Genomics Discussion at Pombe 2000

Discussion chaired by Paul Nurse

Contents: Genome Sequence | Databases | Expression Profiling | Proteomics | Libraries | Communications | Committees

Genome sequence

• The aim is to publish the sequence by the end of 2000. This will hopefully include one centromere but no telomeric sequences and there are 8 gaps (about 50 genes).
• Nature have agreed to publish an article and a letter
• Over the next year the two other centromeres and the telomeres will be done and the whole sequence including the gaps should be finished. If anyone finds they have sequence which is not on the Blast server please let Val Wood know as it would be very helpful for gap filling the sequence .
• It would also be extremely helpful for the annotation if everyone could check the functional assignments of their favourite genes at http://www.sanger.ac.uk/cgi-bin/yeastpub/fun_class_search.p and send any amendments to val@sanger.ac.uk.

• The following databases are being used:- Sanger Centre Commercial eg PombePD
• Resources are needed to keep them going and and the consensus was that this was a good thing .
• The Sanger Centre has submitted a grant to Wellcome Trust for funds to develop a genome database and maintain the annotation
• PombePD^TM will be maintained for the forseeable future. Proteome Inc are committed to the yeast community and PombePD^TM is available free to the academic community. It is updated weekly and is available from their web site at http://www.proteome.com/databases. Laura Robertson would be very pleased to receive any input for improving the database. Her email address is lsr@proteome.com
• Other databases- nothing known.

• Sanger Centre. Jürg Bähler has made PCR products for 4700 genes which will be spotted onto glass slides and he will be using them to look at mitotic cell cycle, meiotic differentiation and stress response expression profiles partly in collaboration with Paul Nurse at ICRF and Nic Jones at the Patterson, CRC. He is also going to make a chromosome microarray. People will be able to go to the Sanger Centre to do their experiments during 2001 and the arrays will be available for the yeast community in about 12 months time.
• MRC Tim Humphrey explained that the MRC have a mouse genome project at Harwell and could incorporate a microarray facility for fission yeast. He wanted to know if there was a case for having additional microarrays. He thought that there was a lot of interest in microarrays and wondered if the demand could be met.
• Japan Yasushi Hiraoka will be making microarrays from 300bp DNA fragments from the 3' end of the ORF for all reported genes. These will eventually be available to the community.
• Sweden Karl Ekwall reported that the Transcriptional Regulation Groups had approached a Belgian biotech company EuroGenTech to make arrays. These will be available to buy from the company. Nothing has been started yet and he was unsure as to whether it was worth doing.

  Questions were raised as to whether it was best to standardise everything or to let the different initiatives go their own way. What were the needs of the community. Paul Nurse thought that it was better to have several initiatives. Others thought that a central resource should be set up to get the microarrays done well and available to all as many people as possible. The cost of the primers was a major concern as many labs were are interested in doing their own particular experiments and not in a genome wide analysis. The question of whether the scanning of the arrays and the bioinformatic analysis should be performed locally or be centralised was also raised with some people thinking that the centralised consortium approach was better whilst others thought that there was room for individuals. The analysis hardware seems to be generally available but not all the scanners are compatible although there are only four major variations. John Sgouros pointed out that advice and support on the analysis would be needed, this would require one person full time. It was suggested that there should be a committee should be elected which could act as a forum for discussion and a point of information for the community about the different initiatives and that we should not rely on commercial enterprise. The main conclusions were that

  1. In about 12 months the Sanger Centre would make the resources publicly available, Other initiatives are only just starting
  2. A discussion committee should be set up (see Committees)

• This was altogether a far more difficult problem. The PIGGI (Pombe Interest Group Genomics Initiative) had failed to get money from the BBSRC (Biotechnology & Biological Sciences Research Council) to support genomic and proteomic analyses. Proteomics needs more people involved who understand it. Ramsay McFarlane from Bangor is setting up Difference Gel Electrophoresis. He says: "DIGE....was developed in J. Minden's lab at Carnegie Mellon. Moreover, it is being set up for pombe at Bangor in collaboration with our resident 2D expert, Dr. Henk Braig (who deserves much credit)." No one knew if anything was happening in Japan or the States.

Libraries

• Yoshida is making an ordered library of all full length ORFs using the "Gateway" system. Yasushi Hiraoka has made the GFP fusion library that has been updated. Images of intracellular localisations are now available on the web at http://www-karc.crl.go.jp/bio/CellMagic/index.html.
• Mitsuhiro Yanagida has a ts mutant library of 1000 mutants. He has images and will make an image database accessible.
• Bea Grallert has a ts mutant library of about 2000 mutants. This is freely available but you need to go to Oslo for about one week (yes honestly) to wake up and reisolate the strains. Because it can only be woken up one or twice many copies will need to be made. It is difficult to get funding for this type of work but it was felt that once the sequence was published it would raise the profile of pombe and it may be easier to attract more funding.
• Tony Carr has also made a few hundred ts mutants and suggested that they should all be kept together somewhere.
• Deletion libraries. Is it worth doing a systematic deletion of all genes in diploids? Steve Oliver at the Edinburgh meeting thought that it was not worth doing a Eurofan type project and there was no strong move to do it at this meeting. Anabelle Decottigies and Paul Nurse are deleting 100 genes from S. pombe that are conserved in higher eukaryotes but not in S. cerevisiae. Yasushi Hiraoka is going to delete 1) meiosis specific genes regulated by Ste11p and 2) Selected genes from the GFP library based on their localisation.

• There was a general feeling that better means of communication between the community would be advantageous eg information about a deletion you are no longer working on could save someone several weeks work, job advertisments, mutants you are not going to work on etc. Was it worth having a newsletter? Susan Forsburg suggested that her web page could be a means of displaying information (Update 4/01: a community news page has been set up at http://pingu.salk.edu/~forsburg/community.html). Val Wood also said that it was possible to post information on the Sanger Centre pombe mailing list at pombelist@sanger.ac.uk.

Committees

• There were several suggestions at this meeting which need further discussion and organisation eg gene names should be consolidated and that a gene naming committee should be set up immediately. Paul Nurse suggested that an interim committee of Mitsuhiro Yanagida, Amar Klar and himself should be formed to oversee some of these suggestions until the 2nd International Fission yeast meeting in Japan, March 2002 when a more democratic committee could be set up.
• Before this interim committee is formed will you please email Jan Ward at j.ward@icrf.icnet.uk saying whether you think it is or is not a good idea. Unless sufficient people reply the committee will not be formed.

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