scholarly journals Identification and analysis of mobile genetic elements in Gibbon genome

2017 ◽  
Author(s):  
Kamal Rawal ◽  
Jaisri Jagannadham ◽  
Chahat Kubba ◽  
Tanya Sharma
Keyword(s):  
Mobile Genetic Elements ◽  
Wide Distribution ◽  
Alu Elements ◽  
Genetic Elements ◽  
Genome Wide ◽  
Nomascus Leucogenys ◽  
Dna Elements ◽  
Insertion Mechanism ◽  
Insertion Sites

AbstractRecent sequencing of genome of northern white-cheeked gibbon (Nomascus leucogenys) has provided important insight into fast evolution of gibbons and signatures relevant to gibbon biology. It was revealed that mobile genetic elements (MGE) seems to play major role in gibbon evolution. Here we report that most of the gibbon genome is occupied by the MGEs such as ALUs, MIRs, LINE1, LINE 2, LINE 3, ERVL, ERV-class1, ERV-class II and other DNA elements which include hAT Charlie and TcMar tigger. We provide detailed description and genome wide distribution of all the MGEs present in gibbon genome. Previously, it was reported that gibbon-specific retrotransposon (LAVA) tend to insert into chromosome segregation genes and alter transcription by providing a premature termination site, suggesting a possible molecular mechanism for the genome plasticity of the gibbon lineage. We show that insertion sites of LAVA elements present atypical signals/patterns which are different from typical signals present at insertion sites of Alu elements. This suggests possibility of distinct insertion mechanism used by LAVA elements for their insertions. We also find similarity in signals of LAVA elements insertion sites with atypical signals present at Alus /L1s insertion sites disrupting the genes leading to diseases such as cancer and Duchenne muscular dystrophy. This suggest role of LAVA in premature transcription termination.

scholarly journals Epigenetic mechanisms in sexual differentiation of the brain and behaviour

2016 ◽  
Vol 371 (1688) ◽  
pp. 20150114 ◽  
Author(s):  
Nancy G. Forger
Keyword(s):  
Gene Expression ◽  
Sex Differences ◽  
Sexual Differentiation ◽  
Wide Distribution ◽  
Epigenetic Modifications ◽  
Epigenetic Mechanism ◽  
Epigenetic Mechanisms ◽  
Genome Wide ◽  
The Brain

Circumstantial evidence alone argues that the establishment and maintenance of sex differences in the brain depend on epigenetic modifications of chromatin structure. More direct evidence has recently been obtained from two types of studies: those manipulating a particular epigenetic mechanism, and those examining the genome-wide distribution of specific epigenetic marks. The manipulation of histone acetylation or DNA methylation disrupts the development of several neural sex differences in rodents. Taken together, however, the evidence suggests there is unlikely to be a simple formula for masculine or feminine development of the brain and behaviour; instead, underlying epigenetic mechanisms may vary by brain region or even by dependent variable within a region. Whole-genome studies related to sex differences in the brain have only very recently been reported, but suggest that males and females may use different combinations of epigenetic modifications to control gene expression, even in cases where gene expression does not differ between the sexes. Finally, recent findings are discussed that are likely to direct future studies on the role of epigenetic mechanisms in sexual differentiation of the brain and behaviour.

scholarly journals A Novel and Direct Metamobilome Approach improves the Detection of Larger-sized Circular Elements across Kingdoms

2019 ◽  
Author(s):  
Katrine Skov Alanin ◽  
Tue Sparholt Jørgensen ◽  
Patrick Browne ◽  
Bent Petersen ◽  
Leise Riber ◽  
...  
Keyword(s):  
Multiple Displacement Amplification ◽  
Bacterial Species ◽  
Human Health Risk ◽  
Prokaryotic Genome ◽  
Mobile Genetic Elements ◽  
Wastewater Sample ◽  
Mobile Dna ◽  
Complex Samples ◽  
Genetic Elements ◽  
Dna Elements

AbstractMobile genetic elements (MGEs) are instrumental in natural prokaryotic genome editing, permitting genome plasticity and allowing microbes to accumulate immense genetic diversity. MGEs include DNA elements such as plasmids, transposons and Insertion Sequences (IS-elements), as well as bacteriophages (phages), and they serve as a vast communal gene pool. These mobile DNA elements represent a human health risk as they can add new traits, such as antibiotic resistance or virulence, to a bacterial strain. Sequencing libraries targeting circular MGEs, referred to as mobilomes, allows the expansion of our current understanding of the mechanisms behind the mobility, prevalence and content of these elements. However, metamobilomes from bacterial communities are not studied to the same extent as metagenomics, partly because of methodological biases arising from multiple displacement amplification (MDA), often used in previous metamobilome publications. In this study, we show that MDA is detrimental to the detection of larger-sized plasmids if small plasmids are present by comparing the abundances of reads mapping to plasmids in a wastewater sample spiked with a mock community of selected plasmids with and without MDA. Furthermore, we show that it is possible to produce samples consisting almost exclusively of circular MGEs and obtain a catalog of larger, complete, circular MGEs from complex samples without the use of MDA.ImportanceMobile genetic elements (MGEs) can transport genetic information between genomes in different bacterial species, adding new traits, potentially generating dangerous multidrug-resistant pathogens. In fact, plasmids and circular MGEs can encode bacterial genetic specializations such as virulence, resistance to metals, antimicrobial compounds, and bacteriophages, as well as the degradation of xenobiotics. For this reason, circular MGEs are crucial to investigate, but they are often missed in metagenomics and ecological studies. In this study, we present, for the first time, an improved method, which reduces the bias towards small MGEs and we demonstrate that this method can unveil larger, complete circular MGEs from complex samples without the use of multiple displacement amplification. This method may result in the detection of larger-sized plasmids that have hitherto remained unnoticed and therefore has the potential to reveal novel accessory genes, acting as possible targets in the development of preventive strategies directed at pathogens.

scholarly journals Directed Evolution of an Enhanced POU Reprogramming Factor for Cell Fate Engineering

2021 ◽  
Author(s):  
Daisylyn Senna Tan ◽  
Yanpu Chen ◽  
Ya Gao ◽  
Anastasia Bednarz ◽  
Yuanjie Wei ◽  
...  
Keyword(s):  
Directed Evolution ◽  
Cell Fate ◽  
Mammalian Cells ◽  
Phenotypic Selection ◽  
Biochemical Assays ◽  
Genome Wide ◽  
Dna Elements ◽  
Pioneer Factor ◽  
Selection Of

Abstract Transcription factor-driven cell fate engineering in pluripotency induction, transdifferentiation, and forward reprogramming requires efficiency, speed, and maturity for widespread adoption and clinical translation. Here, we used Oct4, Sox2, Klf4, and c-Myc driven pluripotency reprogramming to evaluate methods for enhancing and tailoring cell fate transitions, through directed evolution with iterative screening of pooled mutant libraries and phenotypic selection. We identified an artificially evolved and enhanced POU factor (ePOU) that substantially outperforms wild-type Oct4 in terms of reprogramming speed and efficiency. In contrast to Oct4, not only can ePOU induce pluripotency with Sox2 alone, but it can also do so in the absence of Sox2 in a three-factor ePOU/Klf4/c-Myc cocktail. Biochemical assays combined with genome-wide analyses showed that ePOU possesses a new preference to dimerize on palindromic DNA elements. Yet, the moderate capacity of Oct4 to function as a pioneer factor, its preference to bind octamer DNA and its capability to dimerize with Sox2 and Sox17 proteins remain unchanged in ePOU. Compared with Oct4, ePOU is thermodynamically stabilized and persists longer in reprogramming cells. In consequence, ePOU: 1) differentially activates several genes hitherto not implicated in reprogramming, 2) reveals an unappreciated role of thyrotropin-releasing hormone signaling, and 3) binds a distinct class of retrotransposons. Collectively, these features enable ePOU to accelerate the establishment of the pluripotency network. This demonstrates that the phenotypic selection of novel factor variants from mammalian cells with desired properties is key to advancing cell fate conversions with artificially evolved biomolecules.

scholarly journals Type I toxin-antitoxin systems contribute to the maintenance of mobile genetic elements in Clostridioides difficile

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Johann Peltier ◽  
Audrey Hamiot ◽  
Julian R. Garneau ◽  
Pierre Boudry ◽  
Anna Maikova ◽  
...  
Keyword(s):  
Ectopic Expression ◽  
Mobile Genetic Elements ◽  
Toxin Gene ◽  
Type I ◽  
Genetic Elements ◽  
Clostridioides Difficile ◽  
Bacterial Chromosomes ◽  
Toxin Protein

AbstractToxin-antitoxin (TA) systems are widespread on mobile genetic elements and in bacterial chromosomes. In type I TA, synthesis of the toxin protein is prevented by the transcription of an antitoxin RNA. The first type I TA were recently identified in the human enteropathogen Clostridioides difficile. Here we report the characterization of five additional type I TA within phiCD630-1 (CD0977.1-RCd11, CD0904.1-RCd13 and CD0956.3-RCd14) and phiCD630-2 (CD2889-RCd12 and CD2907.2-RCd15) prophages of C. difficile strain 630. Toxin genes encode 34 to 47 amino acid peptides and their ectopic expression in C. difficile induces growth arrest that is neutralized by antitoxin RNA co-expression. We show that type I TA located within the phiCD630-1 prophage contribute to its stability and heritability. We have made use of a type I TA toxin gene to generate an efficient mutagenesis tool for this bacterium that allowed investigation of the role of these widespread TA in prophage maintenance.

scholarly journals Genetic dominance governs the evolution and spread of mobile genetic elements in bacteria

2020 ◽  
Vol 117 (27) ◽  
pp. 15755-15762
Author(s):  
Jerónimo Rodríguez-Beltrán ◽  
Vidar Sørum ◽  
Macarena Toll-Riera ◽  
Carmen de la Vega ◽  
Rafael Peña-Miller ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Mobile Genetic Elements ◽  
Model System ◽  
Host Bacterium ◽  
Wild Type ◽  
Bacterial Evolution ◽  
Human Interest ◽  
Genetic Dominance ◽  
Genetic Elements

Mobile genetic elements (MGEs), such as plasmids, promote bacterial evolution through horizontal gene transfer (HGT). However, the rules governing the repertoire of traits encoded on MGEs remain unclear. In this study, we uncovered the central role of genetic dominance shaping genetic cargo in MGEs, using antibiotic resistance as a model system. MGEs are typically present in more than one copy per host bacterium, and as a consequence, genetic dominance favors the fixation of dominant mutations over recessive ones. In addition, genetic dominance also determines the phenotypic effects of horizontally acquired MGE-encoded genes, silencing recessive alleles if the recipient bacterium already carries a wild-type copy of the gene. The combination of these two effects governs the catalog of genes encoded on MGEs. Our results help to understand how MGEs evolve and spread, uncovering the neglected influence of genetic dominance on bacterial evolution. Moreover, our findings offer a framework to forecast the spread and evolvability of MGE-encoded genes, which encode traits of key human interest, such as virulence or antibiotic resistance.

Sign in / Sign up

Export Citation Format

Share Document