scholarly journals Flanker: a tool for comparative genomics of gene flanking regions

2021 ◽  
Vol 7 (9) ◽  
Author(s):  
William Matlock ◽  
Samuel Lipworth ◽  
Bede Constantinides ◽  
Timothy E. A. Peto ◽  
A. Sarah Walker ◽  
...  
Keyword(s):  
Flanking Sequence ◽  
European Isolate ◽  
Gene Characterization ◽  
Geographical Regions ◽  
Antimicrobial Resistance Genes ◽  
Flanking Sequences ◽  
Flanking Regions ◽  
Fine Tune ◽  
Python Package

Analysing the flanking sequences surrounding genes of interest is often highly relevant to understanding the role of mobile genetic elements (MGEs) in horizontal gene transfer, particular for antimicrobial-resistance genes. Here, we present Flanker, a Python package that performs alignment-free clustering of gene flanking sequences in a consistent format, allowing investigation of MGEs without prior knowledge of their structure. These clusters, known as ‘flank patterns’ (FPs), are based on Mash distances, allowing for easy comparison of similarity across sequences. Additionally, Flanker can be flexibly parameterized to fine-tune outputs by characterizing upstream and downstream regions separately, and investigating variable lengths of flanking sequence. We apply Flanker to two recent datasets describing plasmid-associated carriage of important carbapenemase genes (bla OXA-48 and bla KPC-2/3) and show that it successfully identifies distinct clusters of FPs, including both known and previously uncharacterized structural variants. For example, Flanker identified four Tn4401 profiles that could not be sufficiently characterized using TETyper or MobileElementFinder, demonstrating the utility of Flanker for flanking-gene characterization. Similarly, using a large (n=226) European isolate dataset, we confirm findings from a previous smaller study demonstrating association between Tn1999.2 and bla OXA-48 upregulation and demonstrate 17 FPs (compared to the 5 previously identified). More generally, the demonstration in this study that FPs are associated with geographical regions and antibiotic-susceptibility phenotypes suggests that they may be useful as epidemiological markers. Flanker is freely available under an MIT license at https://github.com/wtmatlock/flanker.

scholarly journals Flanker: a tool for comparative genomics of gene flanking regions

2021 ◽  
Author(s):  
William Matlock ◽  
Samuel Lipworth ◽  
Bede Constantinides ◽  
Timothy E.A. Peto ◽  
A. Sarah Walker ◽  
...  
Keyword(s):  
Flanking Sequence ◽  
Sequencing Data ◽  
Link Type ◽  
Geographical Regions ◽  
Antimicrobial Resistance Genes ◽  
Ncbi Accession ◽  
Flanking Sequences ◽  
Flanking Regions ◽  
Python Package

AbstractAnalysing the flanking sequences surrounding genes of interest is often highly relevant to understanding the role of mobile genetic elements (MGEs) in horizontal gene transfer, particular for antimicrobial resistance genes. Here, we present Flanker, a Python package which performs alignment-free clustering of gene flanking sequences in a consistent format, allowing investigation of MGEs without prior knowledge of their structure. Flanker clusters flanking sequences based on Mash distances, allowing for easy comparison of similarity and the extent of this similarity across sequences. Additionally, Flanker can be flexibly parameterised to finetune outputs by characterising upstream and downstream regions separately and investigating variable lengths of flanking sequence. We apply Flanker to two recent datasets describing plasmid-associated carriage of important carbapenemase genes (blaOXA-48 and blaKPC-2/3) and show that it successfully identifies distinct clusters of flanking sequences (flank patterns), including both known and previously uncharacterised structural variants. We demonstrate that flank patterns are linked to geographical regions and carbapenem phenotypes, suggesting they may be useful as epidemiological markers. Flanker is freely available under an MIT license at https://github.com/wtmatlock/flanker.Data SummaryNCBI accession numbers for all sequencing data used in this study is provided in Supplementary Table 1. The analysis performed in this manuscript can be reproduced in a binder environment provided on the Flanker Github page (https://github.com/wtmatlock/flanker).

scholarly journals Uncovering the repertoire of endogenous flaviviral elements inAedesmosquito genomes

2017 ◽  
Author(s):  
Yasutsugu Suzuki ◽  
Lionel Frangeul ◽  
Laura B. Dickson ◽  
Hervé Blanc ◽  
Yann Verdier ◽  
...  
Keyword(s):  
Cell Lines ◽  
Small Rnas ◽  
Biological Function ◽  
Geographical Regions ◽  
Mosquito Cell Lines ◽  
Flanking Sequences ◽  
Endogenous Viral Elements ◽  
Flanking Regions

AbstractEndogenous viral elements derived from non-retroviral RNA viruses were described in various animal genomes. Whether they have a biological function such as host immune protection against related viruses is a field of intense study. Here, we investigated the repertoire of endogenous flaviviral elements (EFVEs) inAedesmosquitoes, the vectors of arboviruses such as dengue and chikungunya viruses. Previous studies identified three EFVEs fromAe. albopictusand one fromAe. aegypticell lines. However, in-depth characterization of EFVEs in wild-type mosquito populations and individualsin vivohas not been performed. We detected the full-length DNA sequence of the previously described EFVEs and their respective transcripts in severalAe. albopictusandAe. aegyptipopulations from geographically distinct areas. However, EFVE-derived proteins were not detected by mass spectrometry. Using deep sequencing, we detected the production of piRNA-like small RNAs in antisense orientation, targeting the EFVEs and their flanking regionsin vivo. The EFVEs were integrated in repetitive regions of the mosquito genomes, and their flanking sequences varied among mosquito populations from different geographical regions. We bioinformatically predicted several new EFVEs from a VietnameseAe. albopictuspopulation and observed variation in the occurrence of those elements among mosquito populations. Phylogenetic analysis of anAe. aegyptiEFVE suggested that it integrated prior to the global expansion of the species and subsequently diverged among and within populations. Together, this study revealed substantial structural and nucleotide diversity of flaviviral integrations inAedesgenomes. Unraveling this diversity will help to elucidate the potential biological function of these EFVEs.ImportanceEndogenous viral elements (EVEs) are whole or partial viral sequences integrated in host genomes. Interestingly, some EVEs have important functions for host fitness and antiviral defense. Because mosquitoes also have EVEs in their genomes, we decided to thoroughly characterized them to lay the foundation of the potential use of these EVEs to manipulate the mosquito antiviral response. Here, we focused on EVEs related to theFlavivirusgenus, to which dengue and Zika viruses belong, inAedesmosquito individuals from geographically distinct areas. We showed the existencein vivoof flaviviral EVEs previously identified in mosquito cell lines and we detected new ones. We showed that EVEs have evolved differently in each mosquito population. They produced transcripts and small RNAs, but not proteins, suggesting a function at the RNA level. Our study uncovers the diverse repertoire of flaviviral EVEs inAedesmosquito populations and suggests a role in the host antiviral system.

scholarly journals Structural characterization and duplication modes of pseudogenes in plants

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Flavia Mascagni ◽  
Gabriele Usai ◽  
Andrea Cavallini ◽  
Andrea Porceddu
Keyword(s):  
Evolutionary Rate ◽  
Populus Trichocarpa ◽  
Sequence Divergence ◽  
Strand Break ◽  
Whole Genome ◽  
Flanking Sequence ◽  
Plant Genomes ◽  
High Sequence Divergence ◽  
Flanking Regions

AbstractWe identified and characterized the pseudogene complements of five plant species: four dicots (Arabidopsis thaliana, Vitis vinifera, Populus trichocarpa and Phaseolus vulgaris) and one monocot (Oryza sativa). Retroposition was considered of modest importance for pseudogene formation in all investigated species except V. vinifera, which showed an unusually high number of retro-pseudogenes in non coding genic regions. By using a pipeline for the classification of sequence duplicates in plant genomes, we compared the relative importance of whole genome, tandem, proximal, transposed and dispersed duplication modes in the pseudo and functional gene complements. Pseudogenes showed higher tendencies than functional genes to genomic dispersion. Dispersed pseudogenes were prevalently fragmented and showed high sequence divergence at flanking regions. On the contrary, those deriving from whole genome duplication were proportionally less than expected based on observations on functional loci and showed higher levels of flanking sequence conservation than dispersed pseudogenes. Pseudogenes deriving from tandem and proximal duplications were in excess compared to functional loci, probably reflecting the high evolutionary rate associated with these duplication modes in plant genomes. These data are compatible with high rates of sequence turnover at neutral sites and double strand break repairs mediated duplication mechanisms.

scholarly journals The Functional Role of Loops and Flanking Sequences of G-Quadruplex Aptamer to the Hemagglutinin of Influenza a Virus

2021 ◽  
Vol 22 (5) ◽  
pp. 2409
Author(s):  
Anastasia A. Bizyaeva ◽  
Dmitry A. Bunin ◽  
Valeria L. Moiseenko ◽  
Alexandra S. Gambaryan ◽  
Sonja Balk ◽  
...  
Keyword(s):  
Influenza A Virus ◽  
Influenza A ◽  
Core Structure ◽  
Dna Aptamer ◽  
Tertiary Structures ◽  
Quadruplex Dna ◽  
G Quadruplex ◽  
Flanking Sequences ◽  
Related Proteins

Nucleic acid aptamers are generally accepted as promising elements for the specific and high-affinity binding of various biomolecules. It has been shown for a number of aptamers that the complexes with several related proteins may possess a similar affinity. An outstanding example is the G-quadruplex DNA aptamer RHA0385, which binds to the hemagglutinins of various influenza A virus strains. These hemagglutinins have homologous tertiary structures but moderate-to-low amino acid sequence identities. Here, the experiment was inverted, targeting the same protein using a set of related, parallel G-quadruplexes. The 5′- and 3′-flanking sequences of RHA0385 were truncated to yield parallel G-quadruplex with three propeller loops that were 7, 1, and 1 nucleotides in length. Next, a set of minimal, parallel G-quadruplexes with three single-nucleotide loops was tested. These G-quadruplexes were characterized both structurally and functionally. All parallel G-quadruplexes had affinities for both recombinant hemagglutinin and influenza virions. In summary, the parallel G-quadruplex represents a minimal core structure with functional activity that binds influenza A hemagglutinin. The flanking sequences and loops represent additional features that can be used to modulate the affinity. Thus, the RHA0385–hemagglutinin complex serves as an excellent example of the hypothesis of a core structure that is decorated with additional recognizing elements capable of improving the binding properties of the aptamer.

scholarly journals EpCAM promotes endosomal modulation of the cortical RhoA zone for epithelial organization

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Cécile Gaston ◽  
Simon De Beco ◽  
Bryant Doss ◽  
Meng Pan ◽  
Estelle Gauquelin ◽  
...  
Keyword(s):  
Cell Shape ◽  
Specific Protein ◽  
Cell Polarization ◽  
Stress Fiber ◽  
Fiber Formation ◽  
Endosomal Trafficking ◽  
Transient Zone ◽  
And Behavior ◽  
Fine Tune

AbstractAt the basis of cell shape and behavior, the organization of actomyosin and its ability to generate forces are widely studied. However, the precise regulation of this contractile network in space and time is unclear. Here, we study the role of the epithelial-specific protein EpCAM, a contractility modulator, in cell shape and motility. We show that EpCAM is required for stress fiber generation and front-rear polarity acquisition at the single cell level. In fact, EpCAM participates in the remodeling of a transient zone of active RhoA at the cortex of spreading epithelial cells. EpCAM and RhoA route together through the Rab35/EHD1 fast recycling pathway. This endosomal pathway spatially organizes GTP-RhoA to fine tune the activity of actomyosin resulting in polarized cell shape and development of intracellular stiffness and traction forces. Impairment of GTP-RhoA endosomal trafficking either by silencing EpCAM or by expressing Rab35/EHD1 mutants prevents proper myosin-II activity, stress fiber formation and ultimately cell polarization. Collectively, this work shows that the coupling between co-trafficking of EpCAM and RhoA, and actomyosin rearrangement is pivotal for cell spreading, and advances our understanding of how biochemical and mechanical properties promote cell plasticity.

scholarly journals Ability of a bacterial chromosome segment to invert is dictated by included material rather than flanking sequence.

Genetics ◽  
1991 ◽  
Vol 129 (4) ◽  
pp. 1021-1032 ◽  
Author(s):  
M J Mahan ◽  
J R Roth
Keyword(s):  
Homologous Recombination ◽  
Parent Strain ◽  
Genetic Material ◽  
Chromosomal Inversion ◽  
Chromosome Segment ◽  
Bacterial Chromosome ◽  
Flanking Sequence ◽  
Flanking Sequences ◽  
Almost All

Abstract Homologous recombination between sequences present in inverse order within the same chromosome can result in inversion formation. We have previously shown that inverse order sequences at some sites (permissive) recombine to generate the expected inversion; no inversions are found when the same inverse order sequences flank other (nonpermissive) regions of the chromosome. In hopes of defining how permissive and nonpermissive intervals are determined, we have constructed a strain that carries a large chromosomal inversion. Using this inversion mutant as the parent strain, we have determined the "permissivity" of a series of chromosomal sites for secondary inversions. For the set of intervals tested, permissivity seems to be dictated by the nature of the genetic material present within the chromosomal interval being tested rather than the flanking sequences or orientation of this material in the chromosome. Almost all permissive intervals include the origin or terminus of replication. We suggest that the rules for recovery of inversions reflect mechanistic restrictions on the occurrence of inversions rather than lethal consequences of the completed rearrangement.

Distal regulatory elements from the mouse metallothionein locus stimulate gene expression in transgenic mice

1993 ◽  
Vol 13 (9) ◽  
pp. 5266-5275
Author(s):  
R D Palmiter ◽  
E P Sandgren ◽  
D M Koeller ◽  
R L Brinster
Keyword(s):  
Transgenic Mice ◽  
Regulatory Elements ◽  
High Level Expression ◽  
Hypersensitive Sites ◽  
Enhanced Expression ◽  
Rat Growth ◽  
Flanking Sequences ◽  
High Level ◽  
Distal Regulatory Elements ◽  
Flanking Regions

DNA regions of 10 and 7 kb that flank the mouse metallothionein II (MT-II) and MT-I genes, respectively, were combined with a minimally marked MT-I (MT-I*) gene and tested in transgenic mice. This construct resulted in (i) position-independent expression of MT-I* mRNA and copy number-dependent expression, (ii) levels of hepatic MT-I mRNA per cell per transgene that were about half that derived from endogenous MT-I genes, (iii) appropriate regulation by metals and hormones, and (iv) tissue distribution of transgene mRNA that resembled that of endogenous MT-I mRNA. These features were not observed when MT-I* was tested without the flanking regions. These MT-I flanking sequences also improved the expression of rat growth hormone reporter genes, with or without introns, that were under the control of the MT-I promoter. Moreover, they enhanced expression from two of four heterologous promoters/enhancers that were tested. Deletion analysis indicated that regions known to have DNase I-hypersensitive sites were necessary but not sufficient for high-level expression. These data suggest that the DNA regions flanking the mouse MT-I and MT-II genes have functions like the locus control regions described for other genes.

Transcriptional insulation of the human keratin 18 gene in transgenic mice

1993 ◽  
Vol 13 (4) ◽  
pp. 2214-2223
Author(s):  
N Neznanov ◽  
I S Thorey ◽  
G Ceceña ◽  
R G Oshima
Keyword(s):  
Transgenic Mice ◽  
Thymidine Kinase ◽  
Copy Number ◽  
Thymidine Kinase Gene ◽  
Flanking Sequence ◽  
Kinase Gene ◽  
Tissue Specific ◽  
Dependent Behavior ◽  
Flanking Sequences ◽  
Keratin 18

Expression of the 10-kb human keratin 18 (K18) gene in transgenic mice results in efficient and appropriate tissue-specific expression in a variety of internal epithelial organs, including liver, lung, intestine, kidney, and the ependymal epithelium of brain, but not in spleen, heart, or skeletal muscle. Expression at the RNA level is directly proportional to the number of integrated K18 transgenes. These results indicate that the K18 gene is able to insulate itself both from the commonly observed cis-acting effects of the sites of integration and from the potential complications of duplicated copies of the gene arranged in head-to-tail fashion. To begin to identify the K18 gene sequences responsible for this property of transcriptional insulation, additional transgenic mouse lines containing deletions of either the 5' or 3' distal end of the K18 gene have been characterized. Deletion of 1.5 kb of the distal 5' flanking sequence has no effect upon either the tissue specificity or the copy number-dependent behavior of the transgene. In contrast, deletion of the 3.5-kb 3' flanking sequence of the gene results in the loss of the copy number-dependent behavior of the gene in liver and intestine. However, expression in kidney, lung, and brain remains efficient and copy number dependent in these transgenic mice. Furthermore, herpes simplex virus thymidine kinase gene expression is copy number dependent in transgenic mice when the gene is located between the distal 5'- and 3'-flanking sequences of the K18 gene. Each adult transgenic male expressed the thymidine kinase gene in testes and brain and proportionally to the number of integrated transgenes. We conclude that the characteristic of copy number-dependent expression of the K18 gene is tissue specific because the sequence requirements for transcriptional insulation in adult liver and intestine are different from those for lung and kidney. In addition, the behavior of the transgenic thymidine kinase gene in testes and brain suggests that the property of transcriptional insulation of the K18 gene may be conferred by the distal flanking sequences of the K18 gene and, additionally, may function for other genes.

The role of quality seed use for world crop production with special reference to the developing countries

1975 ◽  
Vol 8 (5) ◽  
pp. 268-270 ◽  
Author(s):  
W P Feistritzer
Keyword(s):  
Developing Countries ◽  
Special Reference ◽  
Crop Production ◽  
Stages Of Development ◽  
Short Article ◽  
Geographical Regions ◽  
The World ◽  
The Future ◽  
Pasture Plants

In this short article the author indicates the present stages of development of variety evaluation, testing, certification, production and marketing of quality seed—of cereals, industrial crops, pasture plants and vegetables—in major geographical regions of the world and draws attention to some of the underlying problems which must be faced in the future if further progress is to be made.

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