Alu Elements Research Articles

Alternative polyadenylation determines the functional landscape of inverted Alu repeats

Inverted Alu repeats (IRAlus) are abundantly found in the transcriptome, especially in introns and 3' untranslated regions (UTRs). Yet, the biological significance of IRAlus embedded in 3' UTRs remains largely unknown. Here, we find that 3' UTR IRAlus silences genes involved in essential signaling pathways. We utilize J2 antibody to directly capture and map the double-stranded RNA structure of 3' UTR IRAlus in the transcriptome. Bioinformatic analysis reveals alternative polyadenylation as a major axis of IRAlus-mediated gene regulation. Notably, the expression of mouse double minute 2 (MDM2), an inhibitor of p53, is upregulated by the exclusion of IRAlus during UTR shortening, which is exploited to silence p53 during tumorigenesis. Moreover, the transcriptome-wide UTR lengthening in neural progenitor cells results in the global downregulation of genes associated with neurodegenerative diseases, including amyotrophic lateral sclerosis, via IRAlus inclusion. Our study establishes the functional landscape of 3' UTR IRAlus and its role in human pathophysiology.

Machine learning to detect the SINEs of cancer.

We previously described an approach called RealSeqS to evaluate aneuploidy in plasma cell-free DNA through the amplification of ~350,000 repeated elements with a single primer. We hypothesized that an unbiased evaluation of the large amount of sequencing data obtained with RealSeqS might reveal other differences between plasma samples from patients with and without cancer. This hypothesis was tested through the development of a machine learning approach called Alu Profile Learning Using Sequencing (A-PLUS) and its application to 7615 samples from 5178 individuals, 2073 with solid cancer and the remainder without cancer. Samples from patients with cancer and controls were prespecified into four cohorts used for model training, analyte integration, and threshold determination, validation, and reproducibility. A-PLUS alone provided a sensitivity of 40.5% across 11 different cancer types in the validation cohort, at a specificity of 98.5%. Combining A-PLUS with aneuploidy and eight common protein biomarkers detected 51% of the cancers at 98.9% specificity. We found that part of the power of A-PLUS could be ascribed to a single feature-the global reduction of AluS subfamily elements in the circulating DNA of patients with solid cancer. We confirmed this reduction through the analysis of another independent dataset obtained with a different approach (whole-genome sequencing). The evaluation of Alu elements may therefore have the potential to enhance the performance of several methods designed for the earlier detection of cancer.

Detection of a novel gross deletion in the UNC13D gene ends the diagnostic odyssey for a family with familial hemophagocytic lymphohistiocytosis 3

BackgroundFamilial hemophagocytic lymphohistiocytosis (FHL) is an immunological disorder characterized by overactivation of macrophages and T lymphocytes. This autosomal recessive condition has been characterized into multiple types depending on the genetic etiology. FHL type 3 is associated with bi-allelic pathogenic variants in the UNC13D gene.Case presentationWe present a 12-year diagnostic odyssey for a family with FHL that signifies the advances of FHL genetic testing in a clinical genetic diagnostic laboratory setting. We describe the first case of a large UNC13D gross deletion in trans to a nonsense variant in a family with FHL3, which may have been mediated by Alu elements within introns 12 and 25 of the UNC13D gene.ConclusionsThis case highlights the importance of re-evaluating past genetic testing for a patient and family as test technology evolves in order to end a diagnostic odyssey.

Multi-Omics Factor Analysis (MOFA) Identifies Transposable Element Expression As a Risk Factor and Inflammaging As a Protective Factor in Myelodysplastic Syndromes

Introduction Myelodysplastic syndromes (MDS) are haematological diseases characterised by clonal proliferation due to genetic and epigenetic alterations within haematopoietic stem and progenitor cells. Thus far, the prediction of a patient's overall survival (OS) and event-free survival (EFS) has been dependent predominantly on the degree of peripheral blood cytopenias, bone marrow blast percentage, cytogenetics, and genetic features. However, this may overlook other biological phenotypes, including, for example, the expression of transposable elements (TEs), ageing, and immunology profile. In this study, we present a comprehensive analysis of three data modalities (clinical, genotypic, and transcriptomic) and eight different views derived from these modalities to identify the hidden factors that significantly impact MDS prognosis. Methods Three (immunology, ageing, and cellular composition) out of eight views of the data were derived from RNA-seq by applying singscore, a gene set scoring tool developed by Foroutan et al., 2018, on RNA-seq gene expression from bone marrow samples of 94 MDS patients obtained from Shiozawa et al., 2017 (Fig 1.A). Each of these three views was carried forward in the workflow by a number of gene sets. The other five views were clinical numeric data, clinical categorical data, TE expression, genotype data, and known AML/MDS antigens (obtained from TANTIGEN 2.0), expressed in at least 10% of MDS samples in the study. We then employed Multi-Omics Factor Analysis (MOFA), a computational framework developed by Argelaguet et al., 2018, to uncover hidden phenotypic states within a multi-omic dataset. Through MOFA, we generated factors representing specific biological data modalities, establishing connections between features across these different categories. The total variance ( R2) that can be attributed to specific factors is also exhibited by MOFA. Results Factors were ranked based on their explained variance. We present the 10 factors with a threshold of variance explained of 2% from the 15 default factors generated by MOFA (Fig 1.A). Factor 1 was one of the factors that linked the most categories of data: immunology, cellular composition, ageing, and TEs. Most notably, Factor 1 was aligned with features of less differentiated cells (more HSC-like and less GMP-like). We observed that samples represented by high Factor 1 scores also had a higher expression of SINE:Alu elements. (Fig 1.A). Moreover, Factor 1 aligns the following immunology features: increased T-helper 1 (Th1) cells, macrophages, and T regulatory cells. The relationship between Th1 and SINE elements is particularly interesting, given the role of Th1 cell activation in host defence against infection that may be modulated by SINE activation. Factor 2 comprised of ageing and clinical categorical data, which showed that less inflammaging may lead to a poorer EFS ( P=0.00023) (Fig 1.B). Factor 4 linked immunology, cellular decomposition, ageing and clinical categorical data. The following features mainly influenced Factor 4: increased HSC-like cells, decreased CD8+ T cells, decreased immunosenescence and increased inflammatory chemokines. Using Kaplan-Meier plots to predict OS, we observed that patients with more HSC-like cells, fewer leukocytes and T cells, and less immunosenescence and inflammaging were linked to poorer EFS ( P=0.0001) and OS ( P=0.00017, data not shown). Furthermore, Factor 9 comprised solely of the TEs category and exhibited a correlation between increased TE expression and poorer EFS ( P=0.0074) and OS ( P=0.0065, data not shown) (Fig 1.B). Conclusions Our analysis using MOFA on a diverse set of biological data modalities uncovered hidden factors in MDS, providing insights into the complex interplay between various biological layers. Notably, we identified TE expression as a risk factor and inflammaging as a protective factor in MDS. HSC-like cells and specific immunological profiles were also associated with significantly poor OS and EFS. This study contributes to a deeper understanding of MDS pathogenesis and identifies potential prognostic markers for this disease. It also elucidates the importance of considering the relationships between different pathways, markers, and mutations in predicting patient outcomes, highlighting the efficacy of a comprehensive approach that goes beyond all the scoring systems described thus far for MDS.

Deciphering the role of extrachromosomal circular DNA in adipose stem cells from old and young donors

BackgroundThe functional impairment of adipose stem cells (ASCs) during aging limits their clinical transformation. Studies have shown that extrachromosomal circular DNAs (eccDNAs) are associated with tumor progression and cell aging, but the roles of eccDNAs in ASCs remain unknown.MethodWe conducted Circle sequencing (Circle-seq) to identify eccDNAs in ASCs isolated from young and old donors. The differentially expressed eccDNAs were calculated, annotated and validated via polymerase chain reaction.ResultsThousands of eccDNAs were identified and comprehensively characterized. Most of them were GC-rich, < 1000 base pairs in size, and were enriched on chromosome 19 and 17 with a high density of Alu elements and genes, 2 kb upstream/downstream of genes and satellites. In total, 3025 eccDNAs were differentially expressed among the two ASC groups. Conjoint analysis of the Circle-seq results and previous RNA-seq results revealed that 73 eccDNAs and 55 genes exhibited the same differential expression between the two groups. KEGG and GO analyses revealed that genes encoding differentially expressed eccDNAs were enriched for cell adhesion, cellular senescence and TGF-β receptor signaling pathway. We also found that aged ASCs exhibited loss of eccDNAs, including CAMK2G (chr10: 75577899-75578176), TRABD2B (chr1: 48305638-48307008) and TRABD2B (chr1: 48305425-48307091).ConclusionIn this study, we elucidated the first eccDNA profile relating to ASCs and demonstrated that three eccDNAs are lost in aged ASCs, which may be potential biomarkers of stem cell aging and valuable targets for stem cell rejuvenation.

Targeted long-read sequencing identifies and characterizes structural variants in cases of inherited platelet disorders

BackgroundGenetic diagnosis of inherited platelet disorders (IPDs) is mainly performed by high-throughput sequencing (HTS). These short-read–based sequencing methods sometimes fail to characterize the genetics of the disease. ObjectivesTo evaluate nanopore long-read DNA sequencing for characterization of structural variants (SVs) in patients with IPDs. MethodsFour patients with a clinical and laboratory diagnosis of Glanzmann thrombasthenia (GT) (P1 and P2) and Hermansky–Pudlak syndrome (HPS) (P3 and P4) in whom HTS missed the underlying molecular cause were included. DNA was analyzed by both standard HTS and nanopore sequencing on a MinION device (Oxford Nanopore Technologies) after enrichment of DNA spanning regions covering GT and HPS genes. ResultsIn patients with GT, HTS identified only 1 heterozygous ITGB3 splice variant c.2301+1G>C in P2. In patients with HPS, a homozygous deletion in HPS5 was suspected in P3, and 2 heterozygous HPS3 variants, c.2464C>T (p.Arg822∗) and a deletion affecting 2 exons, were reported in P4. Nanopore sequencing revealed a complex SV affecting exons 2 to 6 in ITGB3 (deletion-inversion-duplication) in homozygosity in P1 and compound heterozygosity with the splice variant in P2. In the 2 patients with HPS, nanopore defined the length of the SVs, which were characterized at nucleotide resolution. This allowed the identification of repetitive Alu elements at the breakpoints and the design of specific polymerase chain reactions for family screening. ConclusionThe nanopore technology overcomes the limitations of standard short-read sequencing techniques in SV characterization. Using nanopore, we characterized novel defects in ITGB3, HPS5, and HPS3, highlighting the utility of long-read sequencing as an additional diagnostic tool in IPDs.

Oligonucleotide skews enable comprehensive and insightful characterization of GC- and TA-skew properties observed throughout the human genome with support of unsupervised AI with reference to gene- and Alu-polarity skews

GC and TA skew are fundamental genomic features observed widely from bacteria to humans. They have been described as replication- and transcription-coupled skews because they are mainly caused by differences in mutation and repair biases between complementary DNA strands in replication and transcription processes. The skews are clearly observed in bacteria, plants and birds, but are more difficult to accurately identify in mammals, including humans. The main reason for this difficulty is that the correlation between GC and TA skew is not high for their variation in the mammalian genomes. In this study, we focused not only on these mononucleotide skews but also on di- and trinucleotide skews, first in 100-kb sequences of two short human chromosomes (chr21 and 22), and by using the conventional distribution map analysis, we clearly observed these skews over these chromosomes, except for centromeric heterochromatin regions where diverse repetitive sequences are densely clustered. Then, by using a batch learning self-organizing map (BLSOM), which can display large amounts of sequence data at once, we detected the oligonucleotide skews across nearly the entire human genome. Next, to understand skews within centromeric heterochromatin regions, we focused on Alu sequences ubiquitously distributed in the human genome and analyzed mono-, di-, and trinucleotide skews by referring to the polarity of Alu sequences. Since this polarity is unevenly distributed in the human genome, a clear TA skew was observed by reflecting the evident A-richness to T of Alu elements. However, due to some degree of their G-richness to C, TA and GC skews showed inversely correlated variations, when analyzing Alu sequences alone. Notably, when we analyzed genome sequences after excluding Alu sequences, the concordant correlation between GC- and TA-skew variations increased, indicating that a large amount of Alu sequences has made the detection of these mononucleotide skews in the human genome more difficult than in other organisms. Analysis of oligonucleotide skews using BLSOM is thought to be suitable for characterizing sequence features in skew transition regions.

Adenosine Deaminase Acting on RNA (ADAR) Enzymes: A Journey from Weird to Wondrous.

The adenosine deaminase acting on RNA (ADAR) enzymes that catalyze the conversion of adenosine to inosine in double-stranded (ds)RNA are evolutionarily conserved and are essential for many biological functions including nervous system function, hematopoiesis, and innate immunity. Initially it was assumed that the wide-ranging biological roles of ADARs are due to inosine in mRNA being read as guanosine by the translational machinery, allowing incomplete RNA editing in a target codon to generate two different proteins from the same primary transcript. In humans, there are approximately seventy-six positions that undergo site-specific editing in tissues at greater than 20% efficiency that result in recoding. Many of these transcripts are expressed in the central nervous system (CNS) and edited by ADAR2. Exploiting mouse genetic models revealed that transgenic mice lacking the gene encoding Adar2 die within 3 weeks of birth. Therefore, the role of ADAR2 in generating protein diversity in the nervous system is clear, but why is ADAR RNA editing activity essential in other biological processes, particularly editing mainly involving ADAR1? ADAR1 edits human transcripts having embedded Alu element inverted repeats (AluIRs), but the link from this activity to innate immunity activation was elusive. Mice lacking the gene encoding Adar1 are embryonically lethal, and a major breakthrough was the discovery that the role of Adar1 in innate immunity is due to its ability to edit such repetitive element inverted repeats which have the ability to form dsRNA in transcripts. The presence of inosine prevents activation of the dsRNA sensor melanoma differentiation-associated protein 5 (Mda5). Thus, inosine helps the cell discriminate self from non-self RNA, acting like a barcode on mRNA. As innate immunity is key to many different biological processes, the basis for this widespread biological role of the ADAR1 enzyme became evident.Our group has been studying ADARs from the outset of research on these enzymes. In this Account, we give a historical perspective, moving from the initial purification of ADAR1 and ADAR2 and cloning of their encoding genes up to the current research focus in the field and what questions still remain to be addressed. We discuss the characterizations of the proteins, their localizations, posttranslational modifications, and dimerization, and how all of these affect their biological activities. Another aspect we explore is the use of mouse and Drosophila genetic models to study ADAR functions and how these were crucial in determining the biological functions of the ADAR proteins. Finally, we describe the severe consequences of rare mutations found in the human genes encoding ADAR1 and ADAR2.

Emerging Opportunities to Study Mobile Element Insertions and Their Source Elements in an Expanding Universe of Sequenced Human Genomes.

Three mobile element classes, namely Alu, LINE-1 (L1), and SVA elements, remain actively mobile in human genomes and continue to produce new mobile element insertions (MEIs). Historically, MEIs have been discovered and studied using several methods, including: (1) Southern blots, (2) PCR (including PCR display), and (3) the detection of MEI copies from young subfamilies. We are now entering a new phase of MEI discovery where these methods are being replaced by whole genome sequencing and bioinformatics analysis to discover novel MEIs. We expect that the universe of sequenced human genomes will continue to expand rapidly over the next several years, both with short-read and long-read technologies. These resources will provide unprecedented opportunities to discover MEIs and study their impact on human traits and diseases. They also will allow the MEI community to discover and study the source elements that produce these new MEIs, which will facilitate our ability to study source element regulation in various tissue contexts and disease states. This, in turn, will allow us to better understand MEI mutagenesis in humans and the impact of this mutagenesis on human biology.

Proximity Proteomics Revealed Aberrant mRNA Splicing Elicited by ALS-Linked Profilin-1 Mutants.

Profilin 1 (PFN1) is a cytoskeleton protein that modulates actin dynamics through binding to monomeric actin and polyproline-containing proteins. Mutations in PFN1 have been linked to the pathogenesis of familial amyotrophic lateral sclerosis (ALS). Here, we employed an unbiased proximity labeling strategy in combination with proteomic analysis for proteome-wide profiling of proteins that differentially interact with mutant and wild-type (WT) PFN1 proteins in human cells. We uncovered 11 mRNA splicing proteins that are preferentially enriched in the proximity proteomes of the two ALS-linked PFN1 variants, C71G and M114T, over that of wild-type PFN1. We validated the preferential interactions of the ALS-linked PFN1 variants with two mRNA splicing factors, hnRNPC and U2AF2, by immunoprecipitation, followed with immunoblotting. We also found that the two ALS-linked PFN1 variants promoted the exonization of Alu elements in the mRNAs of MTO1, TCFL5, WRN and POLE genes in human cells. Together, we showed that the two ALS-linked PFN1 variants interacted preferentially with mRNA splicing proteins, which elicited aberrant exonization of the Alu elements in mRNAs. Thus, our work provided pivotal insights into the perturbations of ALS-linked PFN1 variants in RNA biology and their potential contributions to ALS pathology.

Genome-wide perturbations of A-to-I RNA editing dysregulated circular RNAs promoting the development of cervical cancer

Cervical cancer, the second most common female malignant tumor, seriously threatens women's health and lives. Despite the availability of the HPV vaccine, effective treatment options for cervical cancer are still lacking. New research perspectives now clarify that RNA editing dysregulation and changes in circRNA expression are jointly involved in disease pathogenesis, so molecular changes associated with circRNA and RNA editing may provide clues for the development of new therapeutic strategies for cervical cancer. In this study, we designed a series of pipelines to identify and analyze dysregulated RNA editing events in circRNAs. Our findings indicate a decrease in A-to-I RNA editing levels in cervical cancer compared to normal tissues, and editing may influence the back-splicing process of circRNAs through structural modifications of Alu elements. Moreover, our research reveals that RNA editing could modulate circRNA biogenesis by influencing RNA binding protein (RBP) binding on a transcriptome-wide scale, as well as influence the expression and coding potential of circRNAs. Importantly, we identified three RNA editing sites that could serve as potential biomarkers. In summary, our study presents a comprehensive landscape of RNA editing perturbations in circRNAs, providing new insights into the complex relationship between RNA editing and circRNA dysregulation in cervical cancer.

CircMTA1 promotes glioblastoma angiogenesis by encoding MTA1-134aa.

Glioblastoma multiforme (GBM) is the most malignant brain tumor with rapid angiogenesis. How to inhibit GBM angiogenesis is a key problem to be solved. To explore the targets of inhibiting GBM angiogenesis, this study confirmed that the expression of circMTA1 (hsa_circ_0033614) was significantly upregulated in human brain microvascular endothelial cells exposed to glioma cell-conditioned medium (GECs). The expression of circMTA1 in the cytoplasm was significantly higher than that in the nucleus. Upregulated circMTA1 in GECs can promote cell proliferation, migration, and tube formation. Further exploration of the circularization mechanism of circMTA1 confirmed that KHDRBS1 protein can bind to the upstream and downstream flanking sequences of circMTA1 and promote circMTA1 biogenesis by coordinating Alu element pairing. KHDRBS1 upregulated the proliferation, migration, and tube formation of GECs by promoting the biogenesis of circMTA1. CircMTA1 can encode the protein MTA1-134aa by internal ribosome entry site sequence-mediated translation mechanism, and promote the proliferation, migration, and tube formation of GECs through the encoded MTA1-134aa. This study provides a new target for inhibiting angiogenesis in brain GBM and a new strategy for improving the therapeutic efficacy of GBM.

CapTEs enables locus-specific dissection of transcriptional outputs from reference and nonreference transposable elements

Transposable elements (TEs) serve as both insertional mutagens and regulatory elements in cells, and their aberrant activity is increasingly being revealed to contribute to diseases and cancers. However, measuring the transcriptional consequences of nonreference and young TEs at individual loci remains challenging with current methods, primarily due to technical limitations, including short read lengths generated and insufficient coverage in target regions. Here, we introduce a long-read targeted RNA sequencing method, Cas9-assisted profiling TE expression sequencing (capTEs), for quantitative analysis of transcriptional outputs for individual TEs, including transcribed nonreference insertions, noncanonical transcripts from various transcription patterns and their correlations with expression changes in related genes. This method selectively identified TE-containing transcripts and outputted data with up to 90% TE reads, maintaining a comparable data yield to whole-transcriptome sequencing. We applied capTEs to human cancer cells and found that internal and inserted Alu elements may employ distinct regulatory mechanisms to upregulate gene expression. We expect that capTEs will be a critical tool for advancing our understanding of the biological functions of individual TEs at the locus level, revealing their roles as both mutagens and regulators in biological and pathogenic processes.

Epigenomic signature of accelerated ageing in progeroid Cockayne syndrome.

Cockayne syndrome (CS) and UV-sensitive syndrome (UVSS) are rare genetic disorders caused by mutation of the DNA repair and multifunctional CSA or CSB protein, but only CS patients display a progeroid and neurodegenerative phenotype, providing a unique conceptual and experimental paradigm. As DNA methylation (DNAm) remodelling is a major ageing marker, we performed genome-wide analysis of DNAm of fibroblasts from healthy, UVSS and CS individuals. Differential analysis highlighted a CS-specific epigenomic signature (progeroid-related; not present in UVSS) enriched in three categories: developmental transcription factors, ion/neurotransmitter membrane transporters and synaptic neuro-developmental genes. A large fraction of CS-specific DNAm changes were associated with expression changes in CS samples, including in previously reported post-mortem cerebella. The progeroid phenotype of CS was further supported by epigenomic hallmarks of ageing: the prediction of DNAm of repetitive elements suggested an hypomethylation of Alu sequences in CS, and the epigenetic clock returned a marked increase in CS biological age respect to healthy and UVSS cells. The epigenomic remodelling of accelerated ageing in CS displayed both commonalities and differences with other progeroid diseases and regular ageing. CS shared DNAm changes with normal ageing more than other progeroid diseases do, and included genes functionally validated for regular ageing. Collectively, our results support the existence of an epigenomic basis of accelerated ageing in CS and unveil new genes and pathways that are potentially associated with the progeroid/degenerative phenotype.

Distribution of the macaques genus-specific Alu repeat AluMacYa3 in the MGMT gene orthologs of old world monkeys

Aim. To follow the distribution and evolution of the macaques genus-specific Alu repeat AluMacYa3 in Cercopithecidae MGMT gene orthologs. Methods. The homology between nucleotide sequences has been determined by the BLAST 2.6.1 program. The results of the search and identification of MGE have been obtained by the CENSOR program. Results. It has been shown on the example of Cercopithecidae MGMT gene orthologs that the genus-specific Alu repeat AluMacYa3 is present not only in the intron sequences of macaques, but also in other representatives of the Old World monkeys and in its evolutionary history not a deletion degradation of nucleotide sequences, as it is in the case of species-specific Alu repeats, but a single nucleotide polymorphism is dominated. Conclusions. Thus, the macaque genus-specific Alu repeat AluMacYa3 has been identified in different representatives of the Old World monkeys and its evolutionary history combines nucleotide polymorphism and deletion degradation of nucleotide sequences.

Abstract P150: Dynamic Alu Cpg Methylation Change In Elevated Diastolic Blood Pressure

Hypertension is recognized as age-related disease. However, its interaction with aging at the epigenetic level is still not fully understood. Hypomethylation of Alu elements, the most abundant class of interspersed repetitive sequence in the genome, is associated with global hypomethylation, an important epigenetic event of aging. Dermal fibroblasts have been observed to be affected by hypertension. In vitro study has shown that hypertension accelerated expression of age-related phenotypes. Therefore, in our study, we aimed to examine the relationship between blood pressure, age and Alu methylation status using dermal fibroblasts as a model. Biopsies of dermal fibroblasts were performed on 39 patients with various ages and blood pressure statuses. The patients were grouped into three categories based on their systolic blood pressure (SBP) and diastolic blood pressure (DBP): Normal (SBP = 130 mmHg; DBP = 85 mmHg), High Normal (SBP = 130-139 mmHg; DBP = 85-89 mmHg) and Hypertensive (SBP ≥ 140 mmHg; DBP ≥ 90 mmHg). Combined Bisulfite Restriction Analysis was performed to determine the Alu methylation level and pattern. The data was analyzed using Two Way ANOVA factoring in age groups. The Alu methylation level in the normal, high normal and hypertensive groups according to SBP is 30.3 ± 2.15%, 30.2 ± 2.15%, and 30.1 ± 2.06% and 29.6 ± 1.85%, 31.1 ± 1.78%, and 30.2 ± 2.48% according to DBP (data displaying in mean ± SD). The percentages of u C u C methylation pattern were 42.8 ± 5.57%, 42.7 ± 3.84%, 41.9 ± 4.84%, 44.2 ± 5.19%, 40.4 ± 2.95%, and 42.3 ± 4.79% for normal, high normal and hypertensive group, by SBP and DBP respectively. There were statistically significant differences between groups of DBP status with methylation level lowest in the high normal group. u C u C methylation pattern was the highest in high normal DBP group (p-value &lt; 0.05). There was also a statistically significant interaction between age and DBP level to Alu methylation. However, there was no statistically significant difference between SBP groups. We conclude that there is a dynamic Alu methylation change in the elevation of DBP with overarching trend of Alu hypomethylation. This phenomenon suggests that Alu methylation may have a role in how hypertension accelerate cellular aging in different tissues.

Alu elements confer enhancer-promoter specificity.

Alu elements confer enhancer-promoter specificity.

Alu transposable elements rewire enhancer-promoter network through RNA pairing

A recent study by Liang etal.1 reveals that interacting enhancer RNAs (eRNAs) and promoter-transcribed upstream antisense RNAs (uaRNAs) can identify enhancer-promoter interactions. Complementary sequences within the interacting eRNAs and uaRNAs, predominantly Alu sequences, confer the specificity for eRNA-uaRNA pairing and hence enhancer-promoter recognition.

Reference LINE-1 insertion polymorphisms correlate with Parkinson’s disease progression and differential transcript expression in the PPMI cohort

Long interspersed nuclear element-1 (LINE-1/L1) retrotransposons make up 17% of the human genome. They represent one class of transposable elements with the capacity to both mobilize autonomously and in trans via the mobilization of other elements, primarily Alu and SVA elements. Reference LINE-1 elements are, by definition, found in the reference genome, however, due to the polymorphic nature of these elements, variation for presence or absence is present within the population. We used a combination of clinical and transcriptomic data from the Parkinson’s Progression Markers Initiative (PPMI) and applied matrix expression quantitative trait loci analysis and linear mixed-effects models involving 114 clinical, biochemical and imaging data from the PPMI cohort to elucidate the role of reference LINE-1 insertion polymorphism on both gene expression genome-wide and progression of Parkinson’s disease (PD). We demonstrate that most LINE-1 insertion polymorphisms are capable of regulating gene expression, preferentially in trans, including previously identified PD risk loci. In addition, we show that 70 LINE-1 elements were associated with longitudinal changes of at least one PD progression marker, including ipsilateral count density ratio and UPDRS scores which are indicators of degeneration and severity. In conclusion, this study highlights the effect of the polymorphic nature of LINE-1 retrotransposons on gene regulation and progression of PD which underlines the importance of analyzing transposable elements within complex diseases.

Efficiency of mitochondrial genes and nuclear Alu elements in detecting human DNA in blood meals of Anopheles stephensi mosquitoes: a time-course study

BackgroundThe time required for PCR detection of DNA in human blood meals in vector mosquitoes may vary, depending on the molecular markers used, based on the size and copy number of the amplicons. Detailed knowledge of the blood-feeding behavior of mosquito populations in nature is an essential component for evaluating their vectorial capacity and for assessing the roles of individual vertebrates as potential hosts involved in the transmission of vector-borne diseases.MethodsLaboratory experiments were conducted to compare the time course of PCR detection of DNA in human blood meals from individual blood-fed Anopheles stephensi mosquitoes, using loci with different characteristics, including two mitochondrial DNA (mtDNA) genes, cytB (228 bp) and 16S ribosomal RNA (rRNA) (157 bp) and nuclear Alu-repeat elements (226 bp) at different time points after the blood meal.ResultsHuman DNA was detectable up to 84–120 h post-blood-feeding, depending on the length and copy number of the loci. Our results suggest that 16S rRNA and Alu-repeat markers can be successfully recovered from human DNA up to 5 days post-blood-meal. The 16S rDNA and Alu-repeat loci have a significantly (P = 0.008) slower decline rate than the cytB locus. Median detection periods (T50) for the amplicons were 117, 113 and 86.4 h for Alu-repeat, 16S rDNA and cytB, respectively, suggesting an inverse linear relationship between amplicon size/copy number and digestion time.ConclusionThis comparative study shows that the Alu-repeat locus is the most efficient marker for time-course identification of human DNA from blood meals in female mosquitoes. It is also a promising tool for determining the anthropophilic index (AI) or human blood index (HBI), i.e. the proportion of blood meals from humans, which is often reported as a relative measure of anthropophagy of different mosquito vectors, and hence a measure of the vector competence of mosquito species collected in the field.Graphical