scholarly journals Mouse Mammary Tumor Virus Integration Site Selection in Human and Mouse Genomes

2007 ◽  
Vol 82 (3) ◽  
pp. 1360-1367 ◽  
Author(s):  
Alexander Faschinger ◽  
Francoise Rouault ◽  
Johannes Sollner ◽  
Arno Lukas ◽  
Brian Salmons ◽  
...  
Keyword(s):  
Integration Site ◽  
Leukemia Virus ◽  
Transcription Start Sites ◽  
Mouse Mammary Tumor ◽  
Immunodeficiency Virus ◽  
Integration Sites ◽  
Tumor Virus ◽  
Mouse Cells ◽  
Human And Mouse ◽  
Integration Site Selection

ABSTRACT Based on integration site preferences, retroviruses can be placed into three groups. Viruses that comprise the first group, murine leukemia virus and foamy virus, integrate preferentially near transcription start sites. The second group, notably human immunodeficiency virus and simian immunodeficiency virus, preferentially targets transcription units. Avian sarcoma-leukosis virus (ASLV) and human T-cell leukemia virus (HTLV), forming the third group, show little preference for any genomic feature. We have previously shown that some human cells sustain mouse mammary tumor virus (MMTV) infection; therefore, we infected a susceptible human breast cell line, Hs578T, and, without introducing a species-specific bias, compared the MMTV integration profile to those of other retroviruses. Additionally, we infected a mouse cell line, NMuMG, and thus we could compare MMTV integration site selection in human and mouse cells. In total, we examined 468 unique MMTV integration sites. Irrespective of whether human or mouse cells were infected, no integration bias favoring transcription start sites was detected, a profile that is reminiscent of that of ASLV and HTLV. However, in contrast to ASLV and HTLV, not even a modest tendency in favor of integration within genes was observed. Similarly, repetitive sequences and genes that are frequently tagged by MMTV in mammary tumors were not preferentially targeted in cell culture either in mouse or in human cells; hence, we conclude that MMTV displays the most random dispersion of integration sites among retroviruses determined so far.

scholarly journals Integration Site Choice of a Feline Immunodeficiency Virus Vector

2006 ◽  
Vol 80 (17) ◽  
pp. 8820-8823 ◽  
Author(s):  
Yubin Kang ◽  
Christopher J. Moressi ◽  
Todd E. Scheetz ◽  
Litao Xie ◽  
Diane Thi Tran ◽  
...  
Keyword(s):  
Feline Immunodeficiency Virus ◽  
Integration Site ◽  
Leukemia Virus ◽  
Foamy Virus ◽  
Moloney Murine Leukemia Virus ◽  
Human Hepatoma Cells ◽  
Immunodeficiency Virus ◽  
Integration Sites ◽  
Primate Lentiviruses ◽  
Transcriptional Units

ABSTRACT We mapped 226 unique integration sites in human hepatoma cells following gene transfer with a feline immunodeficiency virus (FIV)-based lentivirus vector. FIV integrated across the entire length of the transcriptional units. Microarray data indicated that FIV integration favored actively transcribed genes. Approximately 21% of FIV integrations within transcriptional units occurred in genes regulated by the LEDGF/p75 transcriptional coactivator. DNA in regions of FIV insertion sites exhibited a “bendable” structure and a pattern of duplex destabilization favoring strand separation. FIV integration preferences are more similar to those of primate lentiviruses and distinct from those of Moloney murine leukemia virus, avian sarcoma leukosis virus, and foamy virus.

scholarly journals The GLN Family of Murine Endogenous Retroviruses Contains an Element Competent for Infectious Viral Particle Formation

2008 ◽  
Vol 82 (9) ◽  
pp. 4413-4419 ◽  
Author(s):  
David Ribet ◽  
Francis Harper ◽  
Cécile Esnault ◽  
Gérard Pierron ◽  
Thierry Heidmann
Keyword(s):  
Viral Particle ◽  
Leukemia Virus ◽  
Endogenous Retroviruses ◽  
Particle Assembly ◽  
New Class ◽  
Mouse Mammary Tumor ◽  
The Family ◽  
Tumor Virus ◽  
Mouse Cells ◽  
Viral Particle Assembly

ABSTRACT Several families of endogenous retroviruses (ERVs) have been identified in the mouse genome, in several instances by in silico searches, but for many of them it remains to be determined whether there are elements that can still encode functional retroviral particles. Here, we identify, within the GLN family of highly reiterated ERVs, one, and only one, copy that encodes retroviral particles prone to infection of mouse cells. We show that its envelope protein confers an ecotropic host range and recognizes a receptor different from mCAT1 and mSMIT1, the two previously identified receptors for other ecotropic mouse retroviruses. Electron microscopy disclosed viral particle assembly and budding at the cell membrane, as well as release of mature particles into the extracellular space. These particles are closely related to murine leukemia virus (MLV) particles, with which they have most probably been confused in the past. This study, therefore, identifies a new class of infectious mouse ERVs belonging to the family Gammaretroviridae, with one family member still functional today. This family is in addition to the two MLV and mouse mammary tumor virus families of active mouse ERVs with an extracellular life cycle.

scholarly journals Genome-Wide Analyses of Avian Sarcoma Virus Integration Sites

2004 ◽  
Vol 78 (21) ◽  
pp. 11656-11663 ◽  
Author(s):  
Anna Narezkina ◽  
Konstantin D. Taganov ◽  
Samuel Litwin ◽  
Radka Stoyanova ◽  
Junpei Hayashi ◽  
...  
Keyword(s):  
Rna Polymerase Ii ◽  
Site Selection ◽  
Target Genes ◽  
Integration Site ◽  
Leukemia Virus ◽  
Avian Sarcoma Virus ◽  
Integration Sites ◽  
Sarcoma Virus ◽  
Avian Sarcoma ◽  
Integration Site Selection

ABSTRACT The chromosomal features that influence retroviral integration site selection are not well understood. Here, we report the mapping of 226 avian sarcoma virus (ASV) integration sites in the human genome. The results show that the sites are distributed over all chromosomes, and no global bias for integration site selection was detected. However, RNA polymerase II transcription units (protein-encoding genes) appear to be favored targets of ASV integration. The integration frequency within genes is similar to that previously described for murine leukemia virus but distinct from the higher frequency observed with human immunodeficiency virus type 1. We found no evidence for preferred ASV integration sites over the length of genes and immediate flanking regions. Microarray analysis of uninfected HeLa cells revealed that the expression levels of ASV target genes were similar to the median level for all genes represented in the array. Although expressed genes were targets for integration, we found no preference for integration into highly expressed genes. Our results provide a more detailed description of the chromosomal features that may influence ASV integration and support the idea that distinct, virus-specific mechanisms mediate integration site selection. Such differences may be relevant to viral pathogenesis and provide utility in retroviral vector design.

scholarly journals SATB1-Binding Sequences and Alu-Like Motifs Define a Unique Chromatin Context in the Vicinity of Human Immunodeficiency Virus Type 1 Integration Sites

2007 ◽  
Vol 81 (11) ◽  
pp. 5617-5627 ◽  
Author(s):  
Pavan P. Kumar ◽  
Sameet Mehta ◽  
Prabhat Kumar Purbey ◽  
Dimple Notani ◽  
Ranveer S. Jayani ◽  
...  
Keyword(s):  
Site Selection ◽  
Binding Sites ◽  
Integration Site ◽  
Viral Integration ◽  
Immunodeficiency Virus ◽  
Integration Sites ◽  
Hiv 1 ◽  
Integration Site Selection

ABSTRACT Retroviral integration has recently been shown to be nonrandom, favoring transcriptionally active regions of chromatin. However, the mechanism for integration site selection by retroviruses is not clear. We show here the occurrence of Alu-like motifs in the sequences flanking the reported viral integration sites that are significantly different from those obtained from the randomly picked sequences from the human genome, suggesting that unique primary sequence features exist in the genomic regions targeted by human immunodeficiency virus type 1 (HIV-1). Additionally, these sequences were preferentially bound by SATB1, the T lineage-restricted chromatin organizer, in vitro and in vivo. Alu repeats make up nearly 10% of the human genome and have been implicated in the regulation of transcription. To specifically isolate sequences flanking the viral integration sites and also harboring both Alu-like repeats and SATB1-binding sites, we combined chromatin immunoprecipitation with sequential PCRs. The cloned sequences flanking HIV-1 integration sites were specifically immunoprecipitated and amplified from the pool of anti-SATB1-immunoprecipitated genomic DNA fragments isolated from HIV-1 NL4.3-infected Jurkat T-cell chromatin. Moreover, many of these sequences were preferentially partitioned in the DNA associated tightly with the nuclear matrix and not in the chromatin loops. Strikingly, many of these regions were disfavored for integration when SATB1 was silenced, providing unequivocal evidence for its role in HIV-1 integration site selection. We propose that definitive sequence features such as the Alu-like motifs and SATB1-binding sites provide a unique chromatin context in vivo which is preferentially targeted by the HIV-1 integration machinery.

Electron Immunochemical Labeling of Ultrathin Sections of Murine Tumor Viruses and Cell Cultures using the Unlabeled Antibody Enzyme Technique

1976 ◽  
Vol 34 ◽  
pp. 266-267
Author(s):  
W. J. Hamilton
Keyword(s):  
Mammary Tumor ◽  
Leukemia Virus ◽  
Parallel Methods ◽  
Tumor Viruses ◽  
Mouse Mammary Tumor ◽  
Tumor Virus ◽  
Antibody Conjugates ◽  
Rauscher Leukemia ◽  
Antigen Localization ◽  
Unlabeled Antibody

The study of RNA tumor viruses has been greatly facilitated by the use of immunochemical tagging methods. In the past these methods have been constrained to antibody conjugates with ferritin or peroxidase. In order to avoid the disadvantages of using conjugated antisera, investigators have applied the unlabeled antibody enzyme method of Sternberger to mammary tumor derived mouse cells prior to embedding for electron microscopy. The current study has successfully applied the Sternberger method to virusproducing cells and purified virus pellets after epoxy-embedding and ultrathin sectioning. The results demonstrate the distinct advantages of this “post-embedding” method for viral antigen localization.Purified Rauscher leukemia virus (RLV) and mouse mammary tumor virus (MMTV) were pelleted, fixed in buffered 2% paraformaldehyde and washed thoroughly. These were dehydrated in acetone, infiltrated and embedded in Spurr resin according to common procedures. A tumor derived cell line, Mm5mt, producing MMTV was embedded by parallel methods.

scholarly journals A Protein Antagonist of Activation-Induced Cytidine Deaminase Encoded by a Complex Mouse Retrovirus

mBio ◽  
2019 ◽  
Vol 10 (4) ◽  
Author(s):  
Gurvani B. Singh ◽  
Hyewon Byun ◽  
Almas F. Ali ◽  
Frank Medina ◽  
Dennis Wylie ◽  
...  
Keyword(s):  
Mouse Mammary Tumor Virus ◽  
Cytidine Deaminase ◽  
Wild Type ◽  
Mammary Tumor Virus ◽  
Mouse Mammary Tumor ◽  
Activation Induced Cytidine Deaminase ◽  
Immunodeficiency Virus ◽  
Tumor Virus ◽  
Hiv 1

ABSTRACT Complex human-pathogenic retroviruses cause high morbidity and mortality worldwide, but resist antiviral drugs and vaccine development due to evasion of the immune response. A complex retrovirus, mouse mammary tumor virus (MMTV), requires replication in B and T lymphocytes for mammary gland transmission and is antagonized by the innate immune restriction factor murine Apobec3 (mA3). To determine whether the regulatory/accessory protein Rem affects innate responses to MMTV, a splice-donor mutant (MMTV-SD) lacking Rem expression was injected into BALB/c mice. Mammary tumors induced by MMTV-SD had a lower proviral load, lower incidence, and longer latency than mammary tumors induced by wild-type MMTV (MMTV-WT). MMTV-SD proviruses had many G-to-A mutations on the proviral plus strand, but also C-to-T transitions within WRC motifs. Similarly, a lymphomagenic MMTV variant lacking Rem expression showed decreased proviral loads and increased WRC motif mutations relative to those in wild-type-virus-induced tumors, consistent with activation-induced cytidine deaminase (AID) mutagenesis in lymphoid cells. These mutations are typical of the Apobec family member AID, a B-cell-specific mutagenic protein involved in antibody variable region hypermutation. In contrast, mutations in WRC motifs and proviral loads were similar in MMTV-WT and MMTV-SD proviruses from tumors in AID-insufficient mice. AID was not packaged in MMTV virions. Rem coexpression in transfection experiments led to AID proteasomal degradation. Our data suggest that rem specifies a human-pathogenic immunodeficiency virus type 1 (HIV-1) Vif-like protein that inhibits AID and antagonizes innate immunity during MMTV replication in lymphocytes. IMPORTANCE Complex retroviruses, such as human-pathogenic immunodeficiency virus type 1 (HIV-1), cause many human deaths. These retroviruses produce lifelong infections through viral proteins that interfere with host immunity. The complex retrovirus mouse mammary tumor virus (MMTV) allows for studies of host-pathogen interactions not possible in humans. A mutation preventing expression of the MMTV Rem protein in two different MMTV strains decreased proviral loads in tumors and increased viral genome mutations typical of an evolutionarily ancient enzyme, AID. Although the presence of AID generally improves antibody-based immunity, it may contribute to human cancer progression. We observed that coexpression of MMTV Rem and AID led to AID destruction. Our results suggest that Rem is the first known protein inhibitor of AID and that further experiments could lead to new disease treatments.

scholarly journals DNA Palindromes with a Modest Arm Length of ≳20 Base Pairs Are a Significant Target for Recombinant Adeno-Associated Virus Vector Integration in the Liver, Muscles, and Heart in Mice

2007 ◽  
Vol 81 (20) ◽  
pp. 11290-11303 ◽  
Author(s):  
Katsuya Inagaki ◽  
Susanna M. Lewis ◽  
Xiaolin Wu ◽  
Congrong Ma ◽  
David J. Munroe ◽  
...  
Keyword(s):  
Mouse Liver ◽  
Integration Site ◽  
Marker Gene ◽  
Cpg Islands ◽  
Previous Method ◽  
Adeno Associated Virus ◽  
Transcription Start Sites ◽  
Vector Integration ◽  
Integration Sites

ABSTRACT Our previous study has shown that recombinant adeno-associated virus (rAAV) vector integrates preferentially in genes, near transcription start sites and CpG islands in mouse liver (H. Nakai, X. Wu, S. Fuess, T. A. Storm, D. Munroe, E. Montini, S. M. Burgess, M. Grompe, and M. A. Kay, J. Virol. 79:3606-3614, 2005). However, the previous method relied on in vivo selection of rAAV integrants and could be employed for the liver but not for other tissues. Here, we describe a novel method for high-throughput rAAV integration site analysis that does not rely on marker gene expression, selection, or cell division, and therefore it can identify rAAV integration sites in nondividing cells without cell manipulations. Using this new method, we identified and characterized a total of 997 rAAV integration sites in mouse liver, skeletal muscle, and heart, transduced with rAAV2 or rAAV8 vector. The results support our previous observations, but notably they have revealed that DNA palindromes with an arm length of ≳20 bp (total length, ≳40 bp) are a significant target for rAAV integration. Up to ∼30% of total integration events occurred in the vicinity of DNA palindromes with an arm length of ≳20 bp. Considering that DNA palindromes may constitute fragile genomic sites, our results support the notion that rAAV integrates at chromosomal sites susceptible to breakage or preexisting breakage sites. The use of rAAV to label fragile genomic sites may provide an important new tool for probing the intrinsic source of ongoing genomic instability in various tissues in animals, studying DNA palindrome metabolism in vivo, and understanding their possible contributions to carcinogenesis and aging.

scholarly journals Integration Site Preference of Xenotropic Murine Leukemia Virus-Related Virus, a New Human Retrovirus Associated with Prostate Cancer

2008 ◽  
Vol 82 (20) ◽  
pp. 9964-9977 ◽  
Author(s):  
Sanggu Kim ◽  
Namshin Kim ◽  
Beihua Dong ◽  
David Boren ◽  
Serena A. Lee ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Virus Type ◽  
Murine Leukemia Virus ◽  
Integration Site ◽  
Leukemia Virus ◽  
Integration Sites ◽  
Cancer Tissues ◽  
Xmrv Infection ◽  
Murine Leukemia

ABSTRACT Xenotropic murine leukemia virus-related virus (XMRV) is a new human gammaretrovirus identified in prostate cancer tissue from patients homozygous for a reduced-activity variant of the antiviral enzyme RNase L. Neither a casual relationship between XMRV infection and prostate cancer nor a mechanism of tumorigenesis has been established. To determine the integration site preferences of XMRV and the potential risk of proviral insertional mutagenesis, we carried out a genome-wide analysis of viral integration sites in the prostate cell line DU145 after an acute XMRV infection and compared the integration site pattern of XMRV with those found for murine leukemia virus and two human retroviruses, human immunodeficiency virus type 1 and human T-cell leukemia virus type 1. Among all retroviruses analyzed, XMRV has the strongest preference for transcription start sites, CpG islands, DNase-hypersensitive sites, and gene-dense regions; all are features frequently associated with structurally open transcription regulatory regions of a chromosome. Analyses of XMRV integration sites in tissues from prostate cancer patients found a similar preference for the aforementioned chromosomal features. Additionally, XMRV integration sites in cancer tissues were associated with cancer breakpoints, common fragile sites, microRNA, and cancer-related genes, suggesting a selection process that favors certain chromosomal integration sites. In both acutely infected cells and cancer tissues, no common integration site was detected within or near proto-oncogenes or tumor suppressor genes. These results are consistent with a model in which XMRV may contribute to tumorigenicity via a paracrine mechanism.

scholarly journals Viral Determinants of Integration Site Preferences of Simian Immunodeficiency Virus-Based Vectors

2006 ◽  
Vol 80 (16) ◽  
pp. 8145-8150 ◽  
Author(s):  
Hella Monse ◽  
Stephanie Laufs ◽  
Seraphin Kuate ◽  
W. Jens Zeller ◽  
Stefan Fruehauf ◽  
...  
Keyword(s):  
Simian Immunodeficiency Virus ◽  
Integration Site ◽  
Active Regions ◽  
Retroviral Vectors ◽  
Site Preferences ◽  
Accessory Genes ◽  
Immunodeficiency Virus ◽  
Integration Sites ◽  
Viral Determinants ◽  
Viral Components

ABSTRACT Preferential integration into transcriptionally active regions of genomes has been observed for retroviral vectors based on gamma-retroviruses and lentiviruses. However, differences in the integration site preferences were detected, which might be explained by differences in viral components of the preintegration complexes. Viral determinants of integration site preferences have not been defined. Therefore, integration sites of simian immunodeficiency virus (SIV)-based vectors produced in the absence of accessory genes or lacking promoter and enhancer elements were compared. Similar integration patterns for the different SIV vectors indicate that vif, vpr, vpx, nef, env, and promoter or enhancer elements are not required for preferential integration of SIV into transcriptionally active regions of genomes.

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