Single molecule sequencing and biophysical properties of oxidized genomic DNA using magnetic tweezers.

Descrizione del progetto

Forbici e pinzette potrebbero presto guidare il pacchetto di metodi avanzati di sequenziamento del DNA

Il DNA è sottoposto a numerosi cambiamenti biochimici e biofisici per modulare l’espressione genica. Queste modifiche epigenetiche non alterano la sequenza del DNA, ma possono influenzare il modo in cui questa viene «letta». Un esempio comune è la metilazione (aggiunta di CH3), che impedisce fisicamente la trascrizione e l’espressione genica. Anche se la chimica sintetica e le tecniche di sequenziamento del DNA sono progredite enormemente, tuttavia non conservano informazioni epigenetiche di fondamentale importanza. Il progetto EpiSeq, finanziato dall’UE, utilizza «forbici molecolari» ad alta tecnologia (tecnologia CRISPR/Cas9) per tagliare la piccola sequenza di DNA di interesse e pinzette magnetiche per manipolare la molecola e determinarne la sequenza epigenetica. La conoscenza dei cambiamenti epigenetici informerà gli studi su come i cambiamenti di espressione genica sono alla base di determinate malattie con implicazioni per diagnosi e trattamento migliori.

Obiettivo

Next-generation DNA sequencing technologies are at the core of modern molecular biology and are rapidly entering the technological arsenal for personalized medicine. The recent explosion of sequencing technologies has provided researchers with various solutions to fit their sequencing needs, with a large spectrum of costs and limitations. However, most sequencing methods use enzymatic duplication of DNA to generate a strong enough sequencing signal. Therefore, chemical modifications potentially present on native bases are lost, and with them, an entire level of epigenetic information about. Although some workarounds are emerging, they are indirect, costly, and not yet amenable for the targeted sequencing of a given native genomic locus or biophysical analysis of the modified DNA. Given the need to understand the epigenetic layer of genetic information, I propose to develop a reliable and cheap method to map, at the single-molecule resolution, the epigenetic status of a genomic DNA locus of interest. This will be achieved through biochemical capture of this locus using CRISPR/Cas9 technology, and its epigenetic sequencing via single-molecule manipulation by magnetic tweezers. In addition to identifying the nature and the position of the modified bases at a given genomic DNA locus, I will use this magnetic tweezer technology to address fundamental questions about the effect of epigenetic modifications on the biophysical properties of DNA (formation of DNA structures and protein interactions). Specifically, I will focus on 8-oxoguanine, for which there is increasing interest since it is a hallmark of degenerative pathologies like cancer or Alzheimer’s Disease, and since it has recently entered the known epigenetic arsenal. This project has great potential applications in medical diagnosis. It will give me a first-hand experience in developing a cutting-edge technology, which will be of great benefit to my future independent research career.