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Genes & Development Feb 2017Overlapping gene arrangements can potentially contribute to gene expression regulation. A mammalian interspersed repeat (MIR) nested in antisense orientation within the...
Overlapping gene arrangements can potentially contribute to gene expression regulation. A mammalian interspersed repeat (MIR) nested in antisense orientation within the first intron of the gene, encoding an RNA polymerase III (Pol III) subunit, is conserved in mammals and highly occupied by Pol III. Using a fluorescence assay, CRISPR/Cas9-mediated deletion of the MIR in mouse embryonic stem cells, and chromatin immunoprecipitation assays, we show that the MIR affects expression through transcriptional interference. Our study reveals a mechanism by which a Pol II gene can be regulated at the transcription elongation level by transcription of an embedded antisense Pol III gene.
Topics: Animals; Conserved Sequence; DNA, Antisense; Embryonic Stem Cells; Gene Expression Regulation; Interspersed Repetitive Sequences; Introns; Mice; RNA Polymerase II; RNA Polymerase III; RNA, Messenger; Sequence Deletion
PubMed: 28289142
DOI: 10.1101/gad.293324.116 -
Molecular Microbiology Nov 2020XerCD-dif site-specific recombination is a well characterized system, found in most bacteria and archaea. Its role is resolution of chromosomal dimers that arise from... (Review)
Review
XerCD-dif site-specific recombination is a well characterized system, found in most bacteria and archaea. Its role is resolution of chromosomal dimers that arise from homologous recombination. Xer-mediated recombination is also used by several plasmids for multimer resolution to enhance stability and by some phage for integration into the chromosome. In the past decade, it has been hypothesized that an alternate and novel function exists for this system in the dissemination of genetic elements, notably antibiotic resistance genes, in Acinetobacter species. Currently the mechanism underlying this apparent genetic mobility is unknown. Multidrug resistant Acinetobacter baumannii is an increasingly problematic pathogen that can cause recurring infections. Sequencing of numerous plasmids from clinical isolates of A. baumannii revealed the presence of possible mobile modules: genes were found flanked by pairs of Xer recombination sites, called plasmid-dif (pdif) sites. These modules have been identified in multiple otherwise unrelated plasmids and in different genetic contexts suggesting they are mobile elements. In most cases, the pairs of sites flanking a gene (or genes) are in inverted repeat, but there can be multiple modules per plasmid providing pairs of recombination sites that can be used for inversion or fusion/deletion reactions; as many as 16 pdif sites have been seen in a single plasmid. Similar modules including genes for surviving environmental toxins have also been found in strains of Acinetobacter Iwoffi isolated from permafrost cores; this suggests that these mobile modules are an ancient adaptation and not a novel response to antibiotic pressure. These modules bear all the hallmarks of mobile genetic elements, yet, their movement has never been directly observed to date. This review gives an overview of the current state of this novel research field.
Topics: Acinetobacter; Anti-Bacterial Agents; Drug Resistance, Bacterial; Homologous Recombination; Integrases; Interspersed Repetitive Sequences; Plasmids; Recombinases; Recombination, Genetic
PubMed: 32594594
DOI: 10.1111/mmi.14563 -
Trends in Microbiology Dec 2018Pollution is the dissemination of material that has harmful effects. Mobile DNA elements and antibiotic-resistance genes are being disseminated into the environment via...
Pollution is the dissemination of material that has harmful effects. Mobile DNA elements and antibiotic-resistance genes are being disseminated into the environment via human activity, and are increasingly being viewed as serious pollutants. These pollutants differ from conventional contaminants in important ways: they can replicate, and they can evolve.
Topics: Anti-Infective Agents; Bacteria; DNA; DNA, Bacterial; Disinfectants; Drug Resistance, Bacterial; Drug Resistance, Microbial; Environmental Monitoring; Environmental Pollutants; Environmental Pollution; Genes, Bacterial; Humans; Interspersed Repetitive Sequences; Metals, Heavy
PubMed: 30170783
DOI: 10.1016/j.tim.2018.08.003 -
American Journal of Medical Genetics.... Nov 2010Jumping translocations (JTs) are rare constitutional or acquired rearrangements involving a donor and several receiver chromosomes. They may be inherited or de novo. JTs... (Review)
Review
Jumping translocations (JTs) are rare constitutional or acquired rearrangements involving a donor and several receiver chromosomes. They may be inherited or de novo. JTs can be found as a cultural artifact, in normal individuals or in pathological conditions. The clinical consequences range from spontaneous abortion, loss of fetus, chromosome syndrome, congenital abnormalities, and infertility to malignancy. Considering the breakpoints of JTs, they are localized predominantly in repeat regions such as pericentromeric, centromeric, subtelomeric, telomeric, and occasionally interstitial regions that may be in a low copy repeats (LCR) or in a telomere like sequence. Differences between the constitutional and acquired JTs donor breakpoints suggest an independent mechanism in their formation. In this review, a new JT involving a donor chromosome 18p10qter and recipients 17q25qter or 1q25qter found by CVS of a twin pregnancy is described. This case illustrates the diagnostic challenges posed by JTs.In this study, our knowledge on JTs is consolidated to improve identification, management, and counseling.
Topics: Adult; Chorionic Villi Sampling; Embryonic Development; Female; Humans; In Situ Hybridization, Fluorescence; Interspersed Repetitive Sequences; Karyotyping; Pregnancy; Translocation, Genetic; Twins
PubMed: 20979197
DOI: 10.1002/ajmg.a.33710 -
Movement Disorders : Official Journal... Jan 2019
Topics: Animals; DNA Transposable Elements; Humans; Interspersed Repetitive Sequences; Tauopathies
PubMed: 30549316
DOI: 10.1002/mds.27551 -
Current Opinion in Microbiology Dec 2022Studies of viral adaptation have focused on the selective pressures imposed by hosts. However, there is increasing evidence that interactions between viruses, cells, and... (Review)
Review
Studies of viral adaptation have focused on the selective pressures imposed by hosts. However, there is increasing evidence that interactions between viruses, cells, and other mobile genetic elements are determinant to the success of infections. These interactions are often associated with antagonism and competition, but sometimes involve cooperation or parasitism. We describe two key types of interactions - defense systems and genetic regulation - that allow the partners of the interaction to destroy or control the others. These interactions evolve rapidly by genetic exchanges, including among competing partners. They are sometimes followed by functional diversification. Gene exchanges also facilitate the emergence of cross-talk between elements in the same bacterium. In the end, these processes produce multilayered networks of interactions that shape the outcome of viral infections.
Topics: Bacteriophages; Viruses; Bacteria; Symbiosis; Interspersed Repetitive Sequences
PubMed: 36335712
DOI: 10.1016/j.mib.2022.102230 -
IUBMB Life Aug 2005The advent of comparative genomics has revolutionized the study of the origin and evolution of eukaryotes and their organelles. Genomic analysis has revealed that the... (Review)
Review
The advent of comparative genomics has revolutionized the study of the origin and evolution of eukaryotes and their organelles. Genomic analysis has revealed that the endosymbiosis that gave rise to plastids--the light-harvesting apparatus of photosynthetic eukaryotes--had a profound impact on the genetic composition of the host, far beyond the contribution of cyanobacterial genes for plastid-specific functions. Here I discuss recent advances in our appreciation of the mosaic nature of the eukaryotic nuclear genome, and the ongoing role endosymbiosis plays in shaping its content.
Topics: Eukaryota; Evolution, Molecular; Genomics; Interspersed Repetitive Sequences; Photosynthesis; Phylogeny; Symbiosis
PubMed: 16118111
DOI: 10.1080/15216540500167732 -
Current Opinion in Microbiology Aug 2017Although the phenomenon of transposition has been known for over 60 years, its overarching importance in modifying and streamlining genomes took some time to recognize.... (Review)
Review
Although the phenomenon of transposition has been known for over 60 years, its overarching importance in modifying and streamlining genomes took some time to recognize. In spite of a robust understanding of transposition of some TE, there remain a number of important TE groups with potential high genome impact and unknown transposition mechanisms and yet others, only recently identified by bioinformatics, yet to be formally confirmed as mobile. Here, we point to some areas of limited understanding concerning well established important TE groups with DDE Tpases, to address central gaps in our knowledge of characterised Tn with other types of Tpases and finally, to highlight new potentially mobile DNA species. It is not exhaustive. Examples have been chosen to provide encouragement in the continued exploration of the considerable prokaryotic mobilome especially in light of the current threat to public health posed by the spread of multiple Ab.
Topics: Archaea; Bacteria; Evolution, Molecular; Interspersed Repetitive Sequences; Recombination, Genetic
PubMed: 28683354
DOI: 10.1016/j.mib.2017.06.005 -
Current Opinion in Microbiology Aug 2017Conjugation is a dominant mechanism of horizontal gene transfer and substantially contributes to the plasticity and evolvability of prokaryotic genomes. The impact of... (Review)
Review
Conjugation is a dominant mechanism of horizontal gene transfer and substantially contributes to the plasticity and evolvability of prokaryotic genomes. The impact of conjugation on genetic flux extends well beyond self-transmissible conjugative elements, because non-conjugative 'mobilizable elements' utilize other elements' conjugative apparatus for transfer. Bacterial genome comparisons highlight plasmids as vehicles for dissemination of pathogenesis and antimicrobial-resistance determinants, but for most non-conjugative plasmids, a mobilization mechanism is not apparent. Recently we discovered many Staphylococcus aureus plasmids lacking mobilization genes carry oriT sequences that mimic those on conjugative plasmids, suggesting that significantly more elements may be mobilizable than previously recognized. Here we summarize our findings, review the diverse mobilization strategies employed by mobile genetic elements and discuss implications for future gene-transfer research.
Topics: Gene Transfer, Horizontal; Interspersed Repetitive Sequences; Plasmids; Staphylococcus aureus
PubMed: 28391142
DOI: 10.1016/j.mib.2017.03.003 -
Bioscience, Biotechnology, and... May 2017Mobile genetic elements (MGEs) including plasmids have an important role in the rapid evolution and adaptation of bacteria. Here, the behavior of MGEs in different... (Review)
Review
Mobile genetic elements (MGEs) including plasmids have an important role in the rapid evolution and adaptation of bacteria. Here, the behavior of MGEs in different environments is reviewed, in particular, behavior of the plasmid pCAR1, a carbazole-degradative plasmid isolated from Pseudomonas resinovorans CA10. pCAR1 belongs to incompatibility P-7 group and is self-transmissible among different bacteria. Comparisons of changes in the transcriptome of different host strains caused by carrying pCAR1 revealed common responses in the hosts and host-specific responses. Monitoring the survival of the host and transfer of the plasmid in artificial and natural environmental samples revealed several environmental factors, including cations and water content, which changed the behavior of both the host and its plasmid. Single-cell level analysis to detect the transconjugants of different plasmids successfully determined the transfer range of the plasmids. Three nucleoid-associated proteins encoded on pCAR1 are important factors affecting its genetic stability, maintenance, and transfer.
Topics: Carbazoles; Genomics; Host Specificity; Interspersed Repetitive Sequences; Plasmids
PubMed: 28077029
DOI: 10.1080/09168451.2016.1270743