S Henikoff

Summary

Affiliation: Fred Hutchinson Cancer Research Center
Country: USA

Publications

  1. pmc Extensive demethylation of repetitive elements during seed development underlies gene imprinting
    Mary Gehring
    Howard Hughes Medical Institute HHMI, Fred Hutchinson Cancer Research Center FHCRC, 1100 Fairview Avenue North, Seattle, WA 98109, USA
    Science 324:1447-51. 2009
  2. doi request reprint Distinct chromatin features characterize different classes of repeat sequences in Drosophila melanogaster
    Kristina Krassovsky
    Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109, USA
    BMC Genomics 15:105. 2014
  3. pmc Epigenetics & chromatin: interactions and processes
    Steven Henikoff
    Howard Hughes Medical Institute and Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, WA, 98109 1024, Seattle, USA
    Epigenetics Chromatin 6:2. 2013
  4. pmc Chromatin roadblocks to reprogramming 50 years on
    Peter J Skene
    Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    BMC Biol 10:83. 2012
  5. pmc The unconventional structure of centromeric nucleosomes
    Steven Henikoff
    Howard Hughes Medical Institute and Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109 1024, USA
    Chromosoma 121:341-52. 2012
  6. pmc A unified phylogeny-based nomenclature for histone variants
    Paul B Talbert
    Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
    Epigenetics Chromatin 5:7. 2012
  7. pmc "Point" centromeres of Saccharomyces harbor single centromere-specific nucleosomes
    Steven Henikoff
    Basic Sciences Division, Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109 1024, USA
    Genetics 190:1575-7. 2012
  8. pmc Adaptive evolution of centromere proteins in plants and animals
    Paul B Talbert
    Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 1024, USA
    J Biol 3:18. 2004
  9. pmc Capturing the dynamic epigenome
    Roger B Deal
    Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    Genome Biol 11:218. 2010
  10. pmc Silencing of transposons in plant genomes: kick them when they're down
    Daniel Zilberman
    Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
    Genome Biol 5:249. 2004

Detail Information

Publications141 found, 100 shown here

  1. pmc Extensive demethylation of repetitive elements during seed development underlies gene imprinting
    Mary Gehring
    Howard Hughes Medical Institute HHMI, Fred Hutchinson Cancer Research Center FHCRC, 1100 Fairview Avenue North, Seattle, WA 98109, USA
    Science 324:1447-51. 2009
    ..These data suggest that imprinting in plants evolved from targeted methylation of transposable element insertions near genic regulatory elements followed by positive selection when the resulting expression change was advantageous...
  2. doi request reprint Distinct chromatin features characterize different classes of repeat sequences in Drosophila melanogaster
    Kristina Krassovsky
    Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109, USA
    BMC Genomics 15:105. 2014
    ..Genome-wide profiling of chromatin features such as histone tail modifications and DNA-binding proteins relies on alignment to the reference genome and hence excludes highly repetitive sequences...
  3. pmc Epigenetics & chromatin: interactions and processes
    Steven Henikoff
    Howard Hughes Medical Institute and Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, WA, 98109 1024, Seattle, USA
    Epigenetics Chromatin 6:2. 2013
    ..Epigenetics & Chromatin has now launched a special article series based on the general themes of the conference...
  4. pmc Chromatin roadblocks to reprogramming 50 years on
    Peter J Skene
    Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    BMC Biol 10:83. 2012
    ..Among the issues addressed in Gurdon's latest work are the chromatin impediments to artificially induced reprogramming, discovered by Shinya Yamanaka, who shared the award with Gurdon...
  5. pmc The unconventional structure of centromeric nucleosomes
    Steven Henikoff
    Howard Hughes Medical Institute and Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109 1024, USA
    Chromosoma 121:341-52. 2012
    ....
  6. pmc A unified phylogeny-based nomenclature for histone variants
    Paul B Talbert
    Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
    Epigenetics Chromatin 5:7. 2012
    ..For clarity and searchability, we encourage the use of descriptors that are separate from the phylogeny-based variant name to indicate developmental and other properties of variants that may be independent of structure...
  7. pmc "Point" centromeres of Saccharomyces harbor single centromere-specific nucleosomes
    Steven Henikoff
    Basic Sciences Division, Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109 1024, USA
    Genetics 190:1575-7. 2012
    ..However, high-resolution mapping demonstrates that there is only one CenH3 nucleosome per centromere, providing biochemical confirmation of the point centromere model...
  8. pmc Adaptive evolution of centromere proteins in plants and animals
    Paul B Talbert
    Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 1024, USA
    J Biol 3:18. 2004
    ..Most plant, animal and fungal centromeres also bind a large protein, centromere protein C (CENP-C), that is characterized by a single 24 amino-acid motif (CENPC motif)...
  9. pmc Capturing the dynamic epigenome
    Roger B Deal
    Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    Genome Biol 11:218. 2010
    ..Recent approaches have allowed direct measurements of chromatin dynamics, providing deeper insights into processes such as transcription, DNA replication and epigenetic inheritance...
  10. pmc Silencing of transposons in plant genomes: kick them when they're down
    Daniel Zilberman
    Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
    Genome Biol 5:249. 2004
    ..DNA and histone methylation are not always sufficient to maintain silencing, and RNA-based reinforcement can be needed to maintain as well as initiate it...
  11. pmc Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis
    Robert K Tran
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    Genome Biol 6:R90. 2005
    ..However, the relationship between different cytosine methylation pathways and their preferred targets is not known...
  12. pmc Tissue-specific variation in DNA methylation levels along human chromosome 1
    Cecilia De Bustos
    Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
    Epigenetics Chromatin 2:7. 2009
    ..CONCLUSION: The varied patterns of methylation differences detected between tissues by our methylation profiling method reinforce the potential functional significance of regional differences in methylation levels outside of CpG islands...
  13. pmc Discovery of chemically induced mutations in rice by TILLING
    Bradley J Till
    Fred Hutchinson Cancer Research Center, Seattle, WA 98107, USA
    BMC Plant Biol 7:19. 2007
    ..TILLING (Targeting Induced Local Lesions in Genomes), a general reverse genetic technique that combines traditional mutagenesis with high throughput methods for mutation discovery, is such a method...
  14. pmc Discovery of induced point mutations in maize genes by TILLING
    Bradley J Till
    Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    BMC Plant Biol 4:12. 2004
    ....
  15. pmc TILLING to detect induced mutations in soybean
    Jennifer L Cooper
    Fred Hutchinson Cancer Research Center, Seattle, WA 98107, USA
    BMC Plant Biol 8:9. 2008
    ..We have applied TILLING to four mutagenized soybean populations, three of which were treated with ethyl methanesulfonate (EMS) and one with N-nitroso-N-methylurea (NMU)...
  16. ncbi request reprint Blocks+: a non-redundant database of protein alignment blocks derived from multiple compilations
    S Henikoff
    Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109 1024, USA
    Bioinformatics 15:471-9. 1999
    ..However, Prosite is incomplete, and families from other databases are now available to expand coverage of the Blocks Database...
  17. pmc Rapid changes in plant genomes
    Steven Henikoff
    Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    Plant Cell 17:2852-5. 2005
  18. ncbi request reprint Assembly of variant histones into chromatin
    Steven Henikoff
    Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    Annu Rev Cell Dev Biol 21:133-53. 2005
    ..Taken together, these findings indicate that chromosome architecture can be highly dynamic at the most fundamental level, with epigenetic consequences...
  19. pmc Heterochromatic deposition of centromeric histone H3-like proteins
    S Henikoff
    Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109 1024, USA
    Proc Natl Acad Sci U S A 97:716-21. 2000
    ..Rather, the heterochromatic state itself may help localize centromeric components...
  20. ncbi request reprint Near the edge of a chromosome's "black hole"
    Steven Henikoff
    Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 1024, USA
    Trends Genet 18:165-7. 2002
    ..However, high-resolution mapping of a human X-centromere border reveals a remarkable structure, including a gradient of alpha-satellite divergence up to the edge of the youngest and most homogeneous repeats...
  21. ncbi request reprint Centromeric chromatin: what makes it unique?
    Steven Henikoff
    Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, PO Box 19024, Seattle, WA 98109 1024, USA
    Curr Opin Genet Dev 15:177-84. 2005
    ..Other studies have taken a comparative approach focusing on centromere-specific proteins, of which mammalian CENP-A and CENP-C are the prototypes. Elucidating the assembly and structure of chromatin at centromeres remain key challenges...
  22. ncbi request reprint Histone variants, nucleosome assembly and epigenetic inheritance
    Steven Henikoff
    Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
    Trends Genet 20:320-6. 2004
  23. pmc TILLING. Traditional mutagenesis meets functional genomics
    Steven Henikoff
    Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    Plant Physiol 135:630-6. 2004
    ..We describe public TILLING efforts in Arabidopsis and other organisms, including maize (Zea mays) and zebrafish. We conclude that TILLING, a technology developed in plants, is rapidly being adopted in other systems...
  24. ncbi request reprint Single-nucleotide mutations for plant functional genomics
    Steven Henikoff
    Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    Annu Rev Plant Biol 54:375-401. 2003
    ..Its general applicability leads to the expectation that traditional mutagenesis followed by high-throughput detection will become increasingly important for plant functional genomics...
  25. ncbi request reprint Nucleosomes at active promoters: unforgettable loss
    Steven Henikoff
    Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
    Cancer Cell 12:407-9. 2007
    ..After demethylation by drug treatment, nucleosomes are permanently lost as transcription becomes reactivated. Thus, epigenetic maintenance of gene expression may require that promoters are maintained free of nucleosomes...
  26. ncbi request reprint Nucleosome destabilization in the epigenetic regulation of gene expression
    Steven Henikoff
    Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109, USA
    Nat Rev Genet 9:15-26. 2008
    ....
  27. ncbi request reprint Blocks-based methods for detecting protein homology
    J G Henikoff
    Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    Electrophoresis 21:1700-6. 2000
    ....
  28. pmc Genome-wide profiling of salt fractions maps physical properties of chromatin
    Steven Henikoff
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109 1024, USA
    Genome Res 19:460-9. 2009
    ....
  29. doi request reprint Summary: The nucleus--a close-knit community of dynamic structures
    S Henikoff
    Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    Cold Spring Harb Symp Quant Biol 75:607-15. 2010
    ..By considering these complex processes in the context of the nucleus, the Symposium provided a coherent view of the genome in its native habitat...
  30. doi request reprint Epigenetic inheritance of centromeres
    S Henikoff
    Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    Cold Spring Harb Symp Quant Biol 75:51-60. 2010
    ..We propose that the opposite wrapping of DNA around a half-nucleosome core particle facilitates a mode of inheritance that does not depend on DNA sequence, DNA modification or protein conformation...
  31. doi request reprint Histone modification: cause or cog?
    Steven Henikoff
    Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
    Trends Genet 27:389-96. 2011
    ..Based on this view, histone modifications and variants contribute to diversification of a chromatin landscape shaped by dynamic processes that are driven primarily by transcription and nucleosome remodeling...
  32. ncbi request reprint Modulation of a transcription factor counteracts heterochromatic gene silencing in Drosophila
    K Ahmad
    Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    Cell 104:839-47. 2001
    ..We propose that variegation occurs because heterochromatin inhibits the transient exposure of factor binding sites...
  33. pmc Adaptive evolution of Cid, a centromere-specific histone in Drosophila
    H S Malik
    Howard Hughes Medical Institute, Seattle, Washington 98109, USA
    Genetics 157:1293-8. 2001
    ..Thus, centromeric H3-like proteins may act as adaptors between evolutionarily labile centromeric DNA and the conserved kinetochore machinery...
  34. ncbi request reprint Nuclear organization and gene expression: homologous pairing and long-range interactions
    S Henikoff
    Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98104, USA
    Curr Opin Cell Biol 9:388-95. 1997
    ..Recent work has revealed that such influences are widespread in eukaryotes and that chromosome architecture is likely to be of fundamental importance for nuclear structure and function...
  35. pmc Pairing-dependent mislocalization of a Drosophila brown gene reporter to a heterochromatic environment
    G L Sass
    Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109 1024, USA
    Genetics 152:595-604. 1999
    ..We also find that an ensnared distal copy of bw that is interrupted by a heterochromatic insertion enhances silencing. This demonstrates that bw can be simultaneously acted upon by pericentric and distal blocks of heterochromatin...
  36. pmc Changes in chromosomal localization of heterochromatin-binding proteins during the cell cycle in Drosophila
    J S Platero
    Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109 1024, USA
    J Cell Biol 140:1297-306. 1998
    ..Upon decondensation, GAGA factor and Prod shift from low affinity sites within satellite DNA back to euchromatic sites as a self-assembly process...
  37. pmc Comparative analysis of position-effect variegation mutations in Drosophila melanogaster delineates the targets of modifiers
    G L Sass
    Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    Genetics 148:733-41. 1998
    ..In addition, our observations support a model in which there are different constraints on the process of heterochromatin-induced silencing in classical vs. nonclassical PEV mutations...
  38. ncbi request reprint Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase
    B van Steensel
    Fred Hutchinson Cancer Research Center and Howard Hughes Medical Institute, Seattle, WA 98109, USA
    Nat Biotechnol 18:424-8. 2000
    ..Using DamID, we identified a number of expected and unexpected target loci for Drosophila heterochromatin protein 1. DamID has potential for genome-wide mapping of in vivo targets of chromatin proteins in various eukaryotes...
  39. pmc Heterochromatic trans-inactivation of Drosophila white transgenes
    L E Martin-Morris
    Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109 1024, USA
    Genetics 147:671-7. 1997
    ..These findings suggest that many Drosophila genes, in many positions in the genome, can sense the heterochromatic state of a paired homologue...
  40. pmc Transgene repeat arrays interact with distant heterochromatin and cause silencing in cis and trans
    D R Dorer
    Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109 1024, USA
    Genetics 147:1181-90. 1997
    ..Such spreading of heterochromatic silencing correlates with array size. Finally, white transgene arrays cause pairing-dependent silencing of a non-variegating white insertion at the homologous position...
  41. ncbi request reprint Dosage-dependent modification of position-effect variegation in Drosophila
    S Henikoff
    Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98104, USA
    Bioessays 18:401-9. 1996
    ....
  42. pmc Conservation of brown gene trans-inactivation in Drosophila
    L E Martin-Morris
    Fred Hutchinson Cancer Research Center, Seattle, Washington 98104, USA
    Genetics 140:193-9. 1995
    ..melanogaster gene, these genes must share regulatory sequences as well as protein coding homology. These results support a model in which trans-inactivation is mediated by a heterochromatin-sensitive transcription factor...
  43. pmc Modification of the Drosophila heterochromatic mutation brownDominant by linkage alterations
    P B Talbert
    Fred Hutchinson Cancer Research Center, Seattle, Washington 98104
    Genetics 136:559-71. 1994
    ..These results support the notion that heterochromatin formation at a genetic locus depends on its location within the nucleus...
  44. ncbi request reprint The centromere paradox: stable inheritance with rapidly evolving DNA
    S Henikoff
    Howard Hughes Medical Institute Research Laboratories, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
    Science 293:1098-102. 2001
    ..Incompatibilities between rapidly evolving centromeric components may be responsible for both the organization of centromeric regions and the reproductive isolation of emerging species...
  45. ncbi request reprint A distal heterochromatic block displays centromeric activity when detached from a natural centromere
    J S Platero
    Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    Mol Cell 4:995-1004. 1999
    ..Our findings suggest that centromere competence is innate to satellite-containing blocks of heterochromatin, challenging models for centromere identity in which competence is an acquired characteristic...
  46. ncbi request reprint Introduction of a DNA methyltransferase into Drosophila to probe chromatin structure in vivo
    D R Wines
    Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98104, USA
    Chromosoma 104:332-40. 1996
    ..Silencing of lacZ during development differed from silencing of an adjacent white eye pigment reporter gene in the adult, as though chromatin structure can undergo dynamic alterations during development...
  47. ncbi request reprint Trans-sensing effects: the ups and downs of being together
    S Henikoff
    Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109 1024, USA
    Cell 93:329-32. 1998
  48. ncbi request reprint Epigenetics, histone H3 variants, and the inheritance of chromatin states
    S Henikoff
    Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    Cold Spring Harb Symp Quant Biol 69:235-43. 2004
  49. pmc A reexamination of spreading of position-effect variegation in the white-roughest region of Drosophila melanogaster
    P B Talbert
    Fred Hutchinson Cancer Research Center and Howard Hughes Medical Institute, Seattle, Washington 98109 1024, USA
    Genetics 154:259-72. 2000
    ..We frequently observed rough eye tissue that is pigmented, as though an active white gene is skipped...
  50. pmc Centromeres are specialized replication domains in heterochromatin
    K Ahmad
    Howard Hughes Medical Institute, and Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    J Cell Biol 153:101-10. 2001
    ..We suggest that late-replicating pericentric heterochromatin helps to maintain embedded centromeres by blocking conventional nucleosome assembly early in S phase, thereby allowing the deposition of centromeric histones...
  51. pmc Conserved arrangement of nested genes at the Drosophila Gart locus
    S Henikoff
    Fred Hutchinson Cancer Research Center, Seattle, Washington 98104
    Genetics 117:711-25. 1987
    ..We discuss the possibility that shared cis-acting regulatory sites might enhance transcription of both genes and help explain their nested arrangement...
  52. pmc Trans-inactivation of the Drosophila brown gene: evidence for transcriptional repression and somatic pairing dependence
    S Henikoff
    Fred Hutchinson Cancer Research Center, Seattle, WA 98104
    Proc Natl Acad Sci U S A 86:6704-8. 1989
    ..We propose that direct transmission of the altered chromatin structure characteristic of position-effect variegation (heterochromatinization) occurs between paired homologs in the region of the brown locus...
  53. pmc The brown protein of Drosophila melanogaster is similar to the white protein and to components of active transport complexes
    T D Dreesen
    Fred Hutchinson Cancer Research Center, Seattle, Washington 98104
    Mol Cell Biol 8:5206-15. 1988
    ....
  54. pmc A reconsideration of the mechanism of position effect
    S Henikoff
    Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98104
    Genetics 138:1-5. 1994
  55. ncbi request reprint Characterization of sequences responsible for trans-inactivation of the Drosophila brown gene
    L E Martin-Morris
    Howard Hughes Medical Institute, Seattle, Washington
    Cold Spring Harb Symp Quant Biol 58:577-84. 1993
  56. pmc Large-scale chromosomal movements during interphase progression in Drosophila
    A K Csink
    Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109 1024, USA
    J Cell Biol 143:13-22. 1998
    ....
  57. ncbi request reprint Expansions of transgene repeats cause heterochromatin formation and gene silencing in Drosophila
    D R Dorer
    Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98104
    Cell 77:993-1002. 1994
    ..We propose that pairing of repeats underlies heterochromatin formation and is responsible for diverse gene silencing phenomena in animals and plants...
  58. ncbi request reprint Protein family classification based on searching a database of blocks
    S Henikoff
    Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98104
    Genomics 19:97-107. 1994
    ..We also show how searching a database of blocks can be used to detect repeated domains and to find distinct cross-family relationships that were missed in searches of sequence databases...
  59. pmc The hinge and chromo shadow domain impart distinct targeting of HP1-like proteins
    J F Smothers
    Howard Hughes Medical Institute, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109 1024, USA
    Mol Cell Biol 21:2555-69. 2001
    ..We propose that these targeting features allow different HP1 complexes to be distinctly sequestered in organisms that harbor multiple HP1-like proteins...
  60. ncbi request reprint The HP1 chromo shadow domain binds a consensus peptide pentamer
    J F Smothers
    Howard Hughes Medical Institute, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109 1024, USA
    Curr Biol 10:27-30. 2000
    ..In general, chromo domains may function by avidly binding short peptides at the surface of chromatin-associated proteins...
  61. ncbi request reprint Position effect and related phenomena
    S Henikoff
    Fred Hutchinson Cancer Research Center, Seattle, Washington
    Curr Opin Genet Dev 2:907-12. 1992
    ..In addition, telomeric position effect in yeast provides a new model system for the study of the quasi-stable inheritance of an inactivated state...
  62. ncbi request reprint Adaptive evolution of the histone fold domain in centromeric histones
    Jennifer L Cooper
    Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
    Mol Biol Evol 21:1712-8. 2004
    ....
  63. ncbi request reprint High-throughput TILLING for Arabidopsis
    Bradley J Till
    Basic Sciences Division, Fred Hutchison Cancer Research Center, Department of Biology, University of Washington, Seattle, USA
    Methods Mol Biol 323:127-35. 2006
    ..High-throughput TILLING has been adopted by the Arabidopsis TILLING Project (ATP) to provide allelic series of point mutations for the general Arabidopsis community...
  64. pmc Spectrum of chemically induced mutations from a large-scale reverse-genetic screen in Arabidopsis
    Elizabeth A Greene
    Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    Genetics 164:731-40. 2003
    ..As expected for alkylation of guanine by EMS, >99% of mutations are G/C-to-A/T transitions. A nearest-neighbor bias around the mutated base pair suggests that mismatch repair counteracts alkylation damage...
  65. pmc Drosophila genomic sequence annotation using the BLOCKS+ database
    J G Henikoff
    Howard Hughes Medical Institute, Seattle, Washington 98109 1024, USA
    Genome Res 10:543-6. 2000
    ..We used the search results to improve BLOCKS+ by identifying compositionally biased blocks. Our results confirm that protein family databases can be used effectively in automated sequence annotation efforts...
  66. ncbi request reprint Position-effect variegation after 60 years
    S Henikoff
    Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA
    Trends Genet 6:422-6. 1990
    ..However, new insights are being gained from recent studies of genetic modifiers, new model systems, and variegating genes showing exceptional behavior...
  67. pmc Distance and pairing effects on the brownDominant heterochromatic element in Drosophila
    S Henikoff
    Fred Hutchinson Cancer Research Center, Seattle, Washington 98104, USA
    Genetics 140:1007-17. 1995
    ....
  68. ncbi request reprint Something from nothing: the evolution and utility of satellite repeats
    A K Csink
    Fred Hutchinson, Cancer Research Center, Seattle, WA 98109 1024, USA
    Trends Genet 14:200-4. 1998
    ..To account for the ubiquity and pericentric localization of satellites, we propose that they are utilized to maintain regions of late replication, thus ensuring that the centromere is the last region to replicate on a chromosome...
  69. ncbi request reprint DNA methylation dynamics in plant genomes
    Mary Gehring
    Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
    Biochim Biophys Acta 1769:276-86. 2007
    ..Therefore, epimutations might be an important source of variation during plant evolution...
  70. ncbi request reprint Conspiracy of silence among repeated transgenes
    S Henikoff
    Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 1024, USA
    Bioessays 20:532-5. 1998
    ....
  71. ncbi request reprint Chromatin profiling using targeted DNA adenine methyltransferase
    B van Steensel
    Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
    Nat Genet 27:304-8. 2001
    ..High-resolution, genome-wide maps of target loci of chromatin proteins ('chromatin profiles') provide new insights into chromatin structure and gene regulation...
  72. ncbi request reprint Genome-scale profiling of histone H3.3 replacement patterns
    Yoshiko Mito
    Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109, USA
    Nat Genet 37:1090-7. 2005
    ..3 from upstream to downstream of transcription units. We propose that deposition and inheritance of actively modified H3.3 in regulatory regions maintains transcriptionally active chromatin...
  73. ncbi request reprint Genome-wide profiling of DNA methylation reveals transposon targets of CHROMOMETHYLASE3
    Rachel Tompa
    Howard Hughes Medical Institute and Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    Curr Biol 12:65-8. 2002
    ..Methylation profiling has potential applications in disease research and diagnostic screening...
  74. pmc Recurrent evolution of DNA-binding motifs in the Drosophila centromeric histone
    Harmit S Malik
    Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    Proc Natl Acad Sci U S A 99:1449-54. 2002
    ..The recurrent evolution of these motifs in CenH3 suggests a packaging function for the N-terminal tail, which results in a unique chromatin organization at the primary constriction, the cytological marker of centromeres...
  75. ncbi request reprint Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription
    Daniel Zilberman
    Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109, USA
    Nat Genet 39:61-9. 2007
    ..Our results indicate that genic transcription and DNA methylation are closely interwoven processes...
  76. pmc Predicting deleterious amino acid substitutions
    P C Ng
    Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    Genome Res 11:863-74. 2001
    ..may be used to identify plausible disease candidates among the SNPs that cause missense substitutions...
  77. pmc Superior performance in protein homology detection with the Blocks Database servers
    S Henikoff
    Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109 1024, USA
    Nucleic Acids Res 26:309-12. 1998
    ..Utilizing the trypsin family to evaluate performance, we illustrate the superiority of blocks-based tools over expert pairwise searching or Hidden Markov Models...
  78. ncbi request reprint A pairing-sensitive element that mediates trans-inactivation is associated with the Drosophila brown gene
    T D Dreesen
    Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98104
    Genes Dev 5:331-40. 1991
    ..The chromosome-local nature of the phenomenon and its extreme sensitivity to small disruptions of somatic pairing leads to a model in which a regulator of the brown gene is inactivated by direct contact with heterochromatic proteins...
  79. ncbi request reprint Poised for contagion: evolutionary origins of the infectious abilities of invertebrate retroviruses
    H S Malik
    Fred Hutchinson Cancer Research Center, Seattle, Washington 98109 USA
    Genome Res 10:1307-18. 2000
    ..This has implications for the evolutionary history of retroviruses as well as for the potential ability of all LTR-retrotransposable elements to become infectious agents...
  80. ncbi request reprint Scores for sequence searches and alignments
    S Henikoff
    Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98104, USA
    Curr Opin Struct Biol 6:353-60. 1996
    ..Comprehensive evaluations can effectively guide the choice of scores for sequence alignment and searching applications, including those that aid in the prediction of protein structures...
  81. ncbi request reprint Genetic modification of heterochromatic association and nuclear organization in Drosophila
    A K Csink
    Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98104, USA
    Nature 381:529-31. 1996
    ..This suggests that heterochromatin and proteins involved in its formation provide a structural framework for the interphase nucleus...
  82. pmc A moveable 5' splice site in adenine phosphoribosyltransferase genes of Drosophila species
    D Johnson
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98104
    Mol Cell Biol 9:2220-3. 1989
    ..The production of aberrantly spliced transcripts as a normal feature of gene expression supports a general model of eucaryotic gene evolution through alternative splicing and moveable splice junctions...
  83. pmc A native chromatin purification system for epigenomic profiling in Caenorhabditis elegans
    Siew Loon Ooi
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
    Nucleic Acids Res 38:e26. 2010
    ..3. This versatile two-component approach has the potential of facilitating genome-wide chromatin dynamics and regulatory site identification in C. elegans...
  84. pmc Centromeric nucleosomes induce positive DNA supercoils
    Takehito Furuyama
    Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    Cell 138:104-13. 2009
    ..The mutual incompatibility of nucleosomes with opposite topologies could explain how centromeres are efficiently maintained as unique loci on chromosomes...
  85. pmc A simple method for gene expression and chromatin profiling of individual cell types within a tissue
    Roger B Deal
    Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    Dev Cell 18:1030-40. 2010
    ..This method should be applicable to any organism that is amenable to transformation...
  86. ncbi request reprint Histone replacement marks the boundaries of cis-regulatory domains
    Yoshiko Mito
    Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
    Science 315:1408-11. 2007
    ..Our results suggest the existence of a continuous process that disrupts nucleosomes and maintains accessibility of cis-regulatory elements...
  87. pmc Tetrameric structure of centromeric nucleosomes in interphase Drosophila cells
    Yamini Dalal
    Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
    PLoS Biol 5:e218. 2007
    ..This demonstration of stable half-nucleosomes in vivo provides a possible basis for the instability of centromeric nucleosomes that are deposited in euchromatic regions, which might help maintain centromere identity...
  88. ncbi request reprint The histone variant H3.3 marks active chromatin by replication-independent nucleosome assembly
    Kami Ahmad
    Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
    Mol Cell 9:1191-200. 2002
    ..RI substitution of H3.3 provides a mechanism for the immediate activation of genes that are silenced by histone modification. Inheritance of newly deposited nucleosomes may then mark sites as active loci...
  89. ncbi request reprint DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes
    Robert K Tran
    Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
    Curr Biol 15:154-9. 2005
    ..We suggest that CG methylation clusters silence cryptic promoters that arise sporadically within transcription units...
  90. ncbi request reprint Visualizing gene expression: an unfolding story
    Steven Henikoff
    Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    Cell 116:633-4. 2004
    ..They find that local decondensation of the template is accompanied by profound changes in chromatin composition...
  91. pmc Embedding strategies for effective use of information from multiple sequence alignments
    S Henikoff
    Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98104, USA
    Protein Sci 6:698-705. 1997
    ..Embedding PSSMs or consensus residues into a representative sequence improves searching performance by extracting multiple alignment information from motif regions while retaining single sequence information where alignment is uncertain...
  92. pmc Somatic instability of a Drosophila chromosome
    D R Wines
    Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98104
    Genetics 131:683-91. 1992
    ..This unique chromosome may provide a tool for the genetic and molecular dissection of a higher eukaryotic centromere...
  93. ncbi request reprint Using substitution probabilities to improve position-specific scoring matrices
    J G Henikoff
    Howard Hughes Medical Institute, Basic Sciences Division, Seattle, WA 98104, USA
    Comput Appl Biosci 12:135-43. 1996
    ..In extensive empirical tests, this position-based method out-performed other pseudo-count methods and was a substantial improvement over the traditional average score method used for constructing profiles...
  94. ncbi request reprint Unusual organizational features of the Drosophila Gart locus are not conserved within Diptera
    D V Clark
    Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98104
    J Mol Evol 35:51-9. 1992
    ..In addition, the extremely rapid divergence of coding sequence seen for members of the tandemly duplicated AIRS domain in Drosophila is found to be much less rapid in Chironomus...
  95. pmc Chaperone-mediated assembly of centromeric chromatin in vitro
    Takehito Furuyama
    Fred Hutchinson Cancer Research Center and Howard Hughes Medical Institute, 1100 Fairview Avenue North, Seattle, WA 98109, USA
    Proc Natl Acad Sci U S A 103:6172-7. 2006
    ..3, suggesting that centromeres are maintained by a passive mechanism that involves exclusion of the complexes that deposit canonical H3s during replication and transcription...
  96. pmc Large-scale discovery of induced point mutations with high-throughput TILLING
    Bradley J Till
    Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    Genome Res 13:524-30. 2003
    ..The tools and methodologies described here can be adapted to create similar facilities for other organisms...
  97. ncbi request reprint Epigenetic inheritance in Arabidopsis: selective silence
    Daniel Zilberman
    Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
    Curr Opin Genet Dev 15:557-62. 2005
    ..Much of the epigenetic machinery of many organisms, including Arabidopsis, appears to be directed at silencing viruses and transposable elements, with epigenetic regulation of endogenous genes being mostly derived from such processes...
  98. ncbi request reprint High-throughput TILLING for functional genomics
    Bradley J Till
    BasicSciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
    Methods Mol Biol 236:205-20. 2003
    ..High-throughput TILLING has been adopted by the Arabidopsis TILLING Project (ATP) to provide allelic series of point mutations for the general Arabidopsis community...
  99. pmc Centromere targeting element within the histone fold domain of Cid
    Danielle Vermaak
    Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    Mol Cell Biol 22:7553-61. 2002
    ..We suggest that the process of deposition of (Cid.H4)2 tetramers allows for discriminating contacts to be made between loop I and DNA, providing the specificity needed for targeting...
  100. ncbi request reprint Predicting in vivo protein peptide interactions with random phage display
    J F Smothers
    Howard Hughes Medical Institute, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
    Comb Chem High Throughput Screen 4:585-91. 2001
    ..This strategy should become increasingly powerful with the growing popularity of interaction studies, sequencing projects and microarray analyses in modern biology...
  101. ncbi request reprint A histone-H3-like protein in C. elegans
    B J Buchwitz
    Division of Basic Sciences, Molecular and Cellular Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    Nature 401:547-8. 1999

Research Grants29

  1. Epigenomic profiling of histone turnover kinetics in mammalian cells
    Steven Henikoff; Fiscal Year: 2010
    ..Our project will explore the application of CATCH-IT to measuring dynamic changes in the epigenome involved developmental regulation, cancer, and DNA damage, with broad diagnostic potential. ..
  2. ALIGNMENT BASED METHODS FOR MOLECULAR SEQUENCE ANALYSIS
    Steven Henikoff; Fiscal Year: 2001
    ..This effort could yield new eukaryotic family members of great importance for understanding epigenetic phenomena, some of which, such as parental imprinting, are relevant to human disease. ..
  3. Genome-wide profiling of histone variants in Drosophila and Caenorhabditis
    Steven Henikoff; Fiscal Year: 2007
    ..Given that the same histone variants are thought to play similar roles in essentially all complex eukaryotes, our basic approach can be immediately applied to the human genome. ..
  4. Maintenance of blocks-based tools for functional genomic
    Steven Henikoff; Fiscal Year: 2006
    ..These various components will be packaged to facilitate updates and local implementations. ..
  5. GENE REGULATION OF THE PURINE SYNTHETIC PATHWAY
    Steven Henikoff; Fiscal Year: 1993
    ..It is likely that some of these other genes that we identify by this approach will correspond to loci that were previously identified by mutation, thus furthering our understanding of the relationship between phenotype and gene function...