Alu mobile elements: from junk DNA to genomic gems

Copy Number Variations in Hereditary Spastic Paraplegia-Related Genes: Evaluation of an Iranian Hereditary Spastic Paraplegia Cohort and Literature Review

Introduction

In human genetic disorders, copy number variations (CNVs) are considered a considerable underlying cause. CNVs are generally detected by array-based methods but can also be discovered by read-depth analysis of whole-exome sequencing (WES) data. We performed WES-based CNV identification in a cohort of 35 Iranian families with hereditary spastic paraplegia (HSP) patients.

Methods

Thirty-five patients whose routine single-nucleotide variants (SNVs) and insertion/deletion analyses from exome data were unrevealing underwent a pipeline of CNV analysis using the read-depth detection method. Subsequently, a comprehensive search about the existence of CNVs in all 84 known HSP-causing genes was carried out in all reported HSP cases, so far.

Results and Discussion

CNV analysis of exome data indicated that 1 patient harbored a heterozygous deletion in exon 17 of the SPAST gene. Multiplex ligation-dependent probe amplification analysis confirmed this deletion in the proband and his affected father. Literature review demonstrated that, to date, pathogenic CNVs have been identified in 30 out of 84 HSP-causing genes (∼36%). However, CNVs in only 17 of these genes were specifically associated with the HSP phenotype. Among them, CNVs were more common in L1CAM, PLP1, SPAST, SPG7, SPG11, and REEP1 genes. The identification of the CNV in 1 of our patients suggests that WES allows the detection of both SNVs and CNVs from a single method without additional costs and execution time. However, because of intrinsic issues of WES in the detection of large rearrangements, it may not yet be exploited to replace the CNV detection methods in standard clinical practice.

B1 repetitive sequence methylation enhances wound healing of second‑degree burns in rats

The accumulation of DNA damage in burn wounds delays wound healing. DNA methylation by short interspersed nuclear element (SINE) small interfering (si)RNA prevents DNA damage and promotes cell proliferation. Therefore, SINE siRNA may be able to promote burn wound healing. Here, a SINE B1 siRNA was used to treat burn wounds in rats. Second-degree burn wounds were introduced on the backs of rats. The rats were then divided into three groups: a B1 siRNA-treated, saline-treated control, and saline + calcium phosphate-nanoparticle-treated control group (n=15/group). The wounds were imaged on days 0, 7, 14, 21 and 28 post-injury. The tissue sections were processed for methylation, histological and immunohistochemical examination, and scored based on the overall expression of histone H2AX phosphorylated on serine 139 (γH2AX) and 8-hydroxy-2'-deoxyguanosine (8-OHdG). Burn wound closure improved in the B1 siRNA-treated group compared with that in the control group, especially from days 14-28 post-injury (P<0.001). The overall pathological score and degree of B1 methylation in the B1 siRNA-treated group improved significantly at days 14-28 post-injury, with the maximum improvement observed on day 14 (P<0.01) compared with the NSS and Ca-P nanoparticle groups. Immunohistochemical staining revealed lower expression of γH2AX and 8-OHdG in the B1 siRNA-treated group than in the control groups at days 14-28 post-injury; the maximum improvement was observed on days 14 and 21. These data imply that administering SINE siRNA is a promising therapeutic option for managing second-degree burns.

A human specific Alu DNA cassette is found flanking the genes of transcription factor AP2

Objective

Alu elements are retroposons that invaded the primate genome and shaped its biology. Some Alus inserted recently and are polymorphic in the human population. It is these Alus that are being sought after in disease association studies and regulatory biology. Discovering polymorphic Alus in the human genome can open areas of new research in these fields.

Results

Using the polymerase chain reaction on genomic DNA, we identified a polymorphic Alu in the flanking region of the TFAP2B and TFAP2D genes. The new insert was found in higher frequency in Europeans (0.4) and Asians (0.38) and lower frequency in Africans (0.25). We also show this Alu to be part of a 3 Alu cassette that is human specific. The TFAP2B and TFAP2D genes encode members of the transcription factor AP-2, which plays a role in organ development. The insertion of this Alu cassette flanking the transcription factor genes distinguishes humans from the primates. This cassette can possibly affect the regulation of both genes or alternately provoke genomic deletions, which we have shown in this study. Its presence in such a location is intriguing and unquestionably opens an investigational window in disease association studies and in the field of gene regulation.

Electronic supplementary material

The online version of this article (10.1186/s13104-019-4247-7) contains supplementary material, which is available to authorized users.

The validation of Short Interspersed Nuclear Elements (SINEs) as a RT-qPCR normalization strategy in a rodent model for temporal lobe epilepsy

Background

In gene expression studies via RT-qPCR many conclusions are inferred by using reference genes. However, it is generally known that also reference genes could be differentially expressed between various tissue types, experimental conditions and animal models. An increasing amount of studies have been performed to validate the stability of reference genes. In this study, two rodent-specific Short Interspersed Nuclear Elements (SINEs), which are located throughout the transcriptome, were validated and assessed against nine reference genes in a model of Temporal Lobe Epilepsy (TLE). Two different brain regions (i.e. hippocampus and cortex) and two different disease stages (i.e. acute phase and chronic phase) of the systemic kainic acid rat model for TLE were analyzed by performing expression analyses with the geNorm and NormFinder algorithms. Finally, we performed a rank aggregation analysis and validated the reference genes and the rodent-specific SINEs (i.e. B elements) individually via Gfap gene expression.

Results

GeNorm ranked Hprt1, Pgk1 and Ywhaz as the most stable genes in the acute phase, while Gusb and B2m were ranked as the most unstable, being significantly upregulated. The two B elements were ranked as most stable for both brain regions in the chronic phase by geNorm. In contrast, NormFinder ranked the B1 element only once as second best in cortical tissue for the chronic phase. Interestingly, using only one of the two algorithms would have led to skewed conclusions. Finally, the rank aggregation method indicated the use of the B1 element as the best option to normalize target genes, independent of the disease progression and brain region. This result was supported by the expression profile of Gfap.

Conclusion

In this study, we demonstrate the potential of implementing SINEs -notably the B1 element- as a stable normalization factor in a rodent model of TLE, independent of brain region or disease progression.

Frequency of Alu insertions within the ACE and PR loci in Northwestern Mexicans

OBJECTIVE

Presently, non-LTR retrotransposons are the most active mobile elements in the human genome. Among these, Alu elements are highly represented in the modern population. Worldwide, distribution of Alu polymorphisms (insertion/deletion; I/D) shows variability between different populations. Two Alu insertion loci, ACE and PR, are significant biomarkers that have served in several genotype-phenotype association studies. In Mexico, studies concerning the frequency of these biomarkers have been conducted mainly in subpopulations from central and southern regions. Here, we screened a population sample of the northwestern region to gain further knowledge regarding the prevalence of Alu polymorphisms within ACE and PR loci.

RESULTS

For ACE locus, the observed genotype frequencies were 26.5, 51.0 and 22.5% for II, ID, and DD, respectively; and allelic frequencies for I and D were 52 and 48%. Whereas respective genotype frequencies for PR locus were 2.7, 26.5 and 70.8%, and the corresponding allele frequencies were 16 and 84%. Furthermore, the insertion frequency within ACE locus was similar between central, western and northwestern subpopulations, and rather higher in southeastern subpopulation (p < 0.05). Although the occurrence of Alu polymorphisms within PR locus has not been widely examined, the insertion frequency was higher in northwestern subpopulation, as compared with western and southeastern subpopulations (p < 0.05). Based on the frequency of Alu insertions found in ACE and PR loci, subpopulations from the northwestern, western and central regions share a common genetic origin, but apparently not with the subpopulation from the southeastern region, in accordance with the notion that assumes the existence of a broad genomic diversity in the Mexican population. In addition, the high prevalence of Alu insertions reveals their potential application as biomarkers with prognostic value for the associated diseases; e.g., as part of the standard protocols for clinical diagnosis.

High-resolution RNA allelotyping along the inactive X chromosome: evidence of RNA polymerase III in regulating chromatin configuration

We carried out padlock capture, a high-resolution RNA allelotyping method, to study X chromosome inactivation (XCI). We examined the gene reactivation pattern along the inactive X (Xi), after Xist (X-inactive specific transcript), a prototype long non-coding RNA essential for establishing X chromosome inactivation (XCI) in early embryos, is conditionally deleted from Xi in somatic cells (Xi^∆Xist). We also monitored the behaviors of X-linked non-coding transcripts before and after XCI. In each mutant cell line, gene reactivation occurs to ~6% genes along Xi^∆Xist in a recognizable pattern. Genes with upstream regions enriched for SINEs are prone to be reactivated. SINE is a class of retrotransposon transcribed by RNA polymerase III (Pol III). Intriguingly, a significant fraction of Pol III transcription from non-coding regions is not subjected to Xist-mediated transcriptional silencing. Pol III inhibition affects gene reactivation status along Xi^∆Xist, alters chromatin configuration and interferes with the establishment XCI during in vitro differentiation of ES cells. These results suggest that Pol III transcription is involved in chromatin structure re-organization during the onset of XCI and functions as a general mechanism regulating chromatin configuration in mammalian cells.

Regulatory roles of Alu transcript on gene expression

Alu element is the most successful transposon and it maintains a high level of content in primate genome. However, despite the fact that the expression level of independent Alu element is rather low under common condition, an increasing number of the observations for the Alu transcripts in cells and tissues have been reported recently. Alu transcripts play key roles in the network of gene expression regulation. The main functions of Alu transcript focus on gene regulation both at transcriptional and post-transcriptional levels. This review summarizes major functions of Alu transcripts on gene expression and highlights molecular mechanisms dependent on conserved sequence or secondary structure in order to unravel a relative ubiquitous way that Alu transcript uses to affect the whole genome.

Footprint of APOBEC3 on the genome of human retroelements

Almost half of the human genome is composed of transposable elements. The genomic structures and life cycles of some of these elements suggest they are a result of waves of retroviral infection and transposition over millions of years. The reduction of retrotransposition activity in primates compared to that in nonprimates, such as mice, has been attributed to the positive selection of several antiretroviral factors, such as apolipoprotein B mRNA editing enzymes. Among these, APOBEC3G is known to mutate G to A within the context of GG in the genome of endogenous as well as several exogenous retroelements (the underlining marks the G that is mutated). On the other hand, APOBEC3F and to a lesser extent other APOBEC3 members induce G-to-A changes within the nucleotide GA. It is known that these enzymes can induce deleterious mutations in the genome of retroviral sequences, but the evolution and/or inactivation of retroelements as a result of mutation by these proteins is not clear. Here, we analyze the mutation signatures of these proteins on large populations of long interspersed nuclear element (LINE), short interspersed nuclear element (SINE), and endogenous retrovirus (ERV) families in the human genome to infer possible evolutionary pressure and/or hypermutation events. Sequence context dependency of mutation by APOBEC3 allows investigation of the changes in the genome of retroelements by inspecting the depletion of G and enrichment of A within the APOBEC3 target and product motifs, respectively. Analysis of approximately 22,000 LINE-1 (L1), 24,000 SINE Alu, and 3,000 ERV sequences showed a footprint of GG→AG mutation by APOBEC3G and GA→AA mutation by other members of the APOBEC3 family (e.g., APOBEC3F) on the genome of ERV-K and ERV-1 elements but not on those of ERV-L, LINE, or SINE.