JASON LIEB

Summary

Affiliation: University of North Carolina
Country: USA

Publications

  1. pmc ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions
    Naim U Rashid
    Department of Biostatistics, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
    Genome Biol 12:R67. 2011
  2. pmc Caenorhabditis elegans chromosome arms are anchored to the nuclear membrane via discontinuous association with LEM-2
    Kohta Ikegami
    Department of Biology, Carolina Center for Genome Sciences and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, 407 Fordham Hall, Chapel Hill, North Carolina 27599, USA
    Genome Biol 11:R120. 2010
  3. pmc ChIPOTle: a user-friendly tool for the analysis of ChIP-chip data
    Michael J Buck
    Department of Biology, Carolina Center for Genome Sciences, CB 3280, University of North Carolina, Chapel Hill, NC 27599 3280, USA
    Genome Biol 6:R97. 2005
  4. ncbi request reprint Control of transcription through intragenic patterns of nucleosome composition
    Jason D Lieb
    Department of Biology and the Carolina Center for Genome Sciences, 202 Fordham Hall, CB 3280, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
    Cell 123:1187-90. 2005
  5. pmc The genomic distribution and function of histone variant HTZ-1 during C. elegans embryogenesis
    Christina M Whittle
    Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
    PLoS Genet 4:e1000187. 2008
  6. pmc Dimethylation of histone H3 at lysine 36 demarcates regulatory and nonregulatory chromatin genome-wide
    Bhargavi Rao
    Department of Biology, CB no 3280, 203 Fordham Hall, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
    Mol Cell Biol 25:9447-59. 2005
  7. doi request reprint C. elegans dosage compensation: a window into mechanisms of domain-scale gene regulation
    Sevinc Ercan
    Department of Biology and Carolina Center for the Genome Sciences, CB 3280, 406 Fordham Hall, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 3280, USA
    Chromosome Res 17:215-27. 2009
  8. pmc High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans
    Sevinc Ercan
    Department of Biology, Carolina Center for the Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599 3280, USA
    Genome Res 21:237-44. 2011
  9. ncbi request reprint Evidence for nucleosome depletion at active regulatory regions genome-wide
    Cheol Koo Lee
    Department of Biology, CB 3280, 202 Fordham Hall, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 3280, USA
    Nat Genet 36:900-5. 2004
  10. pmc Identification of histone H3 lysine 36 acetylation as a highly conserved histone modification
    Stephanie A Morris
    Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA
    J Biol Chem 282:7632-40. 2007

Detail Information

Publications41

  1. pmc ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions
    Naim U Rashid
    Department of Biostatistics, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
    Genome Biol 12:R67. 2011
    ..ZINBA provides a single unified framework for analyzing DNA-seq experiments in challenging genomic contexts...
  2. pmc Caenorhabditis elegans chromosome arms are anchored to the nuclear membrane via discontinuous association with LEM-2
    Kohta Ikegami
    Department of Biology, Carolina Center for Genome Sciences and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, 407 Fordham Hall, Chapel Hill, North Carolina 27599, USA
    Genome Biol 11:R120. 2010
    ..Although Caenorhabditis elegans was the first multicellular organism with a completely sequenced genome, how this genome is arranged within the nucleus is not known...
  3. pmc ChIPOTle: a user-friendly tool for the analysis of ChIP-chip data
    Michael J Buck
    Department of Biology, Carolina Center for Genome Sciences, CB 3280, University of North Carolina, Chapel Hill, NC 27599 3280, USA
    Genome Biol 6:R97. 2005
    ..Implemented as a Microsoft Excel macro written in Visual Basic, ChIPOTle uses a sliding window approach that yields improvements in the identification of bona fide sites of protein-DNA interaction...
  4. ncbi request reprint Control of transcription through intragenic patterns of nucleosome composition
    Jason D Lieb
    Department of Biology and the Carolina Center for Genome Sciences, 202 Fordham Hall, CB 3280, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
    Cell 123:1187-90. 2005
    ..The ultimate target of most epigenetic mechanisms may be the regulation of nucleosome occupancy, which in turn controls access to DNA at specific genomic locations...
  5. pmc The genomic distribution and function of histone variant HTZ-1 during C. elegans embryogenesis
    Christina M Whittle
    Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
    PLoS Genet 4:e1000187. 2008
    ..Our experiments indicate that HTZ-1 functions in establishing or maintaining an essential chromatin state at promoters regulated dynamically during C. elegans embryogenesis...
  6. pmc Dimethylation of histone H3 at lysine 36 demarcates regulatory and nonregulatory chromatin genome-wide
    Bhargavi Rao
    Department of Biology, CB no 3280, 203 Fordham Hall, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
    Mol Cell Biol 25:9447-59. 2005
    ....
  7. doi request reprint C. elegans dosage compensation: a window into mechanisms of domain-scale gene regulation
    Sevinc Ercan
    Department of Biology and Carolina Center for the Genome Sciences, CB 3280, 406 Fordham Hall, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 3280, USA
    Chromosome Res 17:215-27. 2009
    ..We discuss how condensin-like complexes may be targeted to specific chromosomal locations for performance of their functions...
  8. pmc High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans
    Sevinc Ercan
    Department of Biology, Carolina Center for the Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599 3280, USA
    Genome Res 21:237-44. 2011
    ..The nucleosome occupancy differences observed on X promoters may bear on mechanisms of X chromosome dosage compensation in the soma, and chromosome-wide repression of X in the germline...
  9. ncbi request reprint Evidence for nucleosome depletion at active regulatory regions genome-wide
    Cheol Koo Lee
    Department of Biology, CB 3280, 202 Fordham Hall, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 3280, USA
    Nat Genet 36:900-5. 2004
    ..Given the conservation of sequence and function among components of both chromatin and the transcriptional machinery, nucleosome depletion at promoters may be a fundamental feature of eukaryotic transcriptional regulation...
  10. pmc Identification of histone H3 lysine 36 acetylation as a highly conserved histone modification
    Stephanie A Morris
    Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA
    J Biol Chem 282:7632-40. 2007
    ....
  11. pmc Cell cycle-specified fluctuation of nucleosome occupancy at gene promoters
    Gregory J Hogan
    Department of Biology and Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
    PLoS Genet 2:e158. 2006
    ....
  12. pmc X chromosome repression by localization of the C. elegans dosage compensation machinery to sites of transcription initiation
    Sevinc Ercan
    Department of Biology and Carolina Center for the Genome Sciences, 202 Fordham Hall, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 3280, USA
    Nat Genet 39:403-8. 2007
    ..These data aid in understanding how proteins involved in higher-order chromosome dynamics can regulate transcription at individual loci...
  13. pmc DNA-binding specificity and in vivo targets of Caenorhabditis elegans nuclear factor I
    Christina M Whittle
    Department of Biology, Carolina Center for Genome Sciences, and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599 3280, USA
    Proc Natl Acad Sci U S A 106:12049-54. 2009
    ..These experiments provide a foundation for understanding how NFI-1 is recruited to unexpectedly few in vivo sites to perform its developmental functions, despite a vast over-representation of its binding motif...
  14. pmc FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin
    Paul G Giresi
    Department of Biology and the Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 3280, USA
    Genome Res 17:877-85. 2007
    ..FAIRE has utility as a positive selection for genomic regions associated with regulatory activity, including regions traditionally detected by nuclease hypersensitivity assays...
  15. pmc The Saccharomyces cerevisiae histone demethylase Jhd1 fine-tunes the distribution of H3K36me2
    Jia Fang
    Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, NC 27599, USA
    Mol Cell Biol 27:5055-65. 2007
    ..Our studies establish Jhd1 as a histone demethylase in budding yeast and suggest that Jhd1 functions to maintain the fidelity of histone methylation patterns along transcription units...
  16. pmc The Set2/Rpd3S pathway suppresses cryptic transcription without regard to gene length or transcription frequency
    Colin R Lickwar
    Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
    PLoS ONE 4:e4886. 2009
    ..These new results and conclusions have implications for many commonly used genomic analysis approaches, and for the evolution of high-fidelity RNA polymerase II transcriptional initiation in eukaryotes...
  17. pmc The C. elegans dosage compensation complex propagates dynamically and independently of X chromosome sequence
    Sevinc Ercan
    Department of Biology, Carolina Center for Genome Sciences and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
    Curr Biol 19:1777-87. 2009
    ..Five DCC members are homologous to subunits of the evolutionarily conserved condensin complex, and two noncondensin subunits are required for DCC recruitment to X...
  18. pmc A positive but complex association between meiotic double-strand break hotspots and open chromatin in Saccharomyces cerevisiae
    Luke E Berchowitz
    Department of Biology and the Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 3280, USA
    Genome Res 19:2245-57. 2009
    ..Finally, we find evidence for meiosis-specific opening of chromatin at the regions adjacent to boundaries of subtelomeric sequences, which exhibit specific crossover control patterns hypothesized to be regulated by chromatin...
  19. pmc A chromatin-mediated mechanism for specification of conditional transcription factor targets
    Michael J Buck
    Department of Biology and the Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
    Nat Genet 38:1446-51. 2006
    ....
  20. pmc The RNA polymerase II kinase Ctk1 regulates positioning of a 5' histone methylation boundary along genes
    Tiaojiang Xiao
    Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, 405 Mary Ellen Jones, Chapel Hill, NC 27599 7260, USA
    Mol Cell Biol 27:721-31. 2007
    ....
  21. pmc Global analysis of the relationship between the binding of the Bas1p transcription factor and meiosis-specific double-strand DNA breaks in Saccharomyces cerevisiae
    Piotr A Mieczkowski
    Department of Biology and Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 3280, USA
    Mol Cell Biol 26:1014-27. 2006
    ..These results argue that both local and regional factors affect the level of meiotic recombination...
  22. ncbi request reprint Progress and challenges in profiling the dynamics of chromatin and transcription factor binding with DNA microarrays
    Sean E Hanlon
    Department of Biology and Carolina Center for the Genome Sciences, CB 3280, 202 Fordham Hall, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 3280, USA
    Curr Opin Genet Dev 14:697-705. 2004
    ....
  23. pmc Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements)
    Paul G Giresi
    Department of Biology and Carolina Center for the Genome Sciences, University of North Carolina at Chapel Hill, CB 3280, 408 Fordham Hall, Chapel Hill, NC 27599 3280, USA
    Methods 48:233-9. 2009
    ....
  24. ncbi request reprint Regulation of nucleosome stability as a mediator of chromatin function
    Paul G Giresi
    Department of Biology and Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 3280, USA
    Curr Opin Genet Dev 16:171-6. 2006
    ....
  25. pmc Systematic identification of balanced transposition polymorphisms in Saccharomyces cerevisiae
    Dina A Faddah
    Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
    PLoS Genet 5:e1000502. 2009
    ..Our methodology and findings provide a starting point for exploring the origins, phenotypic consequences, and evolutionary fate of this largely unexplored form of genomic polymorphism...
  26. doi request reprint Chromatin proteins do double duty
    Sevinc Ercan
    Department of Biology and Carolina Center for the Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
    Cell 133:763-5. 2008
    ....
  27. ncbi request reprint ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments
    Michael J Buck
    Department of Biology and Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 3280, USA
    Genomics 83:349-60. 2004
    ....
  28. pmc A map of open chromatin in human pancreatic islets
    Kyle J Gaulton
    Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
    Nat Genet 42:255-9. 2010
    ..These findings illuminate the tissue-specific organization of cis-regulatory elements and show that FAIRE-seq can guide the identification of regulatory variants underlying disease susceptibility...
  29. pmc Integrating regulatory motif discovery and genome-wide expression analysis
    Erin M Conlon
    Department of Statistics, Harvard University, 1 Oxford Street, Cambridge, MA 02138, USA
    Proc Natl Acad Sci U S A 100:3339-44. 2003
    ....
  30. pmc Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets
    David S Johnson
    Department of Genetics, Stanford University Medical Center, Stanford, California 94305, USA
    Genome Res 18:393-403. 2008
    ..The spike-in DNA samples and the data presented here provide a stable benchmark against which future ChIP platforms, protocol improvements, and analysis methods can be evaluated...
  31. pmc Forkhead proteins control the outcome of transcription factor binding by antiactivation
    Warren P Voth
    Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA
    EMBO J 26:4324-34. 2007
    ..Thus Fkh proteins, which function initially to activate SWI5 and ACE2, subsequently function as Swi5-specific antiactivators...
  32. pmc Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    Ewan Birney
    Nature 447:799-816. 2007
    ..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function...
  33. ncbi request reprint Genome-wide mapping of protein-DNA interactions by chromatin immunoprecipitation and DNA microarray hybridization
    Jason D Lieb
    Department of Biology and Carolina Center for Genome Sciences, The University of North Carolina at Chapel Hill, USA
    Methods Mol Biol 224:99-109. 2003
  34. pmc Genomewide demarcation of RNA polymerase II transcription units revealed by physical fractionation of chromatin
    Peter L Nagy
    Department of Pathology, Stanford University, CA 94305 5428, USA
    Proc Natl Acad Sci U S A 100:6364-9. 2003
    ..Our approach has broad potential use as a tool for genome annotation and for the characterization of global changes in chromatin structure that accompany different genetic, environmental, and disease states...
  35. pmc Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection
    Xiao Liu
    Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
    Genome Res 16:1517-28. 2006
    ....
  36. ncbi request reprint New evidence that DNA encodes its packaging
    Sevinc Ercan
    Nat Genet 38:1104-5. 2006
  37. ncbi request reprint How to find an opening (or lots of them)
    Paul G Giresi
    Nat Methods 3:501-2. 2006
  38. pmc DIP-chip: rapid and accurate determination of DNA-binding specificity
    Xiao Liu
    Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
    Genome Res 15:421-7. 2005
    ....
  39. pmc Loss of a histone deacetylase dramatically alters the genomic distribution of Spo11p-catalyzed DNA breaks in Saccharomyces cerevisiae
    Piotr A Mieczkowski
    Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
    Proc Natl Acad Sci U S A 104:3955-60. 2007
    ..Some of the genes with altered frequencies of DSBs (including the ribosomal RNA gene cluster) are known targets of Sir2p deacetylation in the wild-type strain...
  40. ncbi request reprint Out with the old, in with the new
    Jason D Lieb
    Nat Genet 37:1024-5. 2005
  41. pmc A molecular link between gene-specific and chromosome-wide transcriptional repression
    Diana S Chu
    Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720 3204, USA
    Genes Dev 16:796-805. 2002
    ....

Research Grants8

  1. Understanding Specificity in Protein-Genome Interactions
    JASON LIEB; Fiscal Year: 2004
    ..The award would greatly facilitate the establishment of a productive laboratory engaged in cutting-edge genomics research. ..
  2. Identification of DNA Elements Governing Chromatin Function in C elegans
    JASON LIEB; Fiscal Year: 2007
    ..elegans research will provide an important milestone in meeting the challenge of using genome sequence information to understand and predict biological functions. ..
  3. Genomic Approaches to DNA-binding Specificity in vivo
    JASON LIEB; Fiscal Year: 2009
    ..FAIRE, a new chromatin assay we have developed, has potential as a prognostic or diagnostic tool for diseases (including cancer) that affect, or arise from defects in, chromatin or transcription. ..