Program

1st International Conference and Workshop

Genomic Impact of Eukaryotic Transposable Elements

Organizers: Mark A. Batzer, Prescott Deininger, Jerzy Jurka (Chair), John Moran

March 31, 2006
15:00-18:00 Registration

18:00-19:00 Dinner

19:00-20:30 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

April 1, 2006
7:30-8:30 Breakfast

8:00-9:00 REGISTRATION

9:00-9:30 Jerzy Jurka - Introduction to the conference and workshop

9:30-10:00 John Moran - Template-specific reverse transcriptase activity in LINE-1 RNPs

10:00-10:30 Prescott Deininger - Does L1 survive despite, or because of, its incompetence?

10:30-11:00 Coffee-break

11:00-11:30 Anthony Furano - The interaction between L1 retrotransposons and their mammalian hosts

11:30-12:00 Holly Wichman - LINE-1 activity and extinction in mammals

12:00-13:00 Lunch

13:30-14:00 Haig Kazazian Jr. - Extensive individual variation in L1 retrotransposition capability contributes to human genetic diversity

14:00-14:30 Mark Batzer - Mobile elements and primate genomic variation

14:30-15:00 Juergen Brosius - Mistaken identity - how repetitive elements only indirectly related to retroposons move around the genome

15:00-15:30 Norihiro Okada - Functional non-coding sequences derived from SINEs in the human genomes

15:30-16:00 Coffee-break

16:00-16:30 Carol Rubin - Alu repeats: From junk to function

16:30-17:00 Nicolai Tomilin - The role of retrotransposons in the maintenance of heterochromatin

17:00-17:30 Carl Schmid - Functional implications of SINE expression

18:00-19:00 Dinner

19:00-19:30 Andrew Gentles - Computational reconstruction of transposable elements

19:30-20:00 Gabor Toth - Methods for de novo identification of repetitive sequences in newly sequenced genomes

20:00-20:30 Arian Smit - RepeatMasker, FEAST and other tools for analyzing and exploiting repetitive DNA

20:30-23:00 Happy Hours

April 2, 2006
7:30-8:30 Breakfast

9:00-9:30 Irina Arkhipova - Transposons, telomeres and rotifers

9:30-10:00 Gill Bejerano - Origins of ultraconservation and distal cis-regulation in vertebrates

10:00-10:30 Sandy Martin - Single Amino Acid Substitutions in L1 ORF1p with Dramatic Effects on Nucleic Acid Chaperone Activity and L1 Retrotransposition

10:30-11:00 Coffee-break

11:00-11:30 Daniel Voytas - Retrotransposon target specificity and genome organization

11:30-12:00 Jiri Hejnar - Human syncytins - an extreme example of transposable element domestication

12:00-13:00 Lunch

13:30-14:00 Dusan Kordis - Enormous impact of retroelements on the genome structure and evolution in land vertebrates

14:00-14:30 Dixie Mager - Effects of LTR elements on mammalian genes

14:30-15:00 Alan Schulman - Parasites and parasites of parasites: Plant retrotransposons and their genomic impact

15:00-15:30 John McDonald - The contribution of LTR retrotransposons to gene evolution: a tale of three genomes.

15:30-16:00 Coffee-break

16:00-16:30 Horacio Naveira - Contrasting patterns of sequence turnover of LTR retrotransposons in different eukaryotes

16:30-17:00 Marie-Anne Van Sluys - A genomic approach to depict transcriptionally active transposable elements in sugarcane

17:00-17:30 Adam Pavlicek - Retroposition of processed pseudogenes: the impact of RNA stability and translational control

18:00-19:00 Dinner

19:00-19:30 Wojtek Makalowski - Validation of diverged repetitive elements using phylogenetic analysis and comparative genomics approach

19:30-20:00 Peter Warburton - Analysis of the relative chronological age of human transposable elements by defragmentation and insertional analysis

20:00-20:15 Vini Pereira - Automated palaeontology of repetitive DNA with REannotate

20:15-20:30 Degui Zhi - Comparative genomics analysis of Alu gene conversions

20:30-22:30 Happy Hours / poster session / workshop appointments

April 3, 2006
7:30-8:30 Breakfast

9:00-9:30 Pierre Capy - Dynamics of transposable elements: first steps of invasion and long-term evolution

9:30-10:00 Andrew Flavell - Conflict, compromise or cooperation - Different ways for transposons and genomes to coexist

10:00-10:30 Dmitri Petrov - Population dynamics of a comprehensive set of transposable elements in the D. melanogaster genome

10:30-11:00 Coffee-break

11:00-11:30 Giorgio Bernardi - The organization of the human genome: from chromosomal bands to isochores

11:30-12:00 Peter Arndt - Substitution pattern of mammalian transposable elements - element specific, regional, and evolutionary aspects.

12:00-13:00 Lunch

13:30-14:00 Cedric Feschotte Life after death: reincarnation of DNA transposons into genetic networks: A case study in the human genome

14:00-14:30 Ning Jiang - The impact of Mutator-like elements on genome evolution

14:30-15:00 Antoni Rafalski - Helitrons and the evolution of DNA sequence diversity in maize

15:00-15:30 Marie-Jose Daboussi - Transposable elements in filamentous fungi

15:30-16:00 Coffee-break

16:00-16:30 Andrew Shedlock - BAC-enabled comparative investigation of CR1 evolutionary dynamics in the reptilian genomic landscape

16:30-17:00 Vladimir Kapitonov - Towards a unified nomenclature and classification of eukaryotic transposable elements

17:00-17:15 Emile Zuckerkandl - Do transposable elements participate in combinatorial epigenetics?

18:00-19:00 Dinner

19:00-19:15 Cristina Vieira - New regulatory regions of Drosophila 412 retrotransposable element generated by recombination

19:15-19:30 Chris Smith - The Drosophila heterochromatin genome project (DHGP): identifying repeats & using comparative sequence analysis to follow heterochromatin evolution

19:30-19:45 Sebastien Tempel - The combinatorics of helitron termini in A. thaliana genome revealed strongly structured superfamilies

19:45-20:00 Victor Zhurkin - The tumor suppressor protein p53 binding sites in the human genome: How are they related to transposons?

20:00-20:30 Clark Jeffries - Hairpin database: why and how?

20:30-22:30 Happy Hours / poster session / workshop appointments

April 4, 2004
7:30-8:30 Breakfast

Mini-workshop on Classification and Nomenclature of TEs
Moderators:
Pierre Capy, Cedric Feschotte, Jerzy Jurka, Vladimir Kapitonov
Preliminary agenda:

8:30 - 9:30 Mini-presentations (5 min. each) by ~10 speakers interested in the topic. Each speaker will address two specific issues: (1) what are the classification/nomenclature problems in the particular area of the speaker's expertise, and (2) a proposal how to address them.
The Speakers will be selected based on particular interest and expertise, and announced in the final program in March. Those interested in making a mini-presentation should send an email to conference@girinst.org stating their particular topic of interest. The deadline is February 28, 2006.
After the meeting, the role of each active participant should be to submit a short summary of a particular topic and of the recommendation agreed upon, or an outline of basic disagreements. The moderators are responsible for collecting and recording what was agreed upon, and for preparing a jointly signed publication.

9:30-11:00 Short summaries by the moderators, additional talking points and discussion how to constitute an international organization devoted to coordination of the classification and nomenclature of TEs.

11:00-12:00 Nominations and secret ballot (if agreed upon).

12:00-13:00 Lunch

March 31, 2006
15:00-18:00	Registration
18:00-19:00	Dinner
19:00-20:30	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
April 1, 2006
7:30-8:30	Breakfast
8:00-9:00	REGISTRATION
9:00-9:30	Jerzy Jurka - Introduction to the conference and workshop
9:30-10:00	John Moran - Template-specific reverse transcriptase activity in LINE-1 RNPs
10:00-10:30	Prescott Deininger - Does L1 survive despite, or because of, its incompetence?
10:30-11:00	Coffee-break
11:00-11:30	Anthony Furano - The interaction between L1 retrotransposons and their mammalian hosts
11:30-12:00	Holly Wichman - LINE-1 activity and extinction in mammals
12:00-13:00	Lunch
13:30-14:00	Haig Kazazian Jr. - Extensive individual variation in L1 retrotransposition capability contributes to human genetic diversity
14:00-14:30	Mark Batzer - Mobile elements and primate genomic variation
14:30-15:00	Juergen Brosius - Mistaken identity - how repetitive elements only indirectly related to retroposons move around the genome
15:00-15:30	Norihiro Okada - Functional non-coding sequences derived from SINEs in the human genomes
15:30-16:00	Coffee-break
16:00-16:30	Carol Rubin - Alu repeats: From junk to function
16:30-17:00	Nicolai Tomilin - The role of retrotransposons in the maintenance of heterochromatin
17:00-17:30	Carl Schmid - Functional implications of SINE expression
18:00-19:00	Dinner
19:00-19:30	Andrew Gentles - Computational reconstruction of transposable elements
19:30-20:00	Gabor Toth - Methods for de novo identification of repetitive sequences in newly sequenced genomes
20:00-20:30	Arian Smit - RepeatMasker, FEAST and other tools for analyzing and exploiting repetitive DNA
20:30-23:00	Happy Hours
April 2, 2006
7:30-8:30	Breakfast
9:00-9:30	Irina Arkhipova - Transposons, telomeres and rotifers
9:30-10:00	Gill Bejerano - Origins of ultraconservation and distal cis-regulation in vertebrates
10:00-10:30	Sandy Martin - Single Amino Acid Substitutions in L1 ORF1p with Dramatic Effects on Nucleic Acid Chaperone Activity and L1 Retrotransposition
10:30-11:00	Coffee-break
11:00-11:30	Daniel Voytas - Retrotransposon target specificity and genome organization
11:30-12:00	Jiri Hejnar - Human syncytins - an extreme example of transposable element domestication
12:00-13:00	Lunch
13:30-14:00	Dusan Kordis - Enormous impact of retroelements on the genome structure and evolution in land vertebrates
14:00-14:30	Dixie Mager - Effects of LTR elements on mammalian genes
14:30-15:00	Alan Schulman - Parasites and parasites of parasites: Plant retrotransposons and their genomic impact
15:00-15:30	John McDonald - The contribution of LTR retrotransposons to gene evolution: a tale of three genomes.
15:30-16:00	Coffee-break
16:00-16:30	Horacio Naveira - Contrasting patterns of sequence turnover of LTR retrotransposons in different eukaryotes
16:30-17:00	Marie-Anne Van Sluys - A genomic approach to depict transcriptionally active transposable elements in sugarcane
17:00-17:30	Adam Pavlicek - Retroposition of processed pseudogenes: the impact of RNA stability and translational control
18:00-19:00	Dinner
19:00-19:30	Wojtek Makalowski - Validation of diverged repetitive elements using phylogenetic analysis and comparative genomics approach
19:30-20:00	Peter Warburton - Analysis of the relative chronological age of human transposable elements by defragmentation and insertional analysis
20:00-20:15	Vini Pereira - Automated palaeontology of repetitive DNA with REannotate
20:15-20:30	Degui Zhi - Comparative genomics analysis of Alu gene conversions
20:30-22:30	Happy Hours / poster session / workshop appointments
April 3, 2006
7:30-8:30	Breakfast
9:00-9:30	Pierre Capy - Dynamics of transposable elements: first steps of invasion and long-term evolution
9:30-10:00	Andrew Flavell - Conflict, compromise or cooperation - Different ways for transposons and genomes to coexist
10:00-10:30	Dmitri Petrov - Population dynamics of a comprehensive set of transposable elements in the D. melanogaster genome
10:30-11:00	Coffee-break
11:00-11:30	Giorgio Bernardi - The organization of the human genome: from chromosomal bands to isochores
11:30-12:00	Peter Arndt - Substitution pattern of mammalian transposable elements - element specific, regional, and evolutionary aspects.
12:00-13:00	Lunch
13:30-14:00	Cedric Feschotte Life after death: reincarnation of DNA transposons into genetic networks: A case study in the human genome
14:00-14:30	Ning Jiang - The impact of Mutator-like elements on genome evolution
14:30-15:00	Antoni Rafalski - Helitrons and the evolution of DNA sequence diversity in maize
15:00-15:30	Marie-Jose Daboussi - Transposable elements in filamentous fungi
15:30-16:00	Coffee-break
16:00-16:30	Andrew Shedlock - BAC-enabled comparative investigation of CR1 evolutionary dynamics in the reptilian genomic landscape
16:30-17:00	Vladimir Kapitonov - Towards a unified nomenclature and classification of eukaryotic transposable elements
17:00-17:15	Emile Zuckerkandl - Do transposable elements participate in combinatorial epigenetics?
18:00-19:00	Dinner
19:00-19:15	Cristina Vieira - New regulatory regions of Drosophila 412 retrotransposable element generated by recombination
19:15-19:30	Chris Smith - The Drosophila heterochromatin genome project (DHGP): identifying repeats & using comparative sequence analysis to follow heterochromatin evolution
19:30-19:45	Sebastien Tempel - The combinatorics of helitron termini in A. thaliana genome revealed strongly structured superfamilies
19:45-20:00	Victor Zhurkin - The tumor suppressor protein p53 binding sites in the human genome: How are they related to transposons?
20:00-20:30	Clark Jeffries - Hairpin database: why and how?
20:30-22:30	Happy Hours / poster session / workshop appointments
April 4, 2004
7:30-8:30	Breakfast
Mini-workshop on Classification and Nomenclature of TEs Moderators: Pierre Capy, Cedric Feschotte, Jerzy Jurka, Vladimir Kapitonov Preliminary agenda:
8:30 - 9:30	Mini-presentations (5 min. each) by ~10 speakers interested in the topic. Each speaker will address two specific issues: (1) what are the classification/nomenclature problems in the particular area of the speaker's expertise, and (2) a proposal how to address them. The Speakers will be selected based on particular interest and expertise, and announced in the final program in March. Those interested in making a mini-presentation should send an email to conference@girinst.org stating their particular topic of interest. The deadline is February 28, 2006. After the meeting, the role of each active participant should be to submit a short summary of a particular topic and of the recommendation agreed upon, or an outline of basic disagreements. The moderators are responsible for collecting and recording what was agreed upon, and for preparing a jointly signed publication.
9:30-11:00	Short summaries by the moderators, additional talking points and discussion how to constitute an international organization devoted to coordination of the classification and nomenclature of TEs.
11:00-12:00	Nominations and secret ballot (if agreed upon).
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 June 16, 2006. Details will be announced during the conference.

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