The SWIRM domain: a conserved module found in chromosomal proteins points to novel chromatin-modifying activities
10.1186/gb-2002-3-8-research0039
Crossref journal-article
Springer Science and Business Media LLC
Genome Biology (297)
Bibliography

Aravind, L., & Iyer, L. M. (2002). The SWIRM domain: a conserved module found in chromosomal proteins points to novel chromatin-modifying activities. Genome Biology, 3(8).

Authors 2
  1. L Aravind (first)
  2. Lakshminarayan M Iyer (additional)
References 53 Referenced 80
  1. Alberts B, Bray D, Lewis J, Raff M, Roberts K, Watson JD: In Molecular Biology of the Cell. New York and London: Garland Publishing;. 1994 / In Molecular Biology of the Cell. New York and London: Garland Publishing; by B Alberts (1994)
  2. Lodish H, Berk A, Zipursky SL, Matsudaira P, Baltimore D, Darnell JE: In Molecular Cell Biology. New York: WH Freeman;. 1999 / In Molecular Cell Biology. New York: WH Freeman; by H Lodish (1999)
  3. Lamond AI, Earnshaw WC: Structure and function in the nucleus. Science. 1998, 280: 547-553. 10.1126/science.280.5363.547. (10.1126/science.280.5363.547) / Science by AI Lamond (1998)
  4. Kouzarides T: Acetylation: a regulatory modification to rival phosphorylation?. EMBO J. 2000, 19: 1176-1179. 10.1093/emboj/19.6.1176. (10.1093/emboj/19.6.1176) / EMBO J by T Kouzarides (2000)
  5. Grant PA: A tale of histone modifications. Genome Biol. 2001, 2: reviews0003.1-0003.6. 10.1186/gb-2001-2-4-reviews0003. (10.1186/gb-2001-2-4-reviews0003) / Genome Biol by PA Grant (2001)
  6. Jenuwein T, Allis CD: Translating the histone code. Science. 2001, 293: 1074-1080. 10.1126/science.1063127. (10.1126/science.1063127) / Science by T Jenuwein (2001)
  7. Strahl BD, Allis CD: The language of covalent histone modifications. Nature. 2000, 403: 41-45. 10.1038/47412. (10.1038/47412) / Nature by BD Strahl (2000)
  8. Turner BM: Histone acetylation and an epigenetic code. BioEssays. 2000, 22: 836-845. 10.1002/1521-1878(200009)22:9<836::AID-BIES9>3.3.CO;2-O. (10.1002/1521-1878(200009)22:9<836::AID-BIES9>3.0.CO;2-X) / BioEssays by BM Turner (2000)
  9. Fry CJ, Peterson CL: Chromatin remodeling enzymes: who's on first?. Curr Biol. 2001, 11: R185-R197. 10.1016/S0960-9822(01)00090-2. (10.1016/S0960-9822(01)00090-2) / Curr Biol by CJ Fry (2001)
  10. Sudarsanam P, Winston F: The Swi/Snf family nucleosome-remodeling complexes and transcriptional control. Trends Genet. 2000, 16: 345-351. 10.1016/S0168-9525(00)02060-6. (10.1016/S0168-9525(00)02060-6) / Trends Genet by P Sudarsanam (2000)
  11. Wade PA, Wolffe AP: Transcriptional regulation: SWItching circuitry. Curr Biol. 1999, 9: R221-R224. 10.1016/S0960-9822(99)80134-1. (10.1016/S0960-9822(99)80134-1) / Curr Biol by PA Wade (1999)
  12. Muchardt C, Yaniv M: ATP-dependent chromatin remodelling: SWI/SNF and Co. are on the job. J Mol Biol. 1999, 293: 187-198. 10.1006/jmbi.1999.2999. (10.1006/jmbi.1999.2999) / J Mol Biol by C Muchardt (1999)
  13. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, et al: Initial sequencing and analysis of the human genome. Nature. 2001, 409: 860-921. 10.1038/35057062. (10.1038/35057062) / Nature by ES Lander (2001)
  14. Jacobson RH, Ladurner AG, King DS, Tjian R: Structure and function of a human TAFII250 double bromodomain module. Science. 2000, 288: 1422-1425. 10.1126/science.288.5470.1422. (10.1126/science.288.5470.1422) / Science by RH Jacobson (2000)
  15. Syntichaki P, Topalidou I, Thireos G: The Gcn5 bromodomain co-ordinates nucleosome remodelling. Nature. 2000, 404: 414-417. 10.1038/35006136. (10.1038/35006136) / Nature by P Syntichaki (2000)
  16. Dhalluin C, Carlson JE, Zeng L, He C, Aggarwal AK, Zhou MM: Structure and ligand of a histone acetyltransferase bromodomain. Nature. 1999, 399: 491-496. 10.1038/20974. (10.1038/20974) / Nature by C Dhalluin (1999)
  17. Jacobs SA, Khorasanizadeh S: Structure of HP1 chromodomain bound to a lysine 9-methylated histone H3 tail. Science. 2002, 295: 2080-2083. 10.1126/science.1069473. (10.1126/science.1069473) / Science by SA Jacobs (2002)
  18. Nakayama J, Rice JC, Strahl BD, Allis CD, Grewal SI: Role of histone H3 lysine 9 methylation in epigenetic control of heterochromatin assembly. Science. 2001, 292: 110-113. 10.1126/science.1060118. (10.1126/science.1060118) / Science by J Nakayama (2001)
  19. Koonin EV, Zhou S, Lucchesi JC: The chromo superfamily: new members, duplication of the chromo domain and possible role in delivering transcription regulators to chromatin. Nucleic Acids Res. 1995, 23: 4229-4233. (10.1093/nar/23.21.4229) / Nucleic Acids Res by EV Koonin (1995)
  20. Akhtar A, Zink D, Becker PB: Chromodomains are protein-RNA interaction modules. Nature. 2000, 407: 405-409. 10.1038/35030169. (10.1038/35030169) / Nature by A Akhtar (2000)
  21. Aasland R, Gibson TJ, Stewart AF: The PHD finger: implications for chromatin-mediated transcriptional regulation. Trends Biochem Sci. 1995, 20: 56-59. 10.1016/S0968-0004(00)88957-4. (10.1016/S0968-0004(00)88957-4) / Trends Biochem Sci by R Aasland (1995)
  22. Aasland R, Stewart AF, Gibson T: The SANT domain: a putative DNA-binding domain in the SWI-SNF and ADA complexes, the transcriptional co-repressor N-CoR and TFIIIB. Trends Biochem Sci. 1996, 21: 87-88. 10.1016/0968-0004(96)30009-1. (10.1016/0968-0004(96)30009-1) / Trends Biochem Sci by R Aasland (1996)
  23. Sterner DE, Wang X, Bloom MH, Simon GM, Berger SL: The SANT domain of Ada2 is required for normal acetylation of histones by the yeast SAGA complex. J Biol Chem. 2002, 277: 8178-8186. 10.1074/jbc.M108601200. (10.1074/jbc.M108601200) / J Biol Chem by DE Sterner (2002)
  24. Aravind L, Koonin EV: SAP - a putative DNA-binding motif involved in chromosomal organization. Trends Biochem Sci. 2000, 25: 112-114. 10.1016/S0968-0004(99)01537-6. (10.1016/S0968-0004(99)01537-6) / Trends Biochem Sci by L Aravind (2000)
  25. Aravind L, Landsman D: AT-hook motifs identified in a wide variety of DNA-binding proteins. Nucleic Acids Res. 1998, 26: 4413-4421. 10.1093/nar/26.19.4413. (10.1093/nar/26.19.4413) / Nucleic Acids Res by L Aravind (1998)
  26. Cairns BR, Lorch Y, Li Y, Zhang M, Lacomis L, Erdjument-Bromage H, Tempst P, Du J, Laurent B, Kornberg RD: RSC, an essential, abundant chromatin-remodeling complex. Cell. 1996, 87: 1249-1260. (10.1016/S0092-8674(00)81820-6) / Cell by BR Cairns (1996)
  27. Wang W, Xue Y, Zhou S, Kuo A, Cairns BR, Crabtree GR: Diversity and specialization of mammalian SWI/SNF complexes. Genes Dev. 1996, 10: 2117-2130. (10.1101/gad.10.17.2117) / Genes Dev by W Wang (1996)
  28. Peterson CL, Dingwall A, Scott MP: Five SWI/SNF gene products are components of a large multisubunit complex required for transcriptional enhancement. Proc Natl Acad Sci USA. 1994, 91: 2905-2908. (10.1073/pnas.91.8.2905) / Proc Natl Acad Sci USA by CL Peterson (1994)
  29. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25: 3389-3402. 10.1093/nar/25.17.3389. (10.1093/nar/25.17.3389) / Nucleic Acids Res by SF Altschul (1997)
  30. Crosby MA, Miller C, Alon T, Watson KL, Verrijzer CP, Goldman-Levi R, Zak NB: The trithorax group gene moira encodes a brahma-associated putative chromatin-remodeling factor in Drosophila melanogaster. Mol Cell Biol. 1999, 19: 1159-1170. (10.1128/MCB.19.2.1159) / Mol Cell Biol by MA Crosby (1999)
  31. Ding DQ, Tomita Y, Yamamoto A, Chikashige Y, Haraguchi T, Hiraoka Y: Large-scale screening of intracellular protein localization in living fission yeast cells by the use of a GFP-fusion genomic DNA library. Genes Cells. 2000, 5: 169-190. 10.1046/j.1365-2443.2000.00317.x. (10.1046/j.1365-2443.2000.00317.x) / Genes Cells by DQ Ding (2000)
  32. Humphrey GW, Wang Y, Russanova VR, Hirai T, Qin J, Nakatani Y, Howard BH: Stable histone deacetylase complexes distinguished by the presence of SANT domain proteins CoREST/kiaa0071 and Mta-L1. J Biol Chem. 2001, 276: 6817-6824. 10.1074/jbc.M007372200. (10.1074/jbc.M007372200) / J Biol Chem by GW Humphrey (2001)
  33. Ballas N, Battaglioli E, Atouf F, Andres M, Chenoweth J, Anderson M, Burger C, Moniwa M, Davie JR, Bowers WJ, et al: Regulation of neuronal traits by a novel transcriptional complex. Neuron. 2001, 31: 353-365. (10.1016/S0896-6273(01)00371-3) / Neuron by N Ballas (2001)
  34. Schaffer AA, Wolf YI, Ponting CP, Koonin EV, Aravind L, Altschul SF: IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices. Bioinformatics. 1999, 15: 1000-1011. 10.1093/bioinformatics/15.12.1000. (10.1093/bioinformatics/15.12.1000) / Bioinformatics by AA Schaffer (1999)
  35. Eddy SR: Profile hidden Markov models. Bioinformatics. 1998, 14: 755-763. 10.1093/bioinformatics/14.9.755. (10.1093/bioinformatics/14.9.755) / Bioinformatics by SR Eddy (1998)
  36. Caryl AP, Armstrong SJ, Jones GH, Franklin FC: A homologue of the yeast HOP1 gene is inactivated in the Arabidopsis meiotic mutant asy1. Chromosoma. 2000, 109: 62-71. 10.1007/s004120050413. (10.1007/s004120050413) / Chromosoma by AP Caryl (2000)
  37. Candau R, Moore PA, Wang L, Barlev N, Ying CY, Rosen CA, Berger SL: Identification of human proteins functionally conserved with the yeast putative adaptors ADA2 and GCN5. Mol Cell Biol. 1996, 16: 593-602. (10.1128/MCB.16.2.593) / Mol Cell Biol by R Candau (1996)
  38. Cuff JA, Clamp ME, Siddiqui AS, Finlay M, Barton GJ: JPred: a consensus secondary structure prediction server. Bioinformatics. 1998, 14: 892-893. 10.1093/bioinformatics/14.10.892. (10.1093/bioinformatics/14.10.892) / Bioinformatics by JA Cuff (1998)
  39. Treich I, Carlson M: Interaction of a Swi3 homolog with Sth1 provides evidence for a Swi/Snf-related complex with an essential function in Saccharomyces cerevisiae. Mol Cell Biol. 1997, 17: 1768-1775. (10.1128/MCB.17.4.1768) / Mol Cell Biol by I Treich (1997)
  40. Treich I, Ho L, Carlson M: Direct interaction between Rsc6 and Rsc8/Swh3, two proteins that are conserved in SWI/SNF-related complexes. Nucleic Acids Res. 1998, 26: 3739-3745. 10.1093/nar/26.16.3739. (10.1093/nar/26.16.3739) / Nucleic Acids Res by I Treich (1998)
  41. Ponting CP, Blake DJ, Davies KE, Kendrick-Jones J, Winder SJ: ZZ and TAZ: new putative zinc fingers in dystrophin and other proteins. Trends Biochem Sci. 1996, 21: 11-13. 10.1016/0968-0004(96)80878-4. (10.1016/S0968-0004(06)80020-4) / Trends Biochem Sci by CP Ponting (1996)
  42. Aravind L, Koonin EV: The HORMA domain: a common structural denominator in mitotic checkpoints, chromosome synapsis and DNA repair. Trends Biochem Sci. 1998, 23: 284-286. 10.1016/S0968-0004(98)01257-2. (10.1016/S0968-0004(98)01257-2) / Trends Biochem Sci by L Aravind (1998)
  43. Aravind L, Watanabe H, Lipman DJ, Koonin EV: Lineage-specific loss and divergence of functionally linked genes in eukaryotes. Proc Natl Acad Sci USA. 2000, 97: 11319-11324. 10.1073/pnas.200346997. (10.1073/pnas.200346997) / Proc Natl Acad Sci USA by L Aravind (2000)
  44. Baxevanis AD, Landsman D: The HMG-1 box protein family: classification and functional relationships. Nucleic Acids Res. 1995, 23: 1604-1613. (10.1093/nar/23.9.1604) / Nucleic Acids Res by AD Baxevanis (1995)
  45. Binda C, Coda A, Angelini R, Federico R, Ascenzi P, Mattevi A: A 30-angstrom-long U-shaped catalytic tunnel in the crystal structure of polyamine oxidase. Structure Fold Des. 1999, 7: 265-276. 10.1016/S0969-2126(99)80037-9. (10.1016/S0969-2126(99)80037-9) / Structure Fold Des by C Binda (1999)
  46. Binda C, Angelini R, Federico R, Ascenzi P, Mattevi A: Structural bases for inhibitor binding and catalysis in polyamine oxidase. Biochemistry. 2001, 40: 2766-2776. 10.1021/bi002751j. (10.1021/bi002751j) / Biochemistry by C Binda (2001)
  47. Sauve AA, Celic I, Avalos J, Deng H, Boeke JD, Schramm VL: Chemistry of gene silencing: the mechanism of NAD+-dependent deacetylation reactions. Biochemistry. 2001, 40: 15456-15463. 10.1021/bi011858j. (10.1021/bi011858j) / Biochemistry by AA Sauve (2001)
  48. Aravind L, Ponting CP: Homologues of 26S proteasome subunits are regulators of transcription and translation. Protein Sci. 1998, 7: 1250-1254. (10.1002/pro.5560070521) / Protein Sci by L Aravind (1998)
  49. Hofmann K, Bucher P: The PCI domain: a common theme in three multiprotein complexes. Trends Biochem Sci. 1998, 23: 204-205. 10.1016/S0968-0004(98)01217-1. (10.1016/S0968-0004(98)01217-1) / Trends Biochem Sci by K Hofmann (1998)
  50. Kim T, Hofmann K, von Arnim AG, Chamovitz DA: PCI complexes: pretty complex interactions in diverse signaling pathways. Trends Plant Sci. 2001, 6: 379-386. 10.1016/S1360-1385(01)02015-5. (10.1016/S1360-1385(01)02015-5) / Trends Plant Sci by T Kim (2001)
  51. Impala (National Center for Biotechnology Information). [ftp://ftp.ncbi.nih.gov/pub/impala/]
  52. CD-search. [http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi]
  53. Notredame C, Higgins DG, Heringa J: T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol. 2000, 302: 205-217. 10.1006/jmbi.2000.4042. (10.1006/jmbi.2000.4042) / J Mol Biol by C Notredame (2000)
Dates
Type When
Created 22 years, 10 months ago (Sept. 26, 2002, 8:07 a.m.)
Deposited 1 year, 3 months ago (April 25, 2024, 12:10 p.m.)
Indexed 22 hours, 31 minutes ago (Aug. 21, 2025, 1:42 p.m.)
Issued 23 years ago (July 24, 2002)
Published 23 years ago (July 24, 2002)
Published Online 23 years ago (July 24, 2002)
Funders 0

None

@article{Aravind_2002, title={The SWIRM domain: a conserved module found in chromosomal proteins points to novel chromatin-modifying activities}, volume={3}, ISSN={1474-760X}, url={http://dx.doi.org/10.1186/gb-2002-3-8-research0039}, DOI={10.1186/gb-2002-3-8-research0039}, number={8}, journal={Genome Biology}, publisher={Springer Science and Business Media LLC}, author={Aravind, L and Iyer, Lakshminarayan M}, year={2002}, month=jul }