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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.

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

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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