Abstract
Integration of retroviral vectors in the human genome follows nonrandom patterns that favor insertional deregulation of gene expression and increase the risk of their use in clinical gene therapy. The molecular basis of retroviral target site selection is still poorly understood. We used deep sequencing technology to build genomewide, high-definition maps of > 60 000 integration sites of Moloney murine leukemia virus (MLV)-and HIV-based retroviral vectors in the genome of human CD34+ multipotent hematopoietic progenitor cells (HPCs) and used gene expression profiling, chromatin immunoprecipitation, and bioinformatics to associate integration to genetic and epigenetic features of the HPC genome. Clusters of recurrent MLV integrations identify regulatory elements (alternative promoters, enhancers, evolutionarily conserved noncoding regions) within or around protein-coding genes and microRNAs with crucial functions in HPC growth and differentiation, bearing epigenetic marks of active or poised transcription (H3K4me1, H3K4me2, H3K4me3, H3K9Ac, Pol II) and specialized chromatin configurations (H2A.Z). Overall, we mapped 3500 high-frequency integration clusters, which represent a new resource for the identification of transcriptionally active regulatory elements. High-definition MLV integration maps provide a rational basis for predicting genotoxic risks in gene therapy and a new tool for genomewide identification of promoters and regulatory elements controlling hematopoietic stem and progenitor cell functions.
| Original language | English |
|---|---|
| Pages (from-to) | 5507-5517 |
| Number of pages | 11 |
| Journal | Blood |
| Volume | 116 |
| Issue number | 25 |
| DOIs | |
| Publication status | Published - Dec 16 2010 |
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ASJC Scopus subject areas
- Hematology
- Biochemistry
- Cell Biology
- Immunology
Cite this
High-definition mapping of retroviral integration sites identifies active regulatory elements in human multipotent hematopoietic progenitors. / Cattoglio, Claudia; Pellin, Danilo; Rizzi, Ermanno; Maruggi, Giulietta; Corti, Giorgio; Miselli, Francesca; Sartori, Daniela; Guffanti, Alessandro; Di Serio, Clelia; Ambrosi, Alessandro; De Bellis, Gianluca; Mavilio, Fulvio.
In: Blood, Vol. 116, No. 25, 16.12.2010, p. 5507-5517.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - High-definition mapping of retroviral integration sites identifies active regulatory elements in human multipotent hematopoietic progenitors
AU - Cattoglio, Claudia
AU - Pellin, Danilo
AU - Rizzi, Ermanno
AU - Maruggi, Giulietta
AU - Corti, Giorgio
AU - Miselli, Francesca
AU - Sartori, Daniela
AU - Guffanti, Alessandro
AU - Di Serio, Clelia
AU - Ambrosi, Alessandro
AU - De Bellis, Gianluca
AU - Mavilio, Fulvio
PY - 2010/12/16
Y1 - 2010/12/16
N2 - Integration of retroviral vectors in the human genome follows nonrandom patterns that favor insertional deregulation of gene expression and increase the risk of their use in clinical gene therapy. The molecular basis of retroviral target site selection is still poorly understood. We used deep sequencing technology to build genomewide, high-definition maps of > 60 000 integration sites of Moloney murine leukemia virus (MLV)-and HIV-based retroviral vectors in the genome of human CD34+ multipotent hematopoietic progenitor cells (HPCs) and used gene expression profiling, chromatin immunoprecipitation, and bioinformatics to associate integration to genetic and epigenetic features of the HPC genome. Clusters of recurrent MLV integrations identify regulatory elements (alternative promoters, enhancers, evolutionarily conserved noncoding regions) within or around protein-coding genes and microRNAs with crucial functions in HPC growth and differentiation, bearing epigenetic marks of active or poised transcription (H3K4me1, H3K4me2, H3K4me3, H3K9Ac, Pol II) and specialized chromatin configurations (H2A.Z). Overall, we mapped 3500 high-frequency integration clusters, which represent a new resource for the identification of transcriptionally active regulatory elements. High-definition MLV integration maps provide a rational basis for predicting genotoxic risks in gene therapy and a new tool for genomewide identification of promoters and regulatory elements controlling hematopoietic stem and progenitor cell functions.
AB - Integration of retroviral vectors in the human genome follows nonrandom patterns that favor insertional deregulation of gene expression and increase the risk of their use in clinical gene therapy. The molecular basis of retroviral target site selection is still poorly understood. We used deep sequencing technology to build genomewide, high-definition maps of > 60 000 integration sites of Moloney murine leukemia virus (MLV)-and HIV-based retroviral vectors in the genome of human CD34+ multipotent hematopoietic progenitor cells (HPCs) and used gene expression profiling, chromatin immunoprecipitation, and bioinformatics to associate integration to genetic and epigenetic features of the HPC genome. Clusters of recurrent MLV integrations identify regulatory elements (alternative promoters, enhancers, evolutionarily conserved noncoding regions) within or around protein-coding genes and microRNAs with crucial functions in HPC growth and differentiation, bearing epigenetic marks of active or poised transcription (H3K4me1, H3K4me2, H3K4me3, H3K9Ac, Pol II) and specialized chromatin configurations (H2A.Z). Overall, we mapped 3500 high-frequency integration clusters, which represent a new resource for the identification of transcriptionally active regulatory elements. High-definition MLV integration maps provide a rational basis for predicting genotoxic risks in gene therapy and a new tool for genomewide identification of promoters and regulatory elements controlling hematopoietic stem and progenitor cell functions.
UR - http://www.scopus.com/inward/record.url?scp=78650447013&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=78650447013&partnerID=8YFLogxK
U2 - 10.1182/blood-2010-05-283523
DO - 10.1182/blood-2010-05-283523
M3 - Article
C2 - 20864581
AN - SCOPUS:78650447013
VL - 116
SP - 5507
EP - 5517
JO - Blood
JF - Blood
SN - 0006-4971
IS - 25
ER -