the activation of small RNA expression has yet to be determined experimentally. Here we report a global analysis of small RNAs in deep sequencing from L1-active and L1-silenced breast cancer cells. We found that cells in which L1 expression was silenced exhibited greatly increased expression of a number of miRNAs and in particular, members of the let-7 family. In addition, we found differential expression of a few piRNAs that might potentially regulate gene expression. We also report the identification of several repeat RNAs against LTRs, LINEs and SINE elements. Although most of the repeat RNAs mapped to L1 elements, in general we found no significant differences in the expression levels of repeat RNAs in the presence or absence of L1 expression except for a few RNAs targeting subclasses of L1 elements. These differentially expressed small RNAs may function in human genome defence responses.

Dnmt3b Has Few Specific Functions In Adult Hematopoietic Stem Cells But Shows Abnormal Activity In The Absence Of Dnmt3a

DNA methylation is one of the major epigenetic modifications in the vertebrate genome and is important for development, stem cell differentiation, and malignant transformation. DNA methylation is catalyzed by the DNA methyltransferase enzymes Dnmt1, Dnmt3a, and Dnmt3b. We have recently shown that Dnmt3a is essential for hematopoietic stem cell (HSC) differentiation. Ablation of Dnmt3a in hematopoietic cells (Mx1-CRE; Dnmt3a-KO) resulted in HSCs that could not sustain peripheral blood generation after serial transplantation, while phenotypically defined HSCs accumulated in the bone marrow. Recurrent somatic mutations in DNTM3A have been discovered in patients with a wide range of hematopoietic malignancies (AML, MDS, MPN, CML, T-ALL, T-cell lymphoma) suggesting a critical role for de novo DNA methylation in normal and leukemic hematopoiesis. As Dnmt3b is also highly expressed in HSCs and congenital mutations in DNMT3B can cause ICF (immunodeficiency, centromeric instability, and facial anomalies) syndrome, in this study we used a mouse model to investigate if Dnmt3b had distinct roles in HSCs.We conditionally inactivated Dnmt3b in HSCs using the Mx1-CRE system (Dnmt3b-KO) and performed serial competitive transplantation. Loss of Dnmt3b had minimal functional consequences for adult HSC function even after three rounds of transplantation. However, combinatorial deletion of both Dnmt3a and Dnmt3b (Dnmt3ab-dKO) exacerbated the differentiation defect seen in Dnmt3a-KO HSCs, leading to a dramatic accumulation of mutant HSCs in the bone marrow (>50-fold), suggesting a synergistic effect resulting from simultaneous ablation of both de novo DNA methyltransferases. The accumulation of Dnmt3ab-dKO HSCs cannot be attributed to altered proliferation or apoptosis, but is due to an imbalance between self-renewal and differentiation. RNA-SEQ of the mutant HSCs revealed loss of transcriptional integrity in Dnmt3ab-dKO HSCs including increased expression of repetitive elements, inappropriate mRNA splicing, and over-expression of HSC-specific genes.To examine the impact of loss of Dnmt3a and -3b on DNA methylation in HSCs, we performed Whole Genome Bisulfite Sequencing (WGBS). Ablation of both enzymes resulted in loss of DNA methylation that was much more extensive than that seen in the absence of Dnmt3a alone, while loss of Dnmt3b alone showed only minimal changes in DNA methylation compared to control HSCs. One puzzling finding was the observation that a subset of promoter CpG islands (CGIs) actually gained DNA methylation in Dnmt3a-KO HSCs. This CGI hypermethylation is a cancer methylome phenotype and was specific to Dnmt3a-KO HSCs (Figure 1A). The HSC transplant experiments suggest that Dnmt3a can compensate for Dnmt3b in HSCs, but Dnmt3b cannot reciprocate in the reverse situation. An explanation for increases in DNA methylation is that in the absence of Dnmt3a, abnormal function of Dnmt3b may lead to aberrant CGI hypermethylation as the hypermethylation was lost when both enzymes were conditionally inactivated. To confirm the mechanism, post-transplant Dnmt3ab-dKO HSCs were transduced with a retroviral vector encoding ectopic expression of Dnmt3b (MIG-Dnmt3b) or a control empty vector (MIG) and assessed for DNA methylation by bisulfite PCR. Using the promoter CGI of Praf2 as an example, enforced expression of Dnmt3b in Dnmt3ab-dKO HSCs resulted in increased DNA methylation at this loci compared to Dnmt3ab-dKO HSCs transduced with a control empty vector (MIG), control HSCs transduced with either MIG or MIG-Dnmt3b and untransduced HSCs (Figure 1B). It is possible that when Dnmt3b tries to compensate for Dnmt3a, the locus-specificity for targets is reduced, leading to aberrant DNA methylation patterns. Promoter CGI hypermethylation is a cancer phenotype observed in a wide range of tumors, including hematopoietic neoplasms driven by mutation in DNMT3A. Targeting DNMT3B in DNMT3A-mutation hematopoietic pathologies may be a therapeutic option for restoring normal DNA methylation and gene expression patterns. [Display omitted] Disclosures:No relevant conflicts of interest to declare.

Chromatin signatures and retrotransposon profiling in mouse embryos reveal regulation of LINE-1 by RNA

How a more plastic chromatin state is maintained and reversed during development is unknown. Heterochromatin-mediated silencing of repetitive elements occurs in differentiated cells. Here, we used repetitive elements, including retrotransposons, as model loci to address how and when heterochromatin forms during development. RNA sequencing throughout early mouse embryogenesis revealed that repetitive-element expression is dynamic and stage specific, with most repetitive elements becoming repressed before implantation. We show that LINE-1 and IAP retrotransposons become reactivated from both parental genomes after fertilization. Chromatin immunoprecipitation for H3K4me3 and H3K9me3 in 2- and 8-cell embryos indicates that their developmental silencing follows loss of activating marks rather than acquisition of conventional heterochromatic marks. Furthermore, short LINE-1 RNAs regulate LINE-1 transcription in vivo. Our data indicate that reprogramming after mammalian fertilization comprises a robust transcriptional activation of retrotransposons and that repetitive elements are initially regulated through RNA.

Dnmt3b Is Dispensable for Hematopoietic Stem Cell Differentiation, but Acts Synergistically with Dnmt3a to Control the Balance Between Self-Renewal and Differentiation

AbstractAbstract 848DNA methylation is an epigenetic modification in vertebrate genomes critical for regulation of gene expression. DNA methylation is catalyzed by a family of DNA methyltransferase enzymes, Dnmt1, Dnmt3a, and Dnmt3b. Dnmt1 is primarily a maintenance methyltransferase, targeting hemimethylated DNA to reestablish methylation marks after DNA replication. Dnmt3a and Dnmt3b are de novo methyltransferases that are essential for normal embryonic development. In humans, somatic mutations in DNTM3A have been identified in ∼20% of human acute myeloid leukemia (AML) and ∼10% of myelodysplastic syndrome (MDS) patients, but the mechanisms through which these mutations contribute to pathogenesis is not well understood. Congenital mutations in DNMT3B can cause ICF (immunodeficiency, centromeric instability, and facial anomalies) syndrome. These patients exhibit chromosomal instability due to heterochromatin decondensation and demethylation of satellite DNA.Our group has recently reported that Dnmt3a is essential for HSC differentiation (Challen Nature Genetics, 2011). Conditional knockout of Dnmt3a (Dnmt3a-KO) resulted in HSCs that could not sustain peripheral blood generation after serial transplantation, but phenotypically defined HSCs accumulated in the bone marrow.Dnmt3b is also highly expressed in HSCs, but its contribution to gene regulation in hematopoiesis is unclear. Here, we examine the role of Dnmt3b, alone and in combination with Dnmt3a KO, in the regulation of hematopoiesis. We performed conditional ablation of Dnmt3b, as well as Dnmt3a and Dnmt3b simultaneously using the Mx1-cre system. Unlike the Dnmt3a-KO HSCs, loss of Dnmt3b had a minimal impact on blood production. Even after several rounds of transplantation, 3b-KO HSCs performed similarly to WT controls. However, the Dnmt3ab-dKO (double knock-out) peripheral blood contribution was quickly and severely diminished, accompanied by a dramatic accumulation of Dnmt3ab-dKO HSCs in the bone marrow (Figure 1). The dKO phenotype paralleled that of the 3a-KO HSC, but was more extreme.To examine the impact of loss of Dnmt3a and -3b on DNA methylation in HSCs, we performed Whole Genome Bisulfite Sequencing (WGBS) on Dnmt3a-KO, Dnmt3ab- dKO and control HSCs. As we previously found with more limited DNA methylation analysis, loss of Dnmt3a led to both increases and decreases of DNA methylation at distinct genomic regions (Challen, Nature Genetics, 2011). However, loss of both Dnmt3a and -3b primarily resulted in loss of DNA methylation that was much more extensive than that seen in the 3a-KO. In addition, RNAseq of the mutant HSCs revealed increased expression of repetitive elements, inappropriate splicing, and truncation of 3ÕUTRs.To gain insight into the accumulation of Dnmt3ab-dKO HSCs in the bone marrow, we performed a time course analysis of the proliferation and apoptosis status of the HSCs. Every four weeks after transplantation of HSCs, we sacrificed a cohort of 3 control and 3 dKO mice, counted donor derived HSCs in the bone marrow, and analyzed their Ki67 and Annexin V expression. Up to 12 weeks post-transplant, no significant differences are seen in the expression of Ki67 or Annexin V.These data show that while Dnmt3b alone has minimal impact on DNA methylation in HSCs, Dnmt3a and -3b act synergistically to effect gene expression changes that permit HSC differentiation. In the absence of both of these de novo DNA methyltransferases, there is an immediate and extreme shift toward self-renewal of dKO HSCs. The Ki67 and Annexin V expression patterns suggest that a lack of de novo DNA methylation does not affect the proliferation or apoptosis of HSCs, but instead that the accumulation of HSCs and lack of peripheral blood contribution is primarily due to an imbalance between self-renewal and differentiation. By understanding the mechanisms through which Dnmt3a and -3b exert these effects, we should identify genes that are critical for normal hematopoietic differentiation. These genes may serve as targets for therapeutic intervention in malignancies caused by defective DNA methyltransferases. [Display omitted] Disclosures:No relevant conflicts of interest to declare.

Microarray analysis of LTR retrotransposon silencing identifies Hdac1 as a regulator of retrotransposon expression in mouse embryonic stem cells.

Retrotransposons are highly prevalent in mammalian genomes due to their ability to amplify in pluripotent cells or developing germ cells. Host mechanisms that silence retrotransposons in germ cells and pluripotent cells are important for limiting the accumulation of the repetitive elements in the genome during evolution. However, although silencing of selected individual retrotransposons can be relatively well-studied, many mammalian retrotransposons are seldom analysed and their silencing in germ cells, pluripotent cells or somatic cells remains poorly understood. Here we show, and experimentally verify, that cryptic repetitive element probes present in Illumina and Affymetrix gene expression microarray platforms can accurately and sensitively monitor repetitive element expression data. This computational approach to genome-wide retrotransposon expression has allowed us to identify the histone deacetylase Hdac1 as a component of the retrotransposon silencing machinery in mouse embryonic stem cells, and to determine the retrotransposon targets of Hdac1 in these cells. We also identify retrotransposons that are targets of other retrotransposon silencing mechanisms such as DNA methylation, Eset-mediated histone modification, and Ring1B/Eed-containing polycomb repressive complexes in mouse embryonic stem cells. Furthermore, our computational analysis of retrotransposon silencing suggests that multiple silencing mechanisms are independently targeted to retrotransposons in embryonic stem cells, that different genomic copies of the same retrotransposon can be differentially sensitive to these silencing mechanisms, and helps define retrotransposon sequence elements that are targeted by silencing machineries. Thus repeat annotation of gene expression microarray data suggests that a complex interplay between silencing mechanisms represses retrotransposon loci in germ cells and embryonic stem cells.

Establishing the baseline level of repetitive element expression in the human cortex

BackgroundAlthough nearly half of the human genome is comprised of repetitive sequences, the expression profile of these elements remains largely uncharacterized. Recently developed high throughput sequencing technologies provide us with a powerful new set of tools to study repeat elements. Hence, we performed whole transcriptome sequencing to investigate the expression of repetitive elements in human frontal cortex using postmortem tissue obtained from the Stanley Medical Research Institute.ResultsWe found a significant amount of reads from the human frontal cortex originate from repeat elements. We also noticed that Alu elements were expressed at levels higher than expected by random or background transcription. In contrast, L1 elements were expressed at lower than expected amounts.ConclusionsRepetitive elements are expressed abundantly in the human brain. This expression pattern appears to be element specific and can not be explained by random or background transcription. These results demonstrate that our knowledge about repetitive elements is far from complete. Further characterization is required to determine the mechanism, the control, and the effects of repeat element expression.

Analysis of HIV-1 expression level and sense of transcription by high-throughput sequencing of the infected cell.

Next-generation sequencing offers an unprecedented opportunity to jointly analyze cellular and viral transcriptional activity without prerequisite knowledge of the nature of the transcripts. SupT1 cells were infected with a vesicular stomatitis virus G envelope protein (VSV-G)-pseudotyped HIV vector. At 24 h postinfection, both cellular and viral transcriptomes were analyzed by serial analysis of gene expression followed by high-throughput sequencing (SAGE-Seq). Read mapping resulted in 33 to 44 million tags aligning with the human transcriptome and 0.23 to 0.25 million tags aligning with the genome of the HIV-1 vector. Thus, at peak infection, 1 transcript in 143 is of viral origin (0.7%), including a small component of antisense viral transcription. Of the detected cellular transcripts, 826 (2.3%) were differentially expressed between mock- and HIV-infected samples. The approach also assessed whether HIV-1 infection modulates the expression of repetitive elements or endogenous retroviruses. We observed very active transcription of these elements, with 1 transcript in 237 being of such origin, corresponding on average to 123,123 reads in mock-infected samples (0.40%) and 129,149 reads in HIV-1-infected samples (0.45%) mapping to the genomic Repbase repository. This analysis highlights key details in the generation and interpretation of high-throughput data in the setting of HIV-1 cellular infection.

Detection of nascent RNA, single-copy DNA and protein localization by immunoFISH in mouse germ cells and preimplantation embryos

Dynamic reprogramming of the genome takes place during the gamete-to-embryo transition. This transition defines a period of continuous and global change but has been difficult to study because of extremely limited material and varying degrees of chromatin compaction. Improved methods of detecting chromatin and gene expression changes in the germ line and in the preimplantation embryo would greatly enhance the understanding of this crucial developmental transition. Here we describe a protocol developed and used by us that improves the sensitivity of existing fluorescence in situ hybridization (FISH) methods; the protocol described here has enabled us to visualize single-copy DNA targets and corresponding nascent RNA transcripts in preimplantation embryos and during spermatogenesis. Major improvements over alternative methods involve fixation and permeabilization steps. Chromatin epitopes can be visualized simultaneously by combining FISH with immunofluorescence; multicopy and repetitive element expression can also be reliably measured. This procedure (sample preparation and staining) requires 1-1.5 d to complete and will facilitate detailed examination of spatial relationships between chromatin epitopes, DNA and RNA during the dynamic transition from gamete to embryo.

Active Chromatin Marks Are Retained on X Chromosomes Lacking Gene or Repeat Silencing Despite XIST/Xist Expression in Somatic Cell Hybrids

BackgroundX-chromosome inactivation occurs early in mammalian development and results in the inactive X chromosome acquiring numerous hallmarks of heterochromatin. While XIST is a key player in the inactivation process, the method of action of this ncRNA is yet to be determined.Methodology/Principal FindingsTo assess which features of heterochromatin may be directly recruited by the expression and localization of the XIST RNA we have analyzed a mouse/human somatic cell hybrid in which expression of human and mouse XIST/Xist has been induced from the active X by demethylation. Such hybrids had previously been demonstrated to disconnect XIST/Xist expression from gene silencing and we confirm maintenance of X-linked gene expression, even close to the Xist locus, despite the localized expression of mouse Xist.Conclusions/SignificanceLoss of the active chromatin marks H3 acetylation and H3 lysine 4 methylation was not observed upon XIST/Xist expression, nor was there a gain of DNA methylation; thus these marks of facultative heterochromatin are not solely dependent upon Xist expression. Cot-1 holes, regions of depleted RNA hybridization with a Cot-1 probe, were observed upon Xist expression; however, these were at reduced frequency and intensity in these somatic cells. Domains of human Cot-1 transcription were observed corresponding to the human chromosomes in the somatic cell hybrids. The Cot-1 domain of the X was not reduced with the expression of XIST, which fails to localize to the human X chromosome in a mouse somatic cell background. The human inactive X in a mouse/human hybrid cell also shows delocalized XIST expression and an ongoing Cot-1 domain, despite X-linked gene silencing. These results are consistent with recent reports separating Cot-1 silencing from genic silencing, but also demonstrate repetitive element expression from an otherwise silent X chromosome in these hybrid cells.

Abundant transcripts from retrotransposons are unstable in fully grown mouse oocytes

One physiological function proposed for RNA interference (RNAi) is to constrain expression of repetitive elements and thereby reduce the incidence of retrotransposition. Consistent with this model is that inhibiting the RNAi pathway results in an increase in expression of repetitive elements in preimplantation mouse embryos. Mouse oocytes are essentially transcriptionally quiescent providing a unique opportunity to assess the stability of repetitive element-derived transcripts in these cells. We compared the transcriptome of freshly isolated fully grown germinal vesicle (GV)-intact oocytes to that of oocytes in which meiotic maturation in vitro was inhibited for 48 h by milrinone. Consistent with the aforementioned function for RNAi is that the abundance of only a relatively small number of transcripts decreased in the cultured oocytes, when compared to changes that occur during maturation or following fertilization, and of those, several belonged to mobile elements.

Emerging concepts in tumor progression and therapy

Nearly half of the human genome is comprised of repetitive elements that are tightly regulated to protect the host genome from deleterious consequences associated with their inappropriate activation. Cancer cells often misexpress these elements, in part, due to decreases in DNA methylation. Recent discoveries suggest that tumor suppressor proteins contribute to repression of repetitive elements, and their functional inactivation promotes repeat element misexpression during carcinogenesis. Recent findings also suggest that increased expression of repetitive elements beyond a threshold of tolerance can augment cancer therapy responses. Such advances, reviewed here, paint a picture in which deregulated expression of repetitive genome elements not only contributes to the development of cancer but may also provide a tumor-specific Achilles heel for cancer treatment.