2nd International Conference and Workshop

Genomic Impact of Eukaryotic Transposable Elements

Organizer: Jerzy Jurka, Genetic Information Research Institute

Friday, February 6, 2009

15:00-18:00 REGISTRATION (Phoebe A. Hearst Social Hall)
18:00-19:00 Dinner
19:30-23:00 Warm-up party/poster previews/preparation of audio-visual

The following equipment will be provided in all sessions: an LCD projector, laser pointer and a microphone. Speakers should load their talks at Fred Farr Forum in the evening preceding the presentations. There will be a limited time for last-minute testing (30 min. before the morning session and during breaks). Equipment for 35 mm slides and overhead projector WILL NOT be provided at this meeting.

Saturday, February 7, 2009

7:30-8:30 Breakfast
8:00-9:00 REGISTRATION (Phoebe A. Hearst Social Hall)
9:00-9:10 Jerzy Jurka – Opening remarks
9:10-9:50 Roy Britten - History and relationships of TEs
9:50-10:20 David Haussler - Evidence that transposons shaped vertebrate gene regulatory networks
10:20-10:50 Coffee-break/Group photo
10:50-11:20 Gill Bejerano - A study of co-option in the human genome
11:20-11:50 Michael Savageau - Quantitative evolutionary design of gene circuits: lessons from Bacteria
12:00-13:00 Lunch
13:30-14:00 Juergen Brosius - The retro-look of genomes
14:00-14:30 Norihiro Okada - Multiple SINE insertions made our brain mammalian?
14:30-15:00 Chantal Vaury - Insulators brought by TE contribute to gene regulation in relationship with nuclear architecture
15:00-15:30 Dixie Mager - Complex epigenetics of mammalian endogenous retroviruses
15:30-16:00 Coffee-break
16:00-16:30 Cedric Feschotte - Mammalian transposable elements and the emergence of lineage-specific functions
16:30-17:00 King Jordan - Transposable elements, chromatin and gene regulation
17:00-17:30 Alan Weiner - Human PGBD3: a piggyBac transposon that is both good and bad for us?
18:00-19:00 Dinner
19:15-19:45 John Moran - Studies of a human transposable element
19:45-20:15 Sandy Martin - Mutational analyses of ORF1p function in LINE-1 retrotransposition
20:15-20:45 Thomas Eickbush - Regulating the expression of R2 elements within the nucleolus
20:45-23:00 Happy Hours / poster session (odd numbers)

Sunday, February 8, 2009

7:30-8:30 Breakfast
9:00-9:30 Holly Wichman - Comparative biology of L1 elements
9:30-10:00 Prescott Deininger - Cellular responses to damage by non-LTR retroelements
10:00-10:15 Nicolas Gilbert - LINE-1 mediated mobilization of snRNA
10:15-10:30 Eric Devor - A microRNA incubator on the marsupial (Monodelphis domestica) X-chromosome was created via L1 transposon-mediated serial duplication.
10:30-10:45 Corrado Spadafora - Functional roles for LINE1-encoded reverse transcriptase in embryonic development and tumor progression
10:45-11:00 Coffee-break
11:00-11:30 Josefa Gonzalez - High rate of recent transposable element-induced adaptation in Drosophila melanogaster
11:30-12:00 Mark Batzer - Mobile elements and primate genomic variation
12:00-13:00 Lunch
13:30-14:00 Jeff Bennetzen - The evolution, activities and specificities of transposable elements in grass genomes
14:00-14:30 Zoltan Ivics - Transposon-host cell interactions in the regulation of Sleeping Beauty transposition
14:30-14:45 Marie-Angele Grandbastien – Transposable elements and TE-gene associations in the transcriptome of Solanaceae species
14:45-15:00 R. Keith Slotkin - Germ cell-specific activation and silencing of transposable elements in plants
15:00-15:15 Vincent Colot - A role for RNAi in the correction of transposable element methylation and silencing defects in Arabidopsis
15:15-15:30 Ken Naito - Live watching TE burst: behavior and impact of a rice transposon mPing
15:30-15:50 Coffee-break
15:50-16:20 Arian Smit - Evolution of transposable elements in mammals and birds
16:20-16:50 Andrew Shedlock - The Anolis genome assembly: balancing mammalian and avian perspectives on amniote repeat evolution
16:50-17:20 Vladimir Kapitonov - Stories of outrageous horizontal transfer of DNA transposons
17:20-17:50 Irina Arkhipova - Massive Horizontal gene transfer in bdelloid rotifers
18:30-22:30 Dinner at Monterey Bay Aquarium: buses depart at 18:30

Monday, February 9, 2009

7:30-8:30 Breakfast
9:00-9:30 Hadi Quesneville - REPET: pipelines for the identification and annotation of transposable elements in genomic sequences
9:30-10:00 David Pollock - Identifying repeat-derived regions in the twilight zone
10:00-10:30 Marcelo Bento Soares - High-throughput sequence-based epigenomic analysis of human Alu repeats
10:30-10:45 Coffee-break
10:45-11:00 Guillaume Bourque - Evolution of the mammalian transcription factor binding repertoire via transposable elements
11:00-11:15 Victor Zhurkin - The tumor suppressor protein p53 binding sites in mammalian genomes are related to transposons.
11:15-11:30 Tomasz Zemojtel - Methylation and deamination of CpGs generates p53 binding sites on a genomic scale
11:30-11:45 Geoff Faulkner - The regulated retrotransposon transcriptome of mammalian cells
11:45-12:00 Sebastian Szpakowski - Methylation profiling: repetitive elements and disease progression.
12:00-13:00 Lunch
13:30-14:00 Marlene Belfort - Stressed retrotransposons on the move
14:00-14:15 Nancy Craig - Characterization of an active mammalian DNA transposon
14:15-14:30 Gerald Schumann - 5’-transduced SVA retrotransposon groups spread efficiently throughout the human genome
14:30-14:40 Dustin Hancks - Exon-trapping mediated by the SVA retrotransposon
14:40-14:55 Hidenori Nishihara - Retroposon analysis reveals simultaneous divergence of the placental mammalian ancestor possibly triggered by continental divisions
14:55-15:05 Kamal Rawal - ELAN: A server based tool for genome wide analysis of mobile genetic elements
15:05-15:30 Coffee-break

Mini-workshop on Classification and Nomenclature of TEs

Moderators: Pierre Capy, Cedric Feschotte, Jerzy Jurka, Vladimir Kapitonov, Arian Smit

15:30-16:00 Pierre Capy - Automatic classification of mariner-like elements
16:00-16:30 Ruth Seal/Jens Mayer (joint presentation) - The need for an approved nomenclature for (human) endogenous retroviruses
16:30-16:35 Jonas Blomberg - Optimal taxonomical markers for ERVs
16:35-16:40 Francois Sabot - Non-autonomous and complete derivate elements: how to classify them ?
16:40-16:45 Irina Arkhipova - Superfamily-specific reference datasets as possible aids in resolving classification problems
16:45-17:30 (time for this session can be extended if needed for discussion) Open floor: nominations and election of the International Committee for Classification of TEs (ICCTE).
18:00-19:00 Dinner
19:30-23:00 Happy Hours / poster session (even numbers)

Tuesday, February 10, 2009

7:30-8:30 Breakfast
12:00-13:00 Lunch

Due to high interest in the "Genomic Impact of Eukaryotic Transposable Elements", a special issue of Gene devoted to this topic will be published after the conference. Deadline for manuscript submissions is April 30, 2009. Details will be posted on the conference website after the conference.