Alu pair exclusions in the human genome

<p>Abstract</p> <p>Background</p> <p>The human genome contains approximately one million <it>Alu </it>elements which comprise more than 10% of human DNA by mass. <it>Alu </it>elements possess direction, and are distributed almost equally in positive and negative strand orientations throughout the genome. Previously, it has been shown that closely spaced <it>Alu </it>pairs in opposing orientation (inverted pairs) are found less frequently than <it>Alu </it>pairs having the same orientation (direct pairs). However, this imbalance has only been investigated for <it>Alu </it>pairs separated by 650 or fewer base pairs (bp) in a study conducted prior to the completion of the draft human genome sequence.</p> <p>Results</p> <p>We performed a comprehensive analysis of all (> 800,000) full-length <it>Alu </it>elements in the human genome. This large sample size permits detection of small differences in the ratio between inverted and direct <it>Alu </it>pairs (I:D). We have discovered a significant depression in the full-length <it>Alu </it>pair I:D ratio that extends to repeat pairs separated by ≤ 350,000 bp. Within this imbalance bubble (those <it>Alu </it>pairs separated by ≤ 350,000 bp), direct pairs outnumber inverted pairs. Using PCR, we experimentally verified several examples of inverted <it>Alu </it>pair exclusions that were caused by deletions.</p> <p>Conclusions</p> <p>Over 50 million full-length <it>Alu </it>pairs reside within the I:D imbalance bubble. Their collective impact may represent one source of <it>Alu </it>element-related human genomic instability that has not been previously characterized.</p

Evolutionary Conservation of the Functional Modularity of Primate and Murine LINE-1 Elements

LINE-1 (L1) retroelements emerged in mammalian genomes over 80 million years ago with a few dominant subfamilies amplifying over discrete time periods that led to distinct human and mouse L1 lineages. We evaluated the functional conservation of L1 sequences by comparing retrotransposition rates of chimeric human-rodent L1 constructs to their parental L1 counterparts. Although amino acid conservation varies from ∼35% to 63% for the L1 ORF1p and ORF2p, most human and mouse L1 sequences can be functionally exchanged. Replacing either ORF1 or ORF2 to create chimeric human-mouse L1 elements did not adversely affect retrotransposition. The mouse ORF2p retains retrotransposition-competency to support both Alu and L1 mobilization when any of the domain sequences we evaluated were substituted with human counterparts. However, the substitution of portions of the mouse cys-domain into the human ORF2p reduces both L1 retrotransposition and Alu trans-mobilization by 200–1000 fold. The observed loss of ORF2p function is independent of the endonuclease or reverse transcriptase activities of ORF2p and RNA interaction required for reverse transcription. In addition, the loss of function is physically separate from the cysteine-rich motif sequence previously shown to be required for RNP formation. Our data suggest an additional role of the less characterized carboxy-terminus of the L1 ORF2 protein by demonstrating that this domain, in addition to mediating RNP interaction(s), provides an independent and required function for the retroelement amplification process. Our experiments show a functional modularity of most of the LINE sequences. However, divergent evolution of interactions within L1 has led to non-reciprocal incompatibilities between human and mouse ORF2 cys-domain sequences

Insights into the DNA cleavage mechanism of human LINE-1 retrotransposon endonuclease

The human LINE-1 endonuclease (L1-EN) contributes in defining the genomic integration sites of the abundant human L1 and Alu retrotransposons. LINEs have been considered as possible vehicles for gene delivery and understanding the mechanism of L1-EN could help engineering them as genetic tools. We tested the in vitro activity of point mutants in three L1-EN residues— Asp145, Arg155, Ile204—that are key for DNA cleavage, and determined their crystal structures. The L1-EN structure remains overall unaffected by the mutations, which change the enzyme activity but leave DNA cleavage sequence specificity mostly unaffected. To better understand the mechanism of L1-EN, we performed molecular dynamics simulations using as model the structures of wild type EN-L1, of two βB6-βB5 loop exchange mutants we have described previously to be important for DNA recognition, of the R155A mutant from this study, and of the homologous TRAS1 endonuclease: all confirm a rigid scaffold. The simulations crucially indicate that the βB6- βB5 loop shows an anticorrelated motion with the surface loops βA6-βA5 and βB3-αB1. The latter loop harbors N118, a residue that alters DNA cleavage specificity in homologous endonucleases, and implies that the plasticity and correlated motion of these loops has a functional importance in DNA recognition and binding. To further explore how these loops are possibly involved in DNA binding, we docked computationally two DNA substrates to our structure, one involving a flipped-out nucleotide downstream the scissile phosphodiester; and one not. The models for both scenarios are feasible and agree with the hypotheses derived from the dynamic simulations. The reduced cleavage activity we have observed for the I204Y mutant above however, favors the flipped out nucleotide model

Dissecting the Genetic Basis of the Technological, Functional, and Safety Characteristics of Lacticaseibacillus paracasei SRX10

Nonstarter lactic acid bacteria (NSLAB) are major contributors to the unique characteristics (e.g., aroma, flavor, texture) of dairy and nondairy fermented products. Lc. paracasei SRX10 is an NSLAB strain originally isolated from a traditional Greek cheese and previously shown to exhibit favorable biotechnological characteristics. More specifically, the strain showed tolerance to simulated gastrointestinal conditions, exopolysaccharide (EPS) biosynthetic capacity, and lack of hemolytic activity and was used in the production of yoghurt and feta cheese with distinct organoleptic characteristics. The aim of the present study was to investigate these traits at the genome level through whole-genome sequencing (WGS), annotation, and comparative genomics. Functional annotation of the genome revealed that Lc. paracasei SRX10 can utilize different carbon sources, leading to the generation of flavor compounds, including lactic acid, acetate, ethanol, and acetoin. Similarly, full clusters for fatty acid biosynthesis, protein and peptide degradation, as well as genes related to survival under extreme temperatures, osmotic shock, and oxidative stress were annotated. Importantly, no transferable antibiotic resistance genes or virulence factors were identified. Finally, strain-specific primers based on genome-wide polymorphisms were designed for the efficient and rapid identification of Lc. paracasei SRX10 via multiplex PCR in fermented products

The effect of in-hospital acquired thrombocytopenia on the outcome of patients with acute coronary syndromes: A systematic review and meta-analysis

Background In-hospital acquired thrombocytopenia (TP) is relatively common among patients hospitalized with acute coronary syndromes (ACS). However, its effect on short-term and long-term outcomes has yet to be reviewed systematically. Methods We conducted a systematic review and meta-analysis of clinical studies assessing the relationship between new-onset in-hospital TP and adverse outcomes among ACS patients. MEDLINE, Scopus and the Cochrane Library were searched for eligible studies published before March 20, 2016. Results Ten studies reporting on a total of 142,161 ACS patients were identified. 8133 patients showed evidence of new-onset TP during the course of their hospitalization. Compared with patients with normal platelet counts, patients with new-onset TP had a prolonged in-hospital stay, significantly higher risk of both short-term mortality (< 30 days) (Odds ratio (OR) [95% confidence interval (CI)]: 5.58 [3.63–8.57]) and late death (6 months to 1 year) (OR [95% CI]: 3.45 [2.35–5.07]), as well as a significantly higher risk of major bleeding events in the first 30 days (OR [95% CI]: 6.93 [5.13–9.38]). In addition, risk for other secondary cardiovascular endpoints, including recurrent myocardial infarction, stroke, in-hospital heart failure, stent thrombosis and unplanned revascularization was also significantly higher in the TP versus the no TP group. Conclusions Development of TP during the in-hospital management of ACS patients is a significant predictor of both short- and long-term adverse events, including mortality. In the light of this evidence, clinicians should be cautious and closely monitor abnormal platelet counts that present early following an ACS. © 2016 Elsevier Lt

Permanent pacemaker implantation in pediatric heart transplant recipients: A systematic review and evidence quality assessment

Bradyarrhythmias are a common complication following pediatric OHT and may require permanent pacemaker implantation (PPM). The purpose of this study was to investigate the incidence, predictors, and outcomes of children undergoing PPM implantation following OHT. A PRISMA-compliant systematic literature review was performed using the PubMed database and the Cochrane Library (end-of-search date: January 27, 2019). The Newcastle-Ottawa scale and the Joanna Briggs Institute tool were used to assess the quality of cohort studies and case reports, respectively. We analyzed data from a total of 11 studies recruiting 7198 pediatric patients who underwent heart transplant. PPM implantation was performed in 1.9% (n = 137/7,198; 95% CI: 1.6-2.2) of the patients. Most patients underwent dual-chamber pacing (46%, 95% CI: 32.6-59.7). Male-to-female ratio was 1.3:1. Mean patient age at the time of OHT was 10.1 ± 6.3. Overall, biatrial anastomosis was used in 62.2% (95% CI: 52.8-70.6) of the patients. The bicaval technique was performed in the remaining 37.8% (95% CI: 29.4-47.1). Sinus node dysfunction was the most frequent indication for PPM implantation (54.4%; 95% CI: 42.6-65.7) followed by AV block (45.6%; 95% CI: 34.3-57.3). The median time interval between OHT and PPM implantation ranged from 17 days to 12.5 years. All-cause mortality was 27.9% (95% CI: 18.6-39.6) during a median follow-up of 5 years. PPM implantation is rarely required after pediatric OHT. The most common indication for pacing is sinus node dysfunction, and patients undergoing biatrial anastomosis may be more likely to require PPM. © 2020 Wiley Periodicals, Inc