scholarly journals ZBED6 binding motifs correlate with endogenous retroviruses and syncytin genes

2020 ◽  
Author(s):  
Mats E Pettersson ◽  
Patric Jern
Keyword(s):  
Transposable Elements ◽  
Potential Role ◽  
Endogenous Retroviruses ◽  
Binding Motifs ◽  
Dna Transposons ◽  
Genomic Expression ◽  
Transcription Regulator ◽  
Large Numbers ◽  
Mammalian Genomes

Abstract Retroviruses have infiltrated vertebrate germlines for millions of years as inherited endogenous retroviruses (ERVs). Mammalian genomes host large numbers of ERVs and transposable elements (TEs), including retrotransposons and DNA transposons, that contribute to genomic innovation and evolution as coopted genes and regulators of diverse functions. To explore features distinguishing coopted ERVs and TEs from other integrations, we focus on the potential role of ZBED6 and repeated ERV domestication as repurposed Syncytin genes. The placental mammal-specific ZBED6 is a DNA transposon-derived transcription regulator and we demonstrate that its binding motifs are associated with distinct Syncytins, and that ZBED6 binding motifs are 2-to-3 fold more frequent in ERVs than in flanking DNA. Our observations suggest that ZBED6 could contribute an extended regulatory role of genomic expression, utilizing ERVs as platforms for genomic innovation and evolution.

scholarly journals On transposons and totipotency

2020 ◽  
Vol 375 (1795) ◽  
pp. 20190339 ◽  
Author(s):  
Maria-Elena Torres-Padilla
Keyword(s):  
Large Scale ◽  
Current Knowledge ◽  
Regulation Of Gene Expression ◽  
Endogenous Retrovirus ◽  
Endogenous Retroviruses ◽  
Host Genome ◽  
The Past ◽  
Stage Of Development ◽  
Mammalian Genomes

Our perception of the role of the previously considered ‘selfish’ or ‘junk’ DNA has been dramatically altered in the past 20 years or so. A large proportion of this non-coding part of mammalian genomes is repetitive in nature, classified as either satellites or transposons. While repetitive elements can be termed selfish in terms of their amplification, such events have surely been co-opted by the host, suggesting by itself a likely altruistic function for the organism at the subject of such natural selection. Indeed numerous examples of transposons regulating the functional output of the host genome have been documented. Transposons provide a powerful framework for large-scale relatively rapid concerted regulatory activities with the ability to drive evolution. Mammalian totipotency has emerged as one key stage of development in which transposon-mediated regulation of gene expression has taken centre stage in the past few years. During this period, large-scale (epigenetic) reprogramming must be accomplished in order to activate the host genome. In mice and men, one particular element murine endogenous retrovirus with leucine tRNA primer (MERVL) (and its counterpart human ERVL (HERVL)) appears to have acquired roles as a key driving force in this process. Here, I will discuss and interpret the current knowledge and its implications regarding the role of transposons, particularly of long interspersed nuclear elements (LINE-1s) and endogenous retroviruses (ERVs), in the regulation of totipotency. This article is part of a discussion meeting issue ‘Crossroads between transposons and gene regulation’.

A new species of Balaustium von Heyden, 1826 (Acari: Actinotrichida, Erythraeidae) from Spain

Zootaxa ◽  
2012 ◽  
Vol 3178 (1) ◽  
pp. 1 ◽  
Author(s):  
JOANNA MĄKOL ◽  
YVES ARIJS ◽  
FELIX WÄCKERS
Keyword(s):  
New Species ◽  
Potential Role ◽  
Biological Control Agent ◽  
Feeding Habits ◽  
Control Agent ◽  
Food Spectrum ◽  
Mode Of Reproduction ◽  
Large Numbers ◽  
A New Species

An erythraeid mite, Balaustium hernandezi sp. nov., was found in large numbers in a greenhouse in Spain. The larva,deutonymph and female of the new species are described based on material obtained during experimental rearing. Dataand information on feeding habits, food spectrum, mode of reproduction and life cycle are provided. The potential role of the species as a biological control agent is discussed.

scholarly journals The Potential Role of Transposable Elements as Molecular Markers

2021 ◽  
Vol 761 (1) ◽  
pp. 012031
Author(s):  
Y. E. Arvas ◽  
M. M. Abed ◽  
Q. A. Zaki ◽  
İ. Kocaçalışkan ◽  
E. K. Haji
Keyword(s):  
Molecular Markers ◽  
Transposable Elements ◽  
Potential Role

The Potential Role of Endogenous Viral Elements in the Evolution of Bats as Reservoirs for Zoonotic Viruses

2020 ◽  
Vol 7 (1) ◽  
pp. 103-119 ◽  
Author(s):  
Emilia C. Skirmuntt ◽  
Marina Escalera-Zamudio ◽  
Emma C. Teeling ◽  
Adrian Smith ◽  
Aris Katzourakis
Keyword(s):  
Immune System ◽  
Genome Size ◽  
Potential Role ◽  
Endogenous Retroviruses ◽  
Small Genome ◽  
Zoonotic Viruses ◽  
Endogenous Viruses ◽  
Foamy Viruses ◽  
Endogenous Viral Elements

Despite a small genome size, bats have comparable diversity of retroviral and non-retroviral endogenous sequences to other mammals. These include Class I and Class II retroviral sequences, foamy viruses, and deltaretroviruses, as well as filovirus, bornavirus, and parvovirus endogenous viral elements. Some of these endogenous viruses are sufficiently preserved in bat genomes to be expressed, with potential effects for host biology. It is clear that the bat immune system differs when compared with other mammals, yet the role that virus-derived endogenous elements may have played in the evolution of bat immunity is poorly understood. In this review, we discuss some of the bat-specific immune mechanisms that may have resulted in a virus-tolerant phenotype and link these to the long-standing virus-host coevolution that may have allowed a large diversity of endogenous retroviruses and other endogenous viral elements to colonize bat genomes. We also consider the possible effects of endogenization in the evolution of the bat immune system.

scholarly journals Identification of an Immunodominant ABC Transporter in Methicillin-Resistant Staphylococcus aureusInfections

2000 ◽  
Vol 68 (6) ◽  
pp. 3200-3209 ◽  
Author(s):  
James P. Burnie ◽  
Ruth C. Matthews ◽  
Tracey Carter ◽  
Elaine Beaulieu ◽  
Michael Donohoe ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Abc Transporter ◽  
Potential Role ◽  
Recombinant Antibodies ◽  
Control Groups ◽  
Expression Library ◽  
Methicillin Resistant ◽  
Genomic Expression

ABSTRACT Immunoblotting sera from 26 patients with septicemia due to an epidemic strain of methicillin-resistant Staphylococcus aureus (EMRSA-15), 6 of whom died, revealed an immunodominant EMRSA-15 antigen at 61 kDa. There was a statistically significant correlate (P < 0.001) between survival and immunoglobulin G to the 61-kDa band. The antigen was identified by sequencing positive clones obtained by screening a genomic expression library of EMRSA-15 with pooled sera from patients taken after the septicemic episode. Eluted antibody reacted with the 61-kDa antigen on immunoblots. The amino terminus was obtained by searching the S. aureus NCTC 8325 and MRSA strain COL databases, and the whole protein was expressed in Escherichia coli TOP 10F′. The derived amino acid sequence showed homology with ABC transporters, with paired Walker A and Walker B motifs and 73% homology to YkpA fromBacillus subtilis. Epitope mapping of the derived amino acid sequence with sera from patients who had recovered from EMRSA-15 septicemia delineated seven epitopes. Three of these epitopes, represented by peptides 1 (KIKVYVGNYDFWYQS), 2 (TVIVVSHDRHFLYNNV), and 3 (TETFLRGFLGRMLFS), were synthesized and used to isolate human recombinant antibodies from a phage antibody display library. Recombinant antibodies against peptides 1 and 2 gave logarithmic reductions in organ colony counts, compared with control groups, in a mouse model of the infection. This study suggests the potential role of an ABC transporter as a target for immunotherapy.

scholarly journals A genomic portrait of zebrafish transposable elements and their spatiotemporal embryonic expression

2021 ◽  
Author(s):  
Ni-Chen Chang ◽  
Quirze Rovira ◽  
Jonathan N Wells ◽  
Cédric Feschotte ◽  
Juan M Vaquerizas
Keyword(s):  
Transposable Elements ◽  
Single Cell ◽  
Expression Patterns ◽  
Endogenous Retroviruses ◽  
Gene Promoters ◽  
Vertebrate Development ◽  
Sequencing Data ◽  
Dna Transposons ◽  
Wide Range ◽  
The Impact

There is considerable interest in understanding the effect of transposable elements (TEs) on embryonic development. Studies in humans and mice are limited by the difficulty of working with mammalian embryos, and by the relative scarcity of active TEs in these organisms. Zebrafish is an outstanding model for the study of vertebrate development and over half of its genome consists of diverse TEs. However, zebrafish TEs remain poorly characterized. Here we describe the demography and genomic distribution of zebrafish TEs and their expression throughout embryogenesis using bulk and single-cell RNA sequencing data. These results reveal a highly dynamic genomic ecosystem comprising nearly 2,000 distinct TE families, which vary in copy number by four orders of magnitude and span a wide range of ages. Longer retroelements tend to be retained in intergenic regions, whilst short interspersed nuclear elements (SINEs) and DNA transposons are more frequently found nearby or within genes. Locus-specific mapping of TE expression reveals extensive TE transcription during development. While two thirds of TE transcripts are likely driven by nearby gene promoters, we still observe stage and tissue-specific expression patterns in self-regulated TEs. Long terminal repeat (LTR) retroelements are most transcriptionally active immediately following zygotic genome activation, whereas DNA transposons are enriched amongst transcripts expressed in later stages of development. Single-cell analysis reveals several endogenous retroviruses expressed in specific somatic cell lineages. Overall, our study provides an important resource for using zebrafish as a model to study the impact of TEs on vertebrate development.

Potential Role of Transposable Elements in the Rapid Reorganization of the Fusarium oxysporum Genome

2001 ◽  
Vol 34 (3) ◽  
pp. 177-192 ◽  
Author(s):  
Jean-Michel Davière ◽  
Thierry Langin ◽  
Marie-Josée Daboussi
Keyword(s):  
Transposable Elements ◽  
Fusarium Oxysporum ◽  
Potential Role

Localization of Intracisternal a Particle Antigens in Neoplastic Cells and Preimplantation Mouse Embryos

1980 ◽  
Vol 38 ◽  
pp. 696-697
Author(s):  
Thomas T.F. Huang ◽  
Patricia G. Calarco
Keyword(s):  
Endoplasmic Reticulum ◽  
Normal Development ◽  
Mouse Embryos ◽  
Neoplastic Cells ◽  
Large Numbers ◽  
Preimplantation Mouse Embryos ◽  
Preimplantation Mouse ◽  
Intracisternal A Particle ◽  
Normal Feature

The stage specific appearance of a retravirus, termed the Intracisternal A particle (IAP) is a normal feature of early preimplantation development. To date, all feral and laboratory strains of Mus musculus and even Asian species such as Mus cervicolor and Mus pahari express the particles during the 2-8 cell stages. IAP form by budding into the endoplasmic reticulum and appear singly or as groups of donut-shaped particles within the cisternae (fig. 1). IAP are also produced in large numbers in several neoplastic cells such as certain plasmacytomas and rhabdomyosarcomas. The role of IAP, either in normal development or in neoplastic behavior, is unknown.

POPDC proteins and cardiac function

2019 ◽  
Vol 47 (5) ◽  
pp. 1393-1404 ◽  
Author(s):  
Thomas Brand
Keyword(s):  
Potential Role ◽  
Striated Muscle ◽  
Short Review ◽  
Effector Proteins ◽  
Muscle Disease ◽  
Disease Genes ◽  
Protein Protein Interaction ◽  
Interaction Partners ◽  
And Function

Abstract The Popeye domain-containing gene family encodes a novel class of cAMP effector proteins in striated muscle tissue. In this short review, we first introduce the protein family and discuss their structure and function with an emphasis on their role in cyclic AMP signalling. Another focus of this review is the recently discovered role of POPDC genes as striated muscle disease genes, which have been associated with cardiac arrhythmia and muscular dystrophy. The pathological phenotypes observed in patients will be compared with phenotypes present in null and knockin mutations in zebrafish and mouse. A number of protein–protein interaction partners have been discovered and the potential role of POPDC proteins to control the subcellular localization and function of these interacting proteins will be discussed. Finally, we outline several areas, where research is urgently needed.

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