Drosophila ENCODE Workshop

December 5-6

**Meeting Summary**

**General Rationale:**

The debut of the Genomic Era has seen the complete sequencing of a
growing number of genomes, but maximally utilizing those sequences
requires mapping all the known features types as well as providing for
the discovery of new ones. Annotated genomes are the maps that all
biologists will be using in the coming years, but these are quite
clearly works in progress. Data collection will drive genome annotation.
Protein encoding genes are first on most annotation priority lists, but
we need to improve on current gene models to account for the largely
unexplored alternative slice variants and untranslated regions.
Additionally, some genes are still very difficult to identify. Protein
coding genes with short open reading frames or exons and nested genes
fall into this problematic category. Clearly, the transcriptional
instructions imbedded within the genome are critical for our
understanding of genome deployment, but these cis-regulatory sequences
are families of very short strings of characters, such that finding
functionally significant control regions is computationally difficult.
Recently, there has been great interest in non-coding RNA genes. Our
ability to identify and refine non-coding RNAs is still in infancy. A
growing body of evidence indicates that much more of the genome is
transcribed than initially thought. How much of this genomic \"dark
matter\" is in the form of \"genes\" that eluded annotation due to short
ORFs or RNA-based function and how much is due to transcriptional noise?
The list of DNA elements is long. The human genome is big. Knowing what
elements are potentially functional, and in a timely manner, is quite
important given the great cost of analysis for all the sequences in the
human genome in every assay.

Needs and questions like those posited above have been recognized by the
NIH, which has launched an Encyclopedia of DNA Elements (ENCODE) pilot
project to help annotate the human genome. The Drosophila ENCODE
workshop was to organize a supporting project for the express purpose of
facilitating human ENCODE. There are significant ancillary benefits for
the research performed by the \~1,600 groups of scientists making
regular use of the Drosophila model. Members of the Drosophila, Genomic,
and NIH funding communities were represented.

**General Conclusions:**

Broadly speaking, D-ENCODE will be a central database where the
sequence/position is the identifier and a D-ENCODE community that
populates the database with computational and experimental evidence.
This generic structure will allow members of the community to attach any
attribute with a defined sequence to the database, including those that
are not currently anticipated.

The group also developed guidelines for determining the scope of the
initial D-ENCODE project. The human ENCODE project is based on the
analysis of 1% of the genome. The Drosophila genome, at \~5% of human,
will be an important stepping stone to a full human ENCODE project.
Significant benefits include a test of scale-up, a test of \"finishing
phase\" annotation, and cost savings by prioritizing element types for
the human ENCODE project.

The expectation is that all D-ENCODE groups will study the entire genome
and will focus on the first tier of genome features such as
transcription units, splicing, factor occupancy, chromatin status, and
sequence conservation. Approaches that generate data on multiple DNA
element types simultaneously should be favored, as improving cost
efficiency will be important for a full human ENCODE project.

Experimentally verified D-ENCODE data (defining the quality of
verification will depend on the data type) will be experimentally
validated by direct assay for genetic function, based on multiple lines
of evidence from knockouts, knockdowns, and allele frequencies in
populations. Many of the unique features of Drosophila (e.g. a complex
CNS and strong genetics) will make Drosophila the primary source of much
validation data, as rigorous tests of human DNA element function is
often not feasible, ethical, or both.

There is no doubt that immediate access to genomic sequence data has
been a boon to biology, but there are associated concerns about ensuring
that the deposited data is of a high quality and in assuring credit for
those that produce the primary data. At the workshop, members of the
Drosophila genomics community (all of whom embrace the long community
tradition of sharing resources) developed framework recommendations for
data sharing with genomics communities. The strong and unanimous
conclusion was that Drosophila ENCODE would set new standards for the
open distribution of verified experimental data, and for assuring the
proper recognition of such data as an e-publication by the data
producer. This is an appropriate mechanism to credit those scientists
devoting a substantial portion of their effort to community projects,
and to assure that released data passes a \"comfort level\" test of
quality. Indeed, D-ENCODE will be a model for the organization of
collaborative biological science in the spirit of open-source software
or large physical science consortiums.

**Technologies and resources:**

Much of the infrastructure for an ENCODE project is already in place or
is coming on-line, including: 12 sequenced Drosophila genomes,
re-sequencing of 50 lines of Drosophila melanogaster, gene disruption
and protein trapping projects, a genomic resources center, genetic
resource centers (for tilling mutation detection, P-element disruption,
deletion sets, and RNAi), full genome tiling path arrays (community and
commercial), assorted public database repositories, and a database of
the Drosophila genome annotation and literature.

It is clear that funding for many of these resources will need to be
augmented to support a D-ENCODE project. In particular, molecular and
whole organism stock centers are absolutely essential and are already at
or over capacity. Creation of affinity-based protein reagents (e.g.
antibodies, tagged proteins) for capturing the associated DNA elements
for ChIP-on-chip studies should be accelerated.

D-ENCODE array resources, especially those covering the full genome,
need to come on-line rapidly and there needs to be continuing pressure
on improving cost efficiency. Array resources for additional species
must also be developed to generate orthogonal sequence-conservation and
functional-genomic datasets. Such resources are essential for exploring
genomic dark matter.

Similarly, lower-level annotation of additional species is required to
inform the annotation of Drosophila melanogaster. Additional resources
will be required to move beyond first-pass automated gene finding in
non-melanogaster genomes. In particular the sequence of additional
species of flies is deemed to be quite important (especially for groups
falling between Drosophila and Anopheles) as is moderate-coverage cDNA
sequencing. The Tucson species group, not the D-ENCODE group, will
address these sequencing issues.

While community species-specific databases are an ideal home for gold
standard validated D-ENCODE data, it should not be the home of
e-published verified data from D-ENCODE members. Different data types
will necessitate data warehousing in distinct established and stable
public repositories. Data should not be stored and displayed exclusively
at lab-based sites with uncertain long-term stability. A working group
will be established to define information/object fields and to maximize
data synchronization and tracking.

**Moving forward:**

The unanimous view of Drosophila community participants is that D-ENCODE
must proceed rapidly. We have developed a general picture of the
consortium scope, and have made strong policy recommendations for data
sharing. The need for physical resource and software
development/enhancement is clearly recognized in so far as it directly
and immediately aids in data collection. The D-ENCODE workshop
recommendations will be summarized and forwarded to the Drosophila Board
for consideration in the form of a D-ENCODE White Paper. A draft
document will be vetted by meeting participants and by the larger
Drosophila community in the next two months. We will also seek input
from the human ENCODE project. A final document will be presented to the
elected Drosophila Board no latter than mid-March. The Drosophila Board
will approve a final document at the annual Drosophila meeting (March
30 - April 3, 2005), and will deliver this document to the NIH by the
first week of April. The D-ENCODE project will also be mentioned in a
more general Drosophila White Paper outlining the pressing needs of the
Drosophila community.

**Organization and Participation:**

A self-identified group has taken a leading role in initial D-ENCODE
discussions. They are Michael Ashburner (Cambridge UK), Hugo Bellen
(Houston TX), Susan Celniker (Berkeley CA), Michael Eisen (Berkeley CA),
William Gelbart (Cambridge MA), Greg Gibson (Raleigh NC), Gene Myers
(Berkeley CA), Brian Oliver (Bethesda MD), Gerald Rubin (Chevy Chase
MD), Steve Russell (Cambridge UK) and Kevin White (New Haven CT).

Attending from the Drosophila and genomics research communities were:
Justen Andrews (Bloomington IN), Spyros Artivanis-Tsakonis (Boston MA),
Michael Ashburner (Cambridge UK), David Begun (Davis CA), Hugo Bellen
(Houston TX), Michael Brent (St. Louis MO), Sue Celniker (Berkeley CA),
Peter Cherbas (Bloomington IN), Andrew Clark (Ithaca NY), Lynn Cooley
(New Haven CT), Ron Edgar (Bethesda MD), Michael Eisen (Berkeley CA),
Sarah Elgin (St. Louis MO), William Gelbart (Cambridge MA), Greg Gibson
(Raleigh NC), Scott Harrison (Palo Alto CA), Steve Henikoff (Seattle
WA), Angie Hinrich (Santa Cruz CA), Ian Holmes (Berkeley CA), Roger
Hoskins (Berkeley CA), Gary Karpen (Berkeley CA), Thom Kaufman
(Bloomington IN), Mel Kronick (Palo Alto CA), Eric Lai (Berkeley CA),
Suzanna Lewis (Berkeley CA), John Manak (Santa Clara CA) Therese Markow
(Tucson AZ), Alan Michelson (Boston MA), Gos Micklem (Cambridge UK),
Kevin Moses (Ashburn VA), Steve Mount (College Park MD), Gene Myers
(Berkeley CA), Brian Oliver (Bethesda MD), Akilesh Pandey (Baltimore
MD), Norbert Perrimon (Boston MA), Eric Pleshko (La Jolla CA), Gerald
Rubin (Chevy Chase MD), Steve Russell (Cambridge UK), Victor
Sementchenko (Santa Clara CA), Kevin White (New Haven CT), Mark Yandell
(Berkeley CA), Julia Zeitlinger (Cambridge MA).

Representatives from publishers were: Myles Axton (Nature Group),
Michael Eisen (PLoS), and Barbara Jasny (Science).

NIH extramural attendees were: Elise Feingold (Functional Analysis
Program Director, NHGRI), Adam Felsenfeld (Genome Sequencing Program
Director, NHGRI), Peter Good (Genome Informatics and Computational
Program Director, NHGRI), Mark Guyer (Director, Extramural Research,
NHGRI), Lorette Javois (Health Science Administrator, Developmental
Biology, Genetic & Teratology Branch, NICHD), Laurie Tompkins (Genetic
Mechanisms Program Director, NIGMS)

Special thanks to Kevin White and Lynn Cooley for providing funds via
NHGRI and The Drosophila Board.