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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.

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

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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