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triloci-seq SIGNED

Triloci-seq - Dechipering the triple helix code

Total Cost €

0

EC-Contrib. €

0

Partnership

0

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 triloci-seq project word cloud

Explore the words cloud of the triloci-seq project. It provides you a very rough idea of what is the project "triloci-seq" about.

segments    acid    synthetic    unlike    minimal    vp64    triplex    genomic    putative    genomes    exists    data    chain    sequencing    hundreds    oligo    fluorescently    ttss    mixed    containing    sequences    position    function    match    first    molecules    helices    molecule    synthesis    coding    sites    poorly    mammalian    site    genome    matching    hoogsteen    forming    natural    rna    synthesized    watson    genetic    upstream    hybrids    gene    multiple    vivo    oligos    chromatin    greatest    labelled    code    interact    chemistry    protein    cassette    transfect    triple    vitro    cells    affinity    possibility    tfos    bioinformatic    confirm    generation    tfo    obstacle    expression    raised    lncrna    tts    lncrnas    prove    pairing    recent    creek    triplx    libraries    seq    whom    join    triloc    nucleic    thousands    feasibility    promoter    unclear    regulate    plan    technological    decipher    will    extract    helix    harbor    interaction    base    transcribed    revealed    click    relies    functional   

Project "triloci-seq" data sheet

The following table provides information about the project.

Coordinator
TECHNION RESEARCH AND DEVELOPMENT FOUNDATION LTD 

Organization address
address: THE SENATE BUILDING TECHNION CITY 1
city: HAIFA
postcode: 32000
website: n.a.

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 Coordinator Country Israel [IL]
 Total cost 181˙365 €
 EC max contribution 181˙365 € (100%)
 Programme 1. H2020-EU.1.3.2. (Nurturing excellence by means of cross-border and cross-sector mobility)
 Code Call H2020-MSCA-IF-2018
 Funding Scheme MSCA-IF-GF
 Starting year 2020
 Duration (year-month-day) from 2020-08-01   to  2022-07-31

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    TECHNION RESEARCH AND DEVELOPMENT FOUNDATION LTD IL (HAIFA) coordinator 181˙365.00
2    MASSACHUSETTS INSTITUTE OF TECHNOLOGY US (CAMBRIDGE) partner 0.00

Map

 Project objective

Recent technological advances revealed that there are many long non (protein)-coding RNA molecules (lncRNA) transcribed in the genome, many of whom regulate gene expression. However, it remains unclear how lncRNA molecule can interact directly with chromatin to regulate gene expression. One possibility that has been raised is via the formation of triple-helices. The potential for the formation of triple helices exists in any nucleic acid chain via an interaction called Hoogsteen base-pairing. However, unlike the genetic code or even Watson-Creek base-pairing, the triplex code or sequences which can function as triplex target sites and triplex-forming oligos is poorly understood. To decipher the triplex code in vivo, I propose a novel research approach based on next generation sequencing that I call Triloc-seq (in vivo). The feasibility this research plan relies on two crucial resources: first, mammalian genomes which can harbor as many as hundreds of thousands of putative high-affinity triplex target sites (TTSs), and second mixed-base oligo synthesis technology. Together these resources will allow us to over-come the greatest obstacle in triplex study, the need to match specifically a target site with its triplx forming oligo (TFO). To study the triple-helix code, we will transfect mammalian cells with a TFO libraries, and use click chemistry to join the TFO to its target site. We will then use previous TFO-TTS data obtained in vitro and multiple advanced bioinformatic approaches to extract the genomic TTSs. Finally, to prove that triplex interaction can be functional in vivo, we will design several applications that will test this functionality. In all cases we will design a cassette of known TTS target sites and position it upstream of a minimal promoter. The TTS cassette will be targeted by natural lncRNAs containing matching TFO segments, synthetic TFO-VP64 hybrids synthesized in vitro, and fluorescently labelled TFOs to confirm TTS-TFO functionality.

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The information about "TRILOCI-SEQ" are provided by the European Opendata Portal: CORDIS opendata.

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