129 research outputs found
Transduplication resulted in the incorporation of two protein-coding sequences into the Turmoil-1 transposable element of C. elegans
Transposable elements may acquire unrelated gene fragments into their
sequences in a process called transduplication. Transduplication of
protein-coding genes is common in plants, but is unknown of in animals. Here,
we report that the Turmoil-1 transposable element in C. elegans has
incorporated two protein-coding sequences into its inverted terminal repeat
(ITR) sequences. The ITRs of Turmoil-1 contain a conserved RNA recognition
motif (RRM) that originated from the rsp- 2 gene and a fragment from the
protein-coding region of the cpg-3 gene. We further report that an open reading
frame specific to C. elegans may have been created as a result of a Turmoil-1
insertion. Mutations at the 5' splice site of this open reading frame may have
reactivated the transduplicated RRM moti
The role of transposable elements in the evolution of non-mammalian vertebrates and invertebrates
Background: Transposable elements (TEs) have played an important role in the diversification and enrichment of mammalian transcriptomes through various mechanisms such as exonization and intronization (the birth of new exons/introns from previously intronic/exonic sequences, respectively), and insertion into first and last exons. However, no extensive analysis has compared the effects of TEs on the transcriptomes of mammals, non-mammalian vertebrates and invertebrates. Results: We analyzed the influence of TEs on the transcriptomes of five species, three invertebrates and two non-mammalian vertebrates. Compared to previously analyzed mammals, there were lower levels of TE introduction into introns, significantly lower numbers of exonizations originating from TEs and a lower percentage of TE insertion within the first and last exons. Although the transcriptomes of vertebrates exhibit significant levels of exonization of TEs, only anecdotal cases were found in invertebrates. In vertebrates, as in mammals, the exonized TEs are mostly alternatively spliced, indicating that selective pressure maintains the original mRNA product generated from such genes. Conclusions: Exonization of TEs is widespread in mammals, less so in non-mammalian vertebrates, and very low in invertebrates. We assume that the exonization process depends on the length of introns. Vertebrates, unlike invertebrates, are characterized by long introns and short internal exons. Our results suggest that there is a direct link between the length of introns and exonization of TEs and that this process became more prevalent following the appearance of mammals
SERpredict: Detection of tissue- or tumor-specific isoforms generated through exonization of transposable elements
Background: Transposed elements (TEs) are known to affect transcriptomes,
because either new exons are generated from intronic transposed elements (this
is called exonization), or the element inserts into the exon, leading to a new
transcript. Several examples in the literature show that isoforms generated by
an exonization are specific to a certain tissue (for example the heart muscle)
or inflict a disease. Thus, exonizations can have negative effects for the
transcriptome of an organism. Results: As we aimed at detecting other tissue-
or tumor-specific isoforms in human and mouse genomes which were generated
through exonization of a transposed element, we designed the automated analysis
pipeline SERpredict (SER = Specific Exonized Retroelement) making use of
Bayesian Statistics. With this pipeline, we found several genes in which a
transposed element formed a tissue- or tumor-specific isoform. Conclusion: Our
results show that SERpredict produces relevant results, demonstrating the
importance of transposed elements in shaping both the human and the mouse
transcriptomes. The effect of transposed elements on the human transcriptome is
several times higher than the effect on the mouse transcriptome, due to the
contribution of the primate-specific Alu element
Comparative analysis of transposed element insertion within human and mouse genomes reveals Alu's unique role in shaping the human transcriptome
Background: Transposed elements (TEs) have a substantial impact on mammalian
evolution and are involved in numerous genetic diseases. We compared the impact
of TEs on the human transcriptome and the mouse transcriptome. Results: We
compiled a dataset of all TEs in the human and mouse genomes, identifying
3,932,058 and 3,122,416 TEs, respectively. We than extracted TEs located within
human and mouse genes and, surprisingly, we found that 60% of TEs in both human
and mouse are located in intronic sequences, even though introns comprise only
24% of the human genome. All TE families in both human and mouse can exonize.
TE families that are shared between human and mouse exhibit the same percentage
of TE exonization in the two species, but the exonization level of Alu, a
primatespecific retroelement, is significantly greater than that of other TEs
within the human genome, leading to a higher level of TE exonization in human
than in mouse (1,824 exons compared with 506 exons, respectively). We detected
a primate-specific mechanism for intron gain, in which Alu insertion into an
exon creates a new intron located in the 3' untranslated region (termed
'intronization'). Finally, the insertion of TEs into the first and last exons
of a gene is more frequent in human than in mouse, leading to longer exons in
human. Conclusion: Our findings reveal many effects of TEs on these two
transcriptomes. These effects are substantially greater in human than in mouse,
which is due to the presence of Alu elements in human
Nonspecific Transcription-Factor-DNA Binding Influences Nucleosome Occupancy in Yeast
AbstractQuantitative understanding of the principles regulating nucleosome occupancy on a genome-wide level is a central issue in eukaryotic genomics. Here, we address this question using budding yeast, Saccharomyces cerevisiae, as a model organism. We perform a genome-wide computational analysis of the nonspecific transcription factor (TF)-DNA binding free-energy landscape and compare this landscape with experimentally determined nucleosome-binding preferences. We show that DNA regions with enhanced nonspecific TF-DNA binding are statistically significantly depleted of nucleosomes. We suggest therefore that the competition between TFs with histones for nonspecific binding to genomic sequences might be an important mechanism influencing nucleosome-binding preferences in vivo. We also predict that poly(dA:dT) and poly(dC:dG) tracts represent genomic elements with the strongest propensity for nonspecific TF-DNA binding, thus allowing TFs to outcompete nucleosomes at these elements. Our results suggest that nonspecific TF-DNA binding might provide a barrier for statistical positioning of nucleosomes throughout the yeast genome. We predict that the strength of this barrier increases with the concentration of DNA binding proteins in a cell. We discuss the connection of the proposed mechanism with the recently discovered pathway of active nucleosome reconstitution
Dimensions of Maternal Parenting and Infants’ Autonomic Functioning Interactively Predict Early Internalizing Behavior Problems
Developmental pathways to childhood internalizing behavior problems are complex, with both environmental and child-level factors contributing to their emergence. The authors use data from a prospective longitudinal study (n = 206) to examine the associations between dimensions of caregiving experiences in the first year of life and anxious/depressed and withdrawn behaviors in early childhood. Additionally, the authors examine the extent to which these associations were moderated by infants’ autonomic functioning in the first year of life indexed using measures of respiratory sinus arrhythmia (RSA) and heart period (HP). Findings suggest that higher levels of maternal sensitivity in infancy are associated with fewer anxious/depressed and withdrawn behaviors at age 3 years. Negative intrusiveness was found to be positively associated with children’s anxious/depressed behaviors but not withdrawn behaviors. Further, moderation analyses suggested that the link between negative intrusive parenting during infancy and subsequent anxious/depressed behaviors is exacerbated for infants with average or low baseline HP and that positive engaging parenting during infancy was negatively related to withdrawn behaviors for infants demonstrating average to high levels baseline HP. Interestingly, RSA was not found to moderate the associations between parenting in infancy and later internalizing behavior problems suggesting that, during infancy, overall autonomic functioning may have greater implications for the development of internalizing behaviors than do parasympathetic influences alone. Implications of these findings and future directions for research are discussed
An Intranuclear Sodalis-Like Symbiont and Spiroplasma Coinfect the Carrot Psyllid, Bactericera trigonica (Hemiptera, Psylloidea)
Endosymbionts harbored inside insects play critical roles in the biology of their insect host and can influence the transmission of pathogens by insect vectors. Bactericera trigonica infests umbelliferous plants and transmits the bacterial plant pathogen Candidatus Liberibacter solanacearum (CLso), causing carrot yellows disease. To characterize the bacterial diversity of B. trigonica, as a first step, we used PCR-restriction fragment length polymorphism (PCR-RFLP) and denaturing gradient gel electrophoresis (DGGE) analyses of 16S rDNA to identify Sodalis and Spiroplasma endosymbionts. The prevalence of both symbionts in field-collected psyllid populations was determined: Sodalis was detected in 100% of field populations, while Spiroplasma was present in 82.5% of individuals. Phylogenetic analysis using 16S rDNA revealed that Sodalis infecting B. trigonica was more closely related to symbionts infecting weevils, stink bugs and tsetse flies than to those from psyllid species. Using fluorescent in situ hybridization and immunostaining, Sodalis was found to be localized inside the nuclei of the midgut cells and bacteriocytes. Spiroplasma was restricted to the cytoplasm of the midgut cells. We further show that a recently reported Bactericera trigonica densovirus (BtDNV), a densovirus infecting B. trigonica was detected in 100% of psyllids and has reduced titers inside CLso-infected psyllids by more than two-fold compared to CLso uninfected psyllids. The findings of this study will help to increase our understanding of psyllid–endosymbiont interactions
Genetic and metabolic analyses of Candidatus Liberibacter solanacearum infecting carrot
Insect-vectored plant bacterial pathogens are gaining attention in recent years due to crop threatening outbreaks around the world. Candidatus Liberibacter spp. are infecting crops of different botanical families: Solanaceae, Rutaceae, and Apiaceae and are vectored by psyllids. Five genetic haplotypes (A-E) have been described thus far for the species Ca. Liberibacter solanacearum (Lso). Haplotypes A and B infecting solanaceous plants, haplotypes C-E infecting Apiaceae crops. To better understand the genetic basis that governs host specificity of Lso haplotypes, we sequenced the genome of haplotype D (LsoD). The LsoD genome size is 1.23 Mbp, with a GC content of 34.8% and 1167 predicted genes. Enzyme Commission (EC) numbers were assigned using the JGI software tool and 358 ECs were identified. ECs were mapped to metabolic pathways and compared with other sequenced Liberibacters. Phylogenetic analysis based on ECs and assigned metabolic pathways shows that LsoD groups together with Lso haplotypes (A and B) and is clearly different than Liberibacter species infecting citrus. Differences between LsoD and LsoA/B haplotypes were also found, hinting on host specific enzymes. The LsoD genome was also scanned to identify putatively secreted proteins using the SignalP tool. Thirty-one putative genes were identified, most of them with unknown function. While some genes have homologous in other Lso haplotypes, some were unique to LsoD. By quantitative-PCR we examined the expression of the putatively secreted proteins in the different hosts; the psyllid vector Bactericera trigonica, and carrot. Several genes with significantly higher expression levels in carrot compared with psyllid and vice versa were identified. These genes may have host specific functions. Overall, our analyses reveal genetic and metabolic elements differentiating the carrot-infecting Lso from Lso haplotypes infecting potato/tomato. Research is underway to identify the function of these elements
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