Schizosaccharomyces pombe Epigenome Home Page

  Pombe Genome Browser
  Welcome to the Schizosaccharomyces pombe Epigenome Home Page. This page is a gateway that provides access to comprehensive analysis of the epigenetic profile of the S. pombe genome. It makes use of the UCSC genome browser to integrate disparate genomic data sets, generated by Shiv Grewal's laboratory, under one common interface.  At the moment, this site contains information related to distributions of histone modifications such as methylation of histone H3 at lysine 4 and lysine 9, heterochromatin and RNAi components, and siRNAs described in Cam et al. Nature Genetics 37, 809 - 819 (2005). As more data sets become available, they will be added and integrated with existing data sets.

[UPDATE: January 7, 2008]: Data has been added for ChIP-chip analysis for the results described in Cam et al., Nature, Dec 19 Advance online publication (2007).

[UPDATE: July 9, 2007]: Data has been added for expression and ChIP-chip analysis for the results described in Nicolas et al. Nature Structural & Molecular Biology, April 2007, 14,372-380

[UPDATE: March 10, 2007]: Data has been added for Clr1, Clr2, Clr3, Mit1 and Ccq1 based on the results described in Sugiyama et al. Cell, Vol 128, Issue 3 , 9 February 2007, 491-504

[UPDATE: February 1, 2007]: Data has been added for SWIRM1 and SWIRM2 based on the results described in Nicolas et al. J. Biol. Chem., Vol. 281, Issue 47, 35983-35988, November 24, 2006

[UPDATE: June 21, 2006]: Data has been added for Pol III and TFIIIC based on the results described in Noma et al. Cell 125, 859-872 2006)



Select one of the buttons below to proceed

The raw data and the ratio data for the papers entitle "Comprehensive analysis of heterochromatin- and RNAi-mediated epigenetic control of the fission yeast genome", "A Role for TFIIIC Transcription Factor Complex in Genome Organization", "Fission Yeast Homologs of Human Histone H3 Lysine 4 Demethylase Regulate a Common Set of Genes with Diverse Functions", "SHREC, an Effector Complex for Heterochromatic Transcriptional Silencing", "Distinct roles of HDAC complexes in promoter silencing, antisense suppression and DNA damage protection", and "Host genome surveillance for retrotransposons by transposon-derived proteins", are available here.

Instructions

For those not familiar with the workings of the UCSC Genome Browser we provide the following brief introduction. More detailed information about the operation of this software can be found on the HELP page.

Default Display The default view shows the S. pombe genome with mapping data of siRNA and chromatin modifications, for the wild-type organism. However, it is possible to surpress, or compress (dense) the display of this data, and it is also possible to display additional tracks showing the same data in a mutant background (clr4D - clr4 deletion ). Also shown in the default view is the genome position of annotated proteins, and the mapping of the probes used in this study.

Displaying Data Each data item is controlled by a button. Clicking on the name above the button provides information about the data being plotted and additional control over the display. Each button offers at least 3 choices:

Navigation Within the browser one can zoom and center the display by clicking within the Base Position ruler at the top of the image. One can also zoom the display in/out by using the buttons at the top of the page. It is also possible to type in a specific chromosome or position range into the box labelled "position" (e.g. chr1 shows all of chromosome 1, while chr1:5000-10000 show chromosome 1 between base 5,000 and 10,000.

Searching It is possible to search for a particular gene by typeing its name into the box labelled "position". Searching is currently limited to gene/protein name. Searches are case insensitive, and are considered to have a wild card following them - thus searching for meu will match all names beginning with meu (e.g. meu1, meu22 etc).

Search examples: ura4 will immediately locate you to the Ura4 gene locus, and SPCC330 will provide a list of matching genes whose name begins with SPCC330.


The UCSC Genome Browser was created by the Genome Bioinformatics Group of UC Santa Cruz. Software Copyright (c) The Regents of the University of California. All rights reserved.
This site is a collaboration between the NIH Helix Systems, CIT the Genome Analysis Unit, NCI and the Grewal Lab, NCI. Technical questions about access and connectivity should be addressed to staff@helix.nih.gov while questions about the scientific content should be addressed to Shiv Grewal