Mission
The broad mission of ChromDB is display, annotate, and curate sequences of
two broad functional classes of biologically important proteins:
chromatin-associated proteins (CAPs) and RNA interference-associated proteins.
Plant proteins are the major focus of the work support by The Plant Genome
Research Program (PGRP) of the National Science Foundation. Our intent is to
produce intensively curated sequence information and make it available to the
research and teaching community in support of comparative analyses toward
understanding the chromatin proteome in plants, especially in important crop
species. In order to take do a comparative analysis, it is necessary to include
non-plant proteins in the database. Non-plant genes are not curated to the
degree carried out for plants and to automate the process of data import, our
non-plant genes are from the RefSeq database of NCBI. We reason that the
inclusion of non-plant, model organisms will broaden the relevance and
usefulness of ChromDB to the entire chromatin community and will provide a more
complete data set for phylogenetic analyses in support of the evolution of the
plant chromatin proteome.
Staff members
Database Documentation
Presentations and Posters
Publications
Gendler K, Paulsen T, Napoli C (2008) ChromDB: The Chromatin Database. Nucleic Acids Res 36:
298-302
Jorgensen RA, Doetsch N, Muller A, Que Q, Gendler K, Napoli CA (2006) A paragenetic perspective on integration
of RNA silencing into the epigenome and its role in the biology of higher plants. Cold Spring Harb Symp
Quant Biol 71: 481-485
Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, Witman GB, Terry A, Salamov A, Fritz-Laylin LK,
Marechal-Drouard L, Marshall WF, Qu LH, Nelson DR, Sanderfoot AA, Spalding MH, Kapitonov VV, Ren Q, Ferris P,
Lindquist E, Shapiro H, Lucas SM, Grimwood J, Schmutz J, Cardol P, Cerutti H, Chanfreau G, Chen CL, Cognat V,
Croft MT, Dent R, Dutcher S, Fernandez E, Fukuzawa H, Gonzalez-Ballester D, Gonzalez-Halphen D, Hallmann A,
Hanikenne M, Hippler M, Inwood W, Jabbari K, Kalanon M, Kuras R, Lefebvre PA, Lemaire SD, Lobanov AV, Lohr M,
Manuell A, Meier I, Mets L, Mittag M, Mittelmeier T, Moroney JV, Moseley J, Napoli C, Nedelcu AM, Niyogi K,
Novoselov SV, Paulsen IT, Pazour G, Purton S, Ral JP, Riano-Pachon DM, Riekhof W, Rymarquis L, Schroda M,
Stern D, Umen J, Willows R, Wilson N, Zimmer SL, Allmer J, Balk J, Bisova K, Chen CJ, Elias M, Gendler K,
Hauser C, Lamb MR, Ledford H, Long JC, Minagawa J, Page MD, Pan J, Pootakham W, Roje S, Rose A, Stahlberg E,
Terauchi AM, Yang P, Ball S, Bowler C, Dieckmann CL, Gladyshev VN, Green P, Jorgensen R, Mayfield S,
Mueller-Roeber B, Rajamani S, Sayre RT, Brokstein P, Dubchak I, Goodstein D, Hornick L, Huang YW, Jhaveri J,
Luo Y, Martinez D, Ngau WC, Otillar B, Poliakov A, Porter A, Szajkowski L, Werner G, Zhou K, Grigoriev IV,
Rokhsar DS, Grossman AR (2007) The Chlamydomonas genome reveals the evolution of key animal and plant
functions. Science 318(5848): 245-250
Palenik B, Grimwood J, Aerts A, Rouze P, Salamov A, Putnam N, Dupont C, Jorgensen R, Derelle E, Rombauts S,
Zhou K, Otillar R, Merchant SS, Podell S, Gaasterland T, Napoli C, Gendler K, Manuell A, Tai V, Vallon O,
Piganeau G, Jancek S, Heijde M, Jabbari K, Bowler C, Lohr M, Robbens S, Werner G, Dubchak I, Pazour GJ, Ren Q,
Paulsen I, Delwiche C, Schmutz J, Rokhsar D, Van de Peer Y, Moreau H, Grigoriev IV (2007) The tiny eukaryote
Ostreococcus provides genomic insights into the paradox of plankton speciation. Proc Natl Acad Sci U S
A 104(18): 7705-7710
Pandey R, Muller A, Napoli CA, Selinger DA, Pikaard CS, Richards EJ, Bender J, Mount DW, Jorgensen RA (2002)
Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests
functional diversification of chromatin modification among multicellular eukaryotes. Nucleic Acids
Res 30(23): 5036-5055
Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov
A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V,
Campbell M, Carlson J, Chalot M, Chapman J, Chen GL, Cooper D, Coutinho PM, Couturier J, Covert S, Cronk Q,
Cunningham R, Davis J, Degroeve S, Dejardin A, Depamphilis C, Detter J, Dirks B, Dubchak I, Duplessis S,
Ehlting J, Ellis B, Gendler K, Goodstein D, Gribskov M, Grimwood J, Groover A, Gunter L, Hamberger B, Heinze
B, Helariutta Y, Henrissat B, Holligan D, Holt R, Huang W, Islam-Faridi N, Jones S, Jones-Rhoades M, Jorgensen
R, Joshi C, Kangasjarvi J, Karlsson J, Kelleher C, Kirkpatrick R, Kirst M, Kohler A, Kalluri U, Larimer F,
Leebens-Mack J, Leple JC, Locascio P, Lou Y, Lucas S, Martin F, Montanini B, Napoli C, Nelson DR, Nelson C,
Nieminen K, Nilsson O, Pereda V, Peter G, Philippe R, Pilate G, Poliakov A, Razumovskaya J, Richardson P,
Rinaldi C, Ritland K, Rouze P, Ryaboy D, Schmutz J, Schrader J, Segerman B, Shin H, Siddiqui A, Sterky F,
Terry A, Tsai CJ, Uberbacher E, Unneberg P, Vahala J, Wall K, Wessler S, Yang G, Yin T, Douglas C, Marra M,
Sandberg G, Van de Peer Y, Rokhsar D (2006) The genome of black cottonwood, Populus trichocarpa (Torr. &
Gray). Science 313(5793): 1596-1604
Lin MK, Belanger H, Lee YJ, Varkonyi-Gasic E, Taoka K, Miura E, Xoconostle-Cazares B, Gendler K, Jorgensen RA,
Phinney B, Lough TJ, Lucas WJ (2007) FLOWERING LOCUS T protein may act as the long-distance florigenic signal
in the cucurbits. Plant Cell 19(5): 1488-1506