Characterization of a Plant Scaffold-Attached Region from a T-DNA Integration Site

1996 ◽  
pp. 261-268
Author(s):  
A. Dietz-Pfeilstetter ◽  
V. Kay ◽  
J. Landsmann ◽  
J. Bode
Keyword(s):  
Integration Site ◽  
Dna Integration

scholarly journals Integrase-Specific Enhancement and Suppression of Retroviral DNA Integration by Compacted Chromatin Structure In Vitro

2004 ◽  
Vol 78 (11) ◽  
pp. 5848-5855 ◽  
Author(s):  
Konstantin D. Taganov ◽  
Isabel Cuesta ◽  
René Daniel ◽  
Lisa Ann Cirillo ◽  
Richard A. Katz ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Chromatin Structure ◽  
Site Selection ◽  
Integration Site ◽  
Histone H1 ◽  
Detectable Effect ◽  
Host Chromosome ◽  
Dna Integration ◽  
Hiv 1

ABSTRACT Integration of viral DNA into the host chromosome is an obligatory step in retroviral replication and is dependent on the activity of the viral enzyme integrase. To examine the influence of chromatin structure on retroviral DNA integration in vitro, we used a model target comprising a 13-nucleosome extended array that includes binding sites for specific transcription factors and can be compacted into a higher-ordered structure. We found that the efficiency of in vitro integration catalyzed by human immunodeficiency virus type 1 (HIV-1) integrase was decreased after compaction of this target with histone H1. In contrast, integration by avian sarcoma virus (ASV) integrase was more efficient after compaction by either histone H1 or a high salt concentration, suggesting that the compacted structure enhances this reaction. Furthermore, although site-specific binding of transcription factors HNF3 and GATA4 blocked ASV DNA integration in extended nucleosome arrays, local opening of H1-compacted chromatin by HNF3 had no detectable effect on integration, underscoring the preference of ASV for compacted chromatin. Our results indicate that chromatin structure affects integration site selection of the HIV-1 and ASV integrases in opposite ways. These distinct properties of integrases may also affect target site selection in vivo, resulting in an important bias against or in favor of integration into actively transcribed host DNA.

Evi-2, a common integration site involved in murine myeloid leukemogenesis

1990 ◽  
Vol 10 (9) ◽  
pp. 4658-4666
Author(s):  
A M Buchberg ◽  
H G Bedigian ◽  
N A Jenkins ◽  
N G Copeland
Keyword(s):  
Leucine Zipper ◽  
Transmembrane Domain ◽  
Integration Site ◽  
Transmembrane Protein ◽  
Structural Features ◽  
Viral Integration ◽  
Integration Sites ◽  
Leukemia Viruses ◽  
Common Integration Site

BXH-2 mice have the highest incidence of spontaneous retrovirally induced myeloid leukemia of any known inbred strain and, as such, represent a valuable model system for identifying cellular proto-oncogenes involved in myeloid disease. Chronic murine leukemia viruses often induce disease by insertional activation or mutation of cellular proto-oncogenes. These loci are identified as common viral integration sites in tumor DNAs. Here we report on the characterization of a novel common viral integration site in BXH-2 myeloid leukemias, designated Evi-2. Within the cluster of viral integration sites that define Evi-2, we identified a gene that has the potential for encoding a novel protein of 223 amino acids. This putative proto-oncogene possesses all of the structural features of a transmembrane protein. Within the transmembrane domain is a "leucine zipper," suggesting that Evi-2 is involved in either homopolymer or heteropolymer formation, which may play an important role in the normal functioning of Evi-2. Interestingly, the human homolog of Evi-2 has recently been shown to be tightly linked to the von Recklinghausen neurofibromatosis locus, suggesting a role for Evi-2 in human disease as well.

scholarly journals Molecular Characterization of HBV DNA Integration in Patients with Hepatitis and Hepatocellular Carcinoma

2018 ◽  
Vol 9 (18) ◽  
pp. 3225-3235 ◽  
Author(s):  
Liu Yang ◽  
Song Ye ◽  
Xinyi Zhao ◽  
Liyan Ji ◽  
Yinxin Zhang ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Molecular Characterization ◽  
Hbv Dna ◽  
Dna Integration ◽  
Hbv Dna Integration

scholarly journals HPV DNA integration site as proof of the origin of ovarian metastasis from endocervical adenocarcinoma: three case reports

BMC Cancer ◽  
2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Alexandra Arfi ◽  
Delphine Hequet ◽  
Guillaume Bataillon ◽  
Carine Tran-Perennou ◽  
Fereshteh Farkhondeh ◽  
...  
Keyword(s):  
Integration Site ◽  
Case Reports ◽  
Ovarian Metastasis ◽  
Dna Integration ◽  
Hpv Dna ◽  
Endocervical Adenocarcinoma

scholarly journals Characterization of a Novel Composite Staphylococcal Cassette Chromosomemecin Methicillin-Resistant Staphylococcus pseudintermedius from Thailand

2015 ◽  
Vol 60 (2) ◽  
pp. 1153-1157 ◽  
Author(s):  
Pattrarat Chanchaithong ◽  
Nuvee Prapasarakul ◽  
Vincent Perreten ◽  
Sybille Schwendener
Keyword(s):  
Integration Site ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
New Combination ◽  
Staphylococcus Pseudintermedius ◽  
Methicillin Resistant ◽  
Content Type ◽  
Class A ◽  
Restriction Modification

ABSTRACTA novel staphylococcal cassette chromosomemec(SCCmec) composite island (SCCmecAI16-SCCczrAI16-CI) was identified inStaphylococcus pseudintermedius. Four integration site sequences for SCC subdivided the 60,734-bp island into 41,232-bp SCCmecAI16, 19,400-bp SCCczrAI16, and 102-bp SCC-likeAI16elements. SCCmecAI16represents a new combination ofccrA1B3genes with a class Ameccomplex. SCCczrAI16containsccrA1B6and genes related to restriction modification and heavy metal resistance. SCCmecAI16-SCCczrAI16-CI was found in methicillin-resistantS. pseudintermediussequence type 112 (ST112) and ST111 isolated from dogs and veterinarians in Thailand.

scholarly journals Characterization of the Mouse Adeno-Associated Virus AAVS1 Ortholog

2004 ◽  
Vol 78 (16) ◽  
pp. 8917-8921 ◽  
Author(s):  
Nathalie Dutheil ◽  
Miran Yoon-Robarts ◽  
Peter Ward ◽  
Els Henckaerts ◽  
Lucy Skrabanek ◽  
...  
Keyword(s):  
Mouse Genome ◽  
Mouse Cell ◽  
Proximal Promoter ◽  
Sequence Motifs ◽  
Adeno Associated Virus ◽  
Site Specific ◽  
Rep Protein ◽  
Dna Integration ◽  
Site Specific Integration

ABSTRACT The nonpathogenic human adeno-associated virus (AAV) has developed a mechanism to integrate its genome into human chromosome 19 at 19q13.4 (termed AAVS1), thereby establishing latency. Here, we provide evidence that the chromosomal signals required for site-specific integration are conserved in the mouse genome proximal to the recently identified Mbs85 gene. These sequence motifs can be specifically nicked by the viral Rep protein required for the initiation of site-specific AAV DNA integration. Furthermore, these signals can serve as a minimal origin for Rep-dependent DNA replication. In addition, we isolated the mouse Mbs85 proximal promoter and show transcriptional activity in three mouse cell lines.

scholarly journals Quantitation of HIV DNA integration: Effects of differential integration site distributions on Alu-PCR assays

2013 ◽  
Vol 189 (1) ◽  
pp. 53-57 ◽  
Author(s):  
Troy Brady ◽  
Brendan J. Kelly ◽  
Frances Male ◽  
Shoshannah Roth ◽  
Aubrey Bailey ◽  
...  
Keyword(s):  
Integration Site ◽  
Dna Integration ◽  
Hiv Dna ◽  
Pcr Assays

scholarly journals Expression of HPV oncogenes from a single integration site in cervical cancer cell lines

2020 ◽  
Author(s):  
Lulu Yu ◽  
Alexei Lobanov ◽  
Vladimir Majerciak ◽  
Sameer Mirza ◽  
Vimla Band ◽  
...  
Keyword(s):  
Cervical Cancer ◽  
Cell Lines ◽  
Cancer Cell ◽  
Integration Site ◽  
Cancer Cell Lines ◽  
Virus Genome ◽  
Cervical Cancer Cell ◽  
Dna Integration ◽  
Siha Cells ◽  
Integration Sites

AbstractIntegration of a virus genome into human chromosomal DNA is critical in viral carcinogenesis. In this report, we discovered that virus-host fusion transcripts are characteristically originated mainly from a single integration site in three cervical cancer cell lines, CaSki and SiHa cells with multiple HPV16 DNA integration sites and HeLa cells with multiple HPV18 DNA integration sites. The host genomic elements surrounding the integrated HPV genome are critical for efficient expression of the viral oncogenes. We found that HPV E6 and E7 are expressed by hijacking a host 3’ splice site and/or RNA polyadenylation signal for their production. The viral-host fusion transcripts may encode a chimeric viral-host fusion protein through alternative RNA splicing. One such E6* protein in SiHa cells was found to antagonize E6 function and knockdown of its expression further decreased p53 protein level and increased cell growth by promoting S phase entry. Together, our findings of the integrated virus genome expression only from a given integrated host genomic site will shed new light on possible application of precision medicine and the understanding of HPV carcinogenesis.

scholarly journals DNA Integration by Ty Integrase in yku70Mutant Saccharomyces cerevisiae Cells

2000 ◽  
Vol 20 (23) ◽  
pp. 8836-8844 ◽  
Author(s):  
Markus Kiechle ◽  
Anna A. Friedl ◽  
Palaniyandi Manivasakam ◽  
Friederike Eckardt-Schupp ◽  
Robert H. Schiestl
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Plasmid Dna ◽  
Integration Site ◽  
Cellular Function ◽  
Target Site ◽  
Target Site Duplication ◽  
Wild Type ◽  
Dna Integration ◽  
Site Preferences

ABSTRACT In the present work we examined nonhomologous integration of plasmid DNA in a yku70 mutant. Ten of 14 plasmids integrated as composite elements, including Ty sequences probably originating from erroneous strand-switching and/or priming events. Three additional plasmids integrated via Ty integrase without cointegrating Ty sequences, as inferred from 5-bp target site duplication and integration site preferences. Ty integrase-mediated integration of non-Ty DNA has never been observed in wild-type cells, although purified integrase is capable of using non-Ty DNA as a substrate in vitro. Hence our data implicate yKu70 as the cellular function preventing integrase from accepting non-Ty DNA as a substrate.

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