Workshop

STUDIUM Workshop July 8, 9 and 10 2015

From July 8 (14h00) through July 10, 2015 (12h00)

Topic: Analysis and Annotation of DNA Repeats and Dark Matter in Eukaryotic Genomes.

 

Summary 1

The topic of the meeting will be the identification and annotation of various repetitive genetic elements found in eukaryotic genomes as well as of genomic dark matter. The challenge set for this meeting will be to come up with novel approaches to further the understanding of non-genic chromosomal sequence features. This is particularly important in order to better understand the signalling networks that regulate chromatin and nuclear compartment organisation.

Following an introductory session (session 1), the next three sessions will be organized to address the questions above using two different approaches. Presentations in sessions 2 and 3 will focus on de novo repeat analysis methods based on the repeated nature of genetic DNA elements and their sequence conservation, as they are found in either assembled or unassembled genomes. On the other hand, in session 4, genetic repeats will be examined from a functional standpoint in their respective host genomes and will focus on two criteria: i) their nuclear location and/or ability to be bound by protein factors associated with their location or activities, and ii) their sequence conservation.

The meeting will end with a last, fifth session, that will address the definition of a “repeated species” and will explore the methods and feasibility of classifying these in the light of their diversity and complexity.

It should be noted that this meeting will take place immediately following the meeting of the transposable elements network (GDR CNRS 3546) that will be held in Tours in July 2015 from the 6th through the 8th. The juxtaposition of the two meetings will provide an opportunity for participants to have a full week of presentations, meetings and discussion on the biology of transposable elements.

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The meeting focuses on the analysis of repetitive elements found in eukaryotic genomes as well as of genomic dark matter. Its challenge is to come up with novel approaches to further the understanding of non-genic chromosomal sequence features. This is particularly important in order to better understand the signalling networks that regulate chromatin and nuclear compartment organisation.

The presentations will first focussed on de novo repeat analysis methods based on the repeated nature of genetic DNA elements and their sequence conservation, in either assembled or unassembled genomes. Genetic repeats will be then examined from a functional standpoint. It will end by addressing the possibilities to define a “repeated species” and to explore the methods and feasibility of classifying these in the light of their diversity and complexity.

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La conférence porte sur l’analyse des éléments répétés et de la matière noire génomique présents dans les génomes eucaryotes. Son objectif est de mettre en avant les approches permettant d’améliorer la description et l’analyse des séquences chromosomiques non-géniques. Cet aspect de la génomique est particulièrement important pour comprendre l’organisation des réseaux de signalisation qui régulent la chromatine et l'organisation des compartiments nucléaires.

Les présentations mettront d'abord l'accent sur les méthodes de novo de détection des répétitions qui sont basées sur la nature répétée des éléments d'ADN et leur conservation de séquence, dans des génomes assemblés ou non-assemblés. La détection de répétitions sera ensuite examinée d'un point de vue fonctionnel. La conférence s’attaquera pour finir aux possibilités de définir une «espèce répétée" puis d'explorer les solutions et la faisabilité de leur classement à la lumière de leur diversité et de leur complexité.

 

Participants and propositions of talks

Day 1

Welcome talks (14h00 - 14h15)

  • Studium representative (STUDIUM ; 10’)
  • Yves Bigot (CNRS - Nouzilly) & Peter Arensburger (California State University, Pomona) ; 5’

 

Session 1 : Introduction talks (14h15 - 14h30)
Chairman : Yves Bigot

  • Yves Bigot (CNRS - Nouzilly ; 15’)
    Introduction to the complexity of eukaryotic genomes - Scientific challenges of the meeting

 

Session 2 : Analysis and annotation of the repeats in assembled eukaryotic genomes - methodological approaches (14h30 - 16h00)
Chairman of session 2: David O’ Pollocq

  • David O Pollocq (University of Colorado, USA ; 30’ + 10’ )
    Identification of repeat structures in large genomes using repeat probability clouds
  • Florian Maumus (INRA Versailles; 30’ + 10’)
    REPET, Repeatscout and Repeatmodeler : principes and efficiencies.

 

Coffee break & with posters (16h00 - 16h30)

 

Session 2 : Analysis and annotation of the repeats in assembled eukaryotic genomes - methodological approaches (14h30 - 16h00)

  • Hadi Quesneville URGI member (INRA Versailles; 30’ + 10’)
    De novo annotation with REPET and P-clouds : beyond default parameters
  • Flash poster presentation1 on a topic related to the session (5’ + 5’)
    1 Selected from abstracts.
  • Flash poster presentation on a topic related to the session (5’ + 5’)

 

Conclusion of the session 2 by the Chairman : David O’ Pollocq (10’)


Day 2

Session 3 : Analysis and annotation of the repeats in eukaryotic genomes (9h00 - 10h40)
Chairman of session 3: Jiri Macas

 

Part 1 of session 3 : Assembled genomes (9h00 - 10h40)

  • Sébastien Guizard (INRA Tours; 30’ + 10’)
    Diving in the deep annotation the genome of the red jungle fowl genome
  • Jean Nicolas Volff (Ecole Normale Supérieure de Lyon ; 30’ + 10’)
    Did alive animal fossils contain DNA fossils in their genomes ?
  • Flash poster presentation on a topic related to the session (5 + 5’)

 

Part 2 of session 3 : Unassembled genomes (11h10 - 13h10)
Chairman : Jiri Macas

  • Jiri Macas (Ceske Budejovice, Czech Republic; 30’ + 10’)
    Repeat Explorer : beyond default parameters
  • Peter Arensburger or Yves Bigot (California State University, Pomona, USA; 30’ + 10’)
    Analyzing repeats in breeds of chickens with RE and complementary approaches
  • Flash poster presentation on a topic related to the session (5 + 5’)

 

Conclusion of the session 3 by the Chairman : Jiri Macas (10’)

 

Lunch (13h15 - 14h30)

 

Session 4 : Analysis and annotation of repeat networks in eukaryotic genomes (14h30 - 16h00)
Chairman of the session 4 : Davide Gebellini

 

Part 1 of session 4 : Repetitive elements involved in chromatin activity (14h30 - 16h00)

  • Davide Gebellini (University Milano, Italy; 30’ + 10’)
    A repetitive elements perspective in Polycomb epigenetics
  • GENOMATIX
    Diversity, dynamics and annotations of functional repeated elements in eukaryotic genomes
  • Flash poster presentation on a topic related to the session (5 + 5’)

 

Coffee break & with posters (16h00 - 16h30)
Part 2 of session 4 : Repetitive elements involved in nuclear organisation (16h30 - 18h00)
Chairman : Nicolas Mermod

  • Philippe Collas (University of Oslo, Oslo; 30’ + 10’)
    Diversity, dynamics and annotations of Lamina Associated Domains in eukaryotic genomes
  • Attila Nemeth (University of Regensburg, Germany; 30’ + 10’)
    Diversity, dynamics and annotations of Nucleolus Associated Domains in eukaryotic genomes

Conclusion of the session 4 by the Chairman : Davide Gebellini (10’)

 

Day 3

Session 5 : Can we annotate without to classify ? (9h00 - 10h00)
Chairman : Hadi Quesneville

  • Jiri Macas (Ceske Budejovice, Czech Republic ; 15’ + 5’)
    How can we model a “repeat species” for annotation ?
  • Sébastien Tempel (INRIA Rennnes ; 30’ + 10’)
    “repeat species” for annotation : using model-based identification tools

 

Coffee break & with posters (10h00 - 10h30)
Session 5 : Can we annotate without to classify ? (10h30 - 11h30)

  • Peter Arensburger (California State University , Pomona, USA ; 30’ + 10’)
    A survey of transposable element classification systems – a call for a fundamental update to meet the challenge of their diversity and complexity

 

Conclusion of the session 5 by the Chairman : Hadi Quesneville (10’)
Conclusions (11h30 - 12h00)

  • Yves Bigot
    Future lanes that could be continued from the Ins and outs of this meeting

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