Research Topics
| T R HughesSummaryAffiliation: University of Toronto Country: Canada Publications
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Detail Information
Publications
The draft genome and transcriptome of Cannabis sativaHarm van Bakel
Banting and Best Department of Medical Research and Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
Genome Biol 12:R102. 2011..The molecular biology underlying cannabinoid biosynthesis and other traits of interest is largely unexplored...- Conservation of core gene expression in vertebrate tissuesEsther T Chan
Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario, Canada
J Biol 8:33. 2009..Alteration of gene regulation is thought to be a major mechanism in phenotypic variation and evolution, but relatively little is known about the broad patterns of conservation in gene expression in non-mammalian vertebrates... 
The functional landscape of mouse gene expressionWen Zhang
Banting and Best Department of Medical Research, University of Toronto, 1 King s College Circle, Toronto, ON M5S 1A8, Canada
J Biol 3:21. 2004....- A race through the maze of genomic evidenceTimothy R Hughes
Genome Biol 9:S1. 2008 - Signals and systemsNevan J Krogan
Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143, USA
Genome Biol 7:313. 2006 - A critical assessment of Mus musculus gene function prediction using integrated genomic evidenceLourdes Pena-Castillo
Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S3E1, Canada
Genome Biol 9:S2. 2008..Several algorithms using diverse genomic data have been applied to this task in model organisms; however, the performance of such approaches in mammals has not yet been evaluated... - TFCat: the curated catalog of mouse and human transcription factorsDebra L Fulton
Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, Canada
Genome Biol 10:R29. 2009..All data and user-feedback mechanisms are available at the TFCat portal (http://www.tfcat.ca)... - Functional coordination of alternative splicing in the mammalian central nervous systemMatthew Fagnani
Banting and Best Department of Medical Research, Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, Canada, M5S 3E1
Genome Biol 8:R108. 2007..However, the extent to which AS coordinates functions in a cell and tissue type specific manner is not known. Moreover, the sequence code that underlies cell and tissue type specific regulation of AS is poorly understood... - Information propagation within the Genetic Network of Saccharomyces cerevisiaeSharif Chowdhury
Laboratory of Biosystem Dynamics, Computational Systems Biology Research Group, Tampere University of Technology, Tampere, Finland
BMC Syst Biol 4:143. 2010..Inferred connections are verified by gene enrichment... - A systematic search for new mammalian noncoding RNAs indicates little conserved intergenic transcriptionTomas Babak
Banting and Best Department of Medical Research, 112 College St, Toronto, ON M5G 1L6, Canada
BMC Genomics 6:104. 2005..However, these non-genic transcripts often appear to be low in abundance, and their functional significance is not known... - Simultaneous host and parasite expression profiling identifies tissue-specific transcriptional programs associated with susceptibility or resistance to experimental cerebral malariaFiona E Lovegrove
Institute of Medical Science, Department of Medicine, University of Toronto, Toronto, ON, Canada
BMC Genomics 7:295. 2006.... - FunSpec: a web-based cluster interpreter for yeastMark D Robinson
Banting and Best Department of Medical Research, University of Toronto, Toronto, Canada
BMC Bioinformatics 3:35. 2002.... - Considerations in the identification of functional RNA structural elements in genomic alignmentsTomas Babak
Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, 160 College St, Toronto, ON M5S 3E1 Canada
BMC Bioinformatics 8:33. 2007.... - G+C content dominates intrinsic nucleosome occupancyDesiree Tillo
Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
BMC Bioinformatics 10:442. 2009..However, the model is complicated, and it is not clear which specific DNA sequence properties are most important for intrinsic nucleosome-forming preferences... 
Introduction to "a handbook of transcription factors"T R Hughes
Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
Subcell Biochem 52:1-6. 2011..This chapter briefly summarizes the topics in this volume...
Yeast and drug discoveryTimothy R Hughes
Banting and Best Department of Medical Research, University of Toronto, 112 College St, Toronto, ON M5G 1L6, Canada
Funct Integr Genomics 2:199-211. 2002..It is likely that most of the benefits of yeast in discovery and development of therapeutic compounds have yet to be realized...- 'Validation' in genome-scale researchTimothy R Hughes
Banting and Best Department of Medical Research, and Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
J Biol 8:3. 2009..The individual 'validation' experiments typically included in papers reporting genome-scale studies often do not reflect the overall merits of the work... - The promise of functional genomics: completing the encyclopedia of a cellTimothy R Hughes
Banting and Best Department of Medical Research, University of Toronto, 112 College St, Room 307, Toronto, ON, M5G 1L6, Canada
Curr Opin Microbiol 7:546-54. 2004..This task seems increasingly feasible; however, progress to date suggests that increased interaction between systematic efforts and individual investigators will be critical to completing the encyclopedia of the yeast cell... - Most "dark matter" transcripts are associated with known genesHarm van Bakel
Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
PLoS Biol 8:e1000371. 2010..We conclude that, while there are bona fide new intergenic transcripts, their number and abundance is generally low in comparison to known exons, and the genome is not as pervasively transcribed as previously reported... - Exploration of essential gene functions via titratable promoter allelesSanie Mnaimneh
Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, ON M5G 1L6, Canada
Cell 118:31-44. 2004..We furthermore show that these strains are compatible with automated genetic analysis. This study underscores the importance of analyzing mutant phenotypes and provides a resource to complement the yeast knockout collection... - Transcriptional networks: reverse-engineering gene regulation on a global scaleGordon Chua
Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Room 307, Toronto, Ontario M5G 1L6, Canada
Curr Opin Microbiol 7:638-46. 2004..The results indicate that a complete and comprehensive yeast transcriptional network will ultimately be achieved... - Genome-wide analysis of mRNA stability using transcription inhibitors and microarrays reveals posttranscriptional control of ribosome biogenesis factorsJorg Grigull
Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5G 1L6, Canada
Mol Cell Biol 24:5534-47. 2004..Our results indicate that the abundance of ribosome biogenesis factors is controlled at the level of mRNA stability... - Mapping pathways and phenotypes by systematic gene overexpressionRichelle Sopko
Department of Medical Genetics and Microbiology, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
Mol Cell 21:319-30. 2006..Large-scale application of this approach should provide a strategy for identifying target molecules regulated by specific signaling pathways... - Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profilingThomas Kislinger
Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5G 1L6, Canada
Cell 125:173-86. 2006..This molecular compendium, fully accessible via a searchable web-browser interface, serves as a reliable reference of the expressed tissue and organelle proteomes of a leading model mammal... - A catalogue of eukaryotic transcription factor types, their evolutionary origin, and species distributionMatthew T Weirauch
Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
Subcell Biochem 52:25-73. 2011..We also examine the species distributions and inferred evolutionary histories of the various families, and the potential roles played by TF family expansion and dimerization... - Global landscape of protein complexes in the yeast Saccharomyces cerevisiaeNevan J Krogan
Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, Ontario M5S 3E1, Canada
Nature 440:637-43. 2006..The data (all of which are available online) will help future studies on individual proteins as well as functional genomics and systems biology... - Genome-wide analysis of mouse transcripts using exon microarrays and factor graphsBrendan J Frey
Electrical and Computer Engineering, University of Toronto, 10 King s College Rd, Toronto, Ontario M5S 3G4, Canada
Nat Genet 37:991-6. 2005..GenRate also detected tens of thousands of potential new exons and reconciled discrepancies in current cDNA databases by 'stitching' new transcribed regions into previously annotated genes... - Identifying transcription factor functions and targets by phenotypic activationGordon Chua
Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, ON, Canada M5S 1A8
Proc Natl Acad Sci U S A 103:12045-50. 2006..The general strategy outlined here presents a straightforward approach to discovery of TF activities and mapping targets that could be adapted to any organism with transgenic technology... - A panoramic view of yeast noncoding RNA processingWen Tao Peng
Banting and Best Department of Medical Research, University of Toronto, 112 College Street, M5G 1L6, Toronto, Ontario, Canada
Cell 113:919-33. 2003..These data present a global view of yeast noncoding RNA processing and confirm that many currently uncharacterized yeast proteins are involved in biogenesis of noncoding RNA... - Global analysis of yeast RNA processing identifies new targets of RNase III and uncovers a link between tRNA 5' end processing and tRNA splicingShawna L Hiley
Banting and Best Department of Medical Research, University of Toronto 112 College Street, Toronto, ON M5G 1L6, Canada
Nucleic Acids Res 33:3048-56. 2005..This analysis demonstrates the applicability of microarray technology to the study of global analysis of ncRNA synthesis and provides an extensive directory of processing events mediated by yeast ncRNA processing enzymes... - Parasite burden and CD36-mediated sequestration are determinants of acute lung injury in an experimental malaria modelFiona E Lovegrove
Institute of Medical Science, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
PLoS Pathog 4:e1000068. 2008..Furthermore, differential susceptibility of mouse strains to malaria-induced ALI and CM suggests that distinct genetic determinants may regulate susceptibility to these two important causes of malaria-associated morbidity and mortality... - High-definition macromolecular composition of yeast RNA-processing complexesNevan J Krogan
Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, Ontario M5G 1L6, Canada
Mol Cell 13:225-39. 2004..This study provides a high-resolution overview of the modular topology of noncoding RNA-processing machinery... - Two-color cell array screen reveals interdependent roles for histone chaperones and a chromatin boundary regulator in histone gene repressionJeffrey Fillingham
Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Canada
Mol Cell 35:340-51. 2009..Our data suggest that this pathway may represent a chromatin regulatory mechanism that is broadly used across the genome... - Integration of chemical-genetic and genetic interaction data links bioactive compounds to cellular target pathwaysAinslie B Parsons
Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario M5G 1L6, Canada
Nat Biotechnol 22:62-9. 2004..This method thus provides a powerful means for inferring mechanism of action... - A Snf2 family ATPase complex required for recruitment of the histone H2A variant Htz1Nevan J Krogan
Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, Ontario, Canada M5G 1L6
Mol Cell 12:1565-76. 2003..We show that recruitment of Htz1 to chromatin requires the SWR-C. Moreover, like Htz1 and Bdf1, the SWR-C promotes gene expression near silent heterochromatin... - GenRate: a generative model that reveals novel transcripts in genome-tiling microarray dataBrendan J Frey
Department of Electrical and Computer Engineering, University of Toronto, Ontario, Canada
J Comput Biol 13:200-14. 2006..As new problems arise, additional hidden variables can be incorporated into the model in a principled fashion, so we believe that GenRate will prove to be a useful tool in the new era of genome-wide tiling microarray analysis... - The synthetic genetic interaction spectrum of essential genesArmaity P Davierwala
Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, Ontario, M5G 1L6, Canada
Nat Genet 37:1147-52. 2005.... - A systematic characterization of Cwc21, the yeast ortholog of the human spliceosomal protein SRm300May Khanna
Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
RNA 15:2174-85. 2009..Together, the results suggest multiple functions for Cwc21/SRm300 in the splicing process, including an important role in the activation of splicing in association with Isy1... - Exploring the mode-of-action of bioactive compounds by chemical-genetic profiling in yeastAinslie B Parsons
Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5G 1L6, Canada
Cell 126:611-25. 2006..This compendium should serve as a valuable key for interpreting cellular effects of novel compounds with similar activities... - A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promotersGwenael Badis
Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada
Mol Cell 32:878-87. 2008.... - Why are there still over 1000 uncharacterized yeast genes?Lourdes Pena-Castillo
Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
Genetics 176:7-14. 2007..Notably, the uncharacterized gene set is highly enriched for genes whose only homologs are in other fungi. Achieving a full catalog of yeast gene functions may require a greater focus on the life of yeast outside the laboratory... - Yeast genomics and proteomics in drug discovery and target validationAinslie B Parsons
Banting and Best Department of Medical Research, Department of Molecular and Medical Genetics, University of Toronto, Toronto, M3G 1L6 Canada
Prog Cell Cycle Res 5:159-66. 2003..This review will focus on current genetic, genomic, and proteomic methodologies in S. cerevisiae that have the potential to be useful in drug discovery and target validation... - Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platformQun Pan
Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, Ontario M5G 1L6, Canada
Mol Cell 16:929-41. 2004..These results demonstrate the utility of our quantitative microarray platform and data for revealing important global regulatory features of AS... - ESF1 is required for 18S rRNA synthesis in Saccharomyces cerevisiaeWen Tao Peng
Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, Ontario M5G 1L6, Canada
Nucleic Acids Res 32:1993-9. 2004..These data indicate that Esf1p plays a direct role in early pre-rRNA processing... - Microarray analysis of RNA processing and modificationTimothy R Hughes
Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
Methods Enzymol 410:300-16. 2006..This chapter also describes practical aspects of microarray design, sample preparation, hybridization, and data analysis... - Using expression profiling data to identify human microRNA targetsJim C Huang
Department of Electrical and Computer Engineering, University of Toronto, 10 King s College Road, Toronto, Ontario M5S 3G4, Canada
Nat Methods 4:1045-9. 2007..Compared to sequence-based predictions, our high-scoring GenMiR++ predictions had much more consistent Gene Ontology annotations and were more accurate predictors of which mRNA levels respond to changes in let-7b levels... - Probing microRNAs with microarrays: tissue specificity and functional inferenceTomas Babak
Banting and Best Department of Medical Research, 112 College St, University of Toronto, Toronto, Ontario M5G 1L6, Canada
RNA 10:1813-9. 2004.... - Detection and discovery of RNA modifications using microarraysShawna L Hiley
Banting and Best Department of Medical Research, University of Toronto 112 College Street, Toronto, ON M5G 1L6, Canada
Nucleic Acids Res 33:e2. 2005..Using this approach, we identified a previously undetected m1A modification in GlnCTG tRNA, the formation of which is catalyzed by the Gcd10/Gcd14 complex. complex... - Molecular chaperone Hsp90 stabilizes Pih1/Nop17 to maintain R2TP complex activity that regulates snoRNA accumulationRongmin Zhao
Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
J Cell Biol 180:563-78. 2008..As a consequence, the chaperone is shown to affect box C/D accumulation and maintenance, especially under stress conditions. Hsp90 and R2TP proteins are also involved in the proper accumulation of box H/ACA small nucleolar RNAs... - A survey of essential gene function in the yeast cell division cycleLisa Yu
Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
Mol Biol Cell 17:4736-47. 2006.... - Establishing legitimacy and function in the new transcriptomeHarm van Bakel
Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada
Brief Funct Genomic Proteomic 8:424-36. 2009..Here, we discuss the challenges associated with discovery and characterization of non-traditional categories of non-coding RNA... - Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteinsDebashish Ray
Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
Nat Biotechnol 27:667-70. 2009..We anticipate that RNAcompete will be a valuable tool for the study of RNA-protein interactions... - High nucleosome occupancy is encoded at human regulatory sequencesDesiree Tillo
Department of Molecular Genetics, University of Toronto, Toronto, Canada
PLoS ONE 5:e9129. 2010..We propose that high nucleosome preference is directly encoded at regulatory sequences in the human genome to restrict access to regulatory information that will ultimately be utilized in only a subset of differentiated cells... - Genetic selection of peptide inhibitors of biological pathwaysT C Norman
Department of Physiology, University of California, San Francisco, CA 94143 0444, USA
Science 285:591-5. 1999.... - Regulation of chromosome stability by the histone H2A variant Htz1, the Swr1 chromatin remodeling complex, and the histone acetyltransferase NuA4Nevan J Krogan
Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada M5G 1L6
Proc Natl Acad Sci U S A 101:13513-8. 2004..Because SWR-C-dependent recruitment of Htz1 occurs in both transcribed and centromeric regions, a NuA4/SWR-C/Htz1 pathway may regulate both transcription and centromere function in S. cerevisiae... - RNAcontext: a new method for learning the sequence and structure binding preferences of RNA-binding proteinsHilal Kazan
Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
PLoS Comput Biol 6:e1000832. 2010..RNAcontext is an accurate and efficient motif finding method ideally suited for using large-scale RNA-binding affinity datasets to determine the relative binding preferences of RBPs for a wide range of RNA sequences and structures... - Comprehensive genetic analysis of transcription factor pathways using a dual reporter gene system in budding yeastPinay Kainth
Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, Ont M5S3E1E1, Canada
Methods 48:258-64. 2009..The method is extensible to any transcription factor or signalling pathway for which an appropriate reporter gene can be devised... - Alternative splicing of conserved exons is frequently species-specific in human and mouseQun Pan
CH Best Institute, University of Toronto, 112 College Street, Toronto, Ontario, Canada M5G 1L6
Trends Genet 21:73-7. 2005..The results thus provide evidence that species-specific AS of conserved exons constitutes an additional potential source of complexity and species-specific differences between mammals... - SMAUG is a major regulator of maternal mRNA destabilization in Drosophila and its translation is activated by the PAN GU kinaseWael Tadros
Graduate Department of Molecular and Medical Genetics, University of Toronto, 1 King s College Circle, Toronto, Ontario M5S 1A8, Canada
Dev Cell 12:143-55. 2007..SMG-dependent mRNAs are enriched for gene ontology annotations for function in the cell cycle, suggesting a possible causal relationship between failure to eliminate these transcripts and the cell cycle defects in smg mutants... - Prediction and testing of novel transcriptional networks regulating embryonic stem cell self-renewal and commitmentEmily Walker
Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON, M5S 3G9, Canada
Cell Stem Cell 1:71-86. 2007..By using this integrative approach, we have formulated novel networks describing gene repression of key developmental regulators in undifferentiated ESCs and successfully predicted the outcomes of genetic manipulation of these networks... - Global analysis of mRNA localization reveals a prominent role in organizing cellular architecture and functionEric Lecuyer
Banting and Best Department of Medical Research, University of Toronto, Toronto, Canada
Cell 131:174-87. 2007..A searchable web resource documenting mRNA expression and localization dynamics has been established and will serve as an invaluable tool for dissecting localization mechanisms and for predicting gene functions and interactions... - Predicting the binding preference of transcription factors to individual DNA k-mersTrevis M Alleyne
Department of Molecular Genetics, Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada
Bioinformatics 25:1012-8. 2009..Nearest neighbour among functionally important residues emerged among the most effective methods. Our results underscore the complexity of TF-DNA recognition, and suggest a rational approach for future analyses of TF families... - Evaluation of data-dependent versus targeted shotgun proteomic approaches for monitoring transcription factor expression in breast cancerCharanjit Sandhu
Program in Proteomics and Bioinformatics, Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research CCBR, and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
J Proteome Res 7:1529-41. 2008.... - Diversity and complexity in DNA recognition by transcription factorsGwenael Badis
Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada
Science 324:1720-3. 2009..This complexity in DNA recognition may be important in gene regulation and in the evolution of transcriptional regulatory networks... - Zfp206 regulates ES cell gene expression and differentiationWen Zhang
Department of Molecular and Medical Genetics, University of Toronto, 4388 Medical Sciences Building, 1 King s College Circle, Toronto, ON M5S 1A8, Canada
Nucleic Acids Res 34:4780-90. 2006..Together, these data indicate that Zfp206 is a regulator of ES cell differentiation that controls a set of genes expressed very early in development, most of which themselves appear to be regulators... - RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factorsXiaoyu Chen
Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada
Bioinformatics 23:i72-9. 2007..Because RankMotif++ makes few assumptions about the relationship between binding affinity and the semi-quantitative readout, it is applicable to a wide variety of experimental assays of DNA-binding preference... - Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clustersLani F Wu
Rosetta Inpharmatics, Kirkland, Washington, USA
Nat Genet 31:255-65. 2002..We present experimental validation confirming the involvement of several of these proteins in ribosomal RNA processing. Our methodology can be applied to a variety of genomics data types and organisms... - RAM: a conserved signaling network that regulates Ace2p transcriptional activity and polarized morphogenesisBryce Nelson
Department of Biology Queen s University, Kingston, Ontario K7L 3N6, Canada
Mol Biol Cell 14:3782-803. 2003..Our data suggest that the functional architecture of RAM signaling is similar to the S. cerevisiae mitotic exit network and Schizosaccharomyces pombe septation initiation network and is likely conserved among eukaryotes... - How many new genes are there?Leo J Lee
Science 311:1709-11; author reply 1709-11. 2006 - Rapid tRNA decay can result from lack of nonessential modificationsAndrei Alexandrov
Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, New York 14642, USA
Mol Cell 21:87-96. 2006..The degradation of an endogenous tRNA species at a rate typical of mRNA decay demonstrates a critical role of nonessential modifications for tRNA stability and cell survival... - The specificities of four yeast dihydrouridine synthases for cytoplasmic tRNAsFeng Xing
Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, New York 14642, USA
J Biol Chem 279:17850-60. 2004..We show that each of the four Dus proteins has a distinct position specificity: Dus1p for U(16) and U(17), Dus2p for U(20), Dus3p for U(47), and Dus4p for U(20a) and U(20b)... - Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complexMichael Christopher Keogh
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
Cell 123:593-605. 2005..This pathway apparently acts to negatively regulate transcription because deleting the genes for Set2 or Rpd3C(S) bypasses the requirement for the positive elongation factor Bur1/Bur2... - A high-resolution atlas of nucleosome occupancy in yeastWilliam Lee
Department of Genetics, Stanford University School of Medicine, Stanford, California 94305 5120, USA
Nat Genet 39:1235-44. 2007..A quantitative model of nucleosome occupancy indicates that DNA structural features may account for much of the global nucleosome occupancy... - Identification of a bacterial type III effector family with G protein mimicry functionsNeal M Alto
Department of Pharmacology, Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
Cell 124:133-45. 2006..The activities of IpgB2, IpgB1, and Map are dependent on an invariant WxxxE motif found in numerous effectors leading to the speculation that they all function by a similar molecular mechanism... - RPAP1, a novel human RNA polymerase II-associated protein affinity purified with recombinant wild-type and mutated polymerase subunitsCélia Jeronimo
Laboratory of Gene Transcription, Institut de Recherches Cliniques de Montreal, Montreal, Quebec, Canada H2W 1R7
Mol Cell Biol 24:7043-58. 2004.... - Genetic interactions of MAF1 identify a role for Med20 in transcriptional repression of ribosomal protein genesIan M Willis
Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
PLoS Genet 4:e1000112. 2008..The data suggest that Mediator and Maf1 function in parallel pathways to negatively regulate RP mRNA and tRNA synthesis... - Esf2p, a U3-associated factor required for small-subunit processome assembly and compactionTran Hoang
Fonds National de la Recherche Scientifique, Universite Libre de Bruxelles, Institut de Biologie et de Médecine Moléculaires, Charleroi Gosselies, Belgium
Mol Cell Biol 25:5523-34. 2005..The identification of ABT1 in a large-scale analysis of the human nucleolar proteome indicates that its role may also be conserved in mammals... - Plasmodium falciparum shows transcriptional versatility within the human hostFiona E Lovegrove
McLaughlin Rotman Centre for Global Health, McLaughlin Centre for Molecular Medicine, MaRS Centre, Toronto ON, Canada
Trends Parasitol 24:288-91. 2008..These findings suggest that parasites exist in different physiological states in vivo, providing an important foundation for future studies investigating how these states might contribute to malaria pathogenesis and outcome... - GenXHC: a probabilistic generative model for cross-hybridization compensation in high-density genome-wide microarray dataJim C Huang
Probabilistic and Statistical Inference Group, Department of Electrical and Computer Engineering, University of Toronto Toronto, ON, Canada M5S 3G4
Bioinformatics 21:i222-31. 2005..The algorithm is found to outperform robust multi-array analysis, another method for cross-hybridization compensation... - H2B ubiquitylation acts as a barrier to Ctk1 nucleosomal recruitment prior to removal by Ubp8 within a SAGA-related complexAnastasia Wyce
Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA 19104, USA
Mol Cell 27:275-88. 2007..These findings reveal a mechanism by which H2B ubiquitylation acts as a barrier to Ctk1 association with active genes, while subsequent deubiquitylation by Ubp8 triggers Ctk1 recruitment at the appropriate point in activation... - H2B ubiquitin protease Ubp8 and Sgf11 constitute a discrete functional module within the Saccharomyces cerevisiae SAGA complexKristin Ingvarsdottir
The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
Mol Cell Biol 25:1162-72. 2005..These data indicate that Ubp8 and Sgf11 likely represent a new functional module within SAGA that is involved in gene regulation through H2B deubiquitylation... - A novel role of Sp1 and Sp3 in the interferon-gamma -mediated suppression of macrophage lipoprotein lipase gene transcriptionTimothy R Hughes
Cardiff School of Biosciences, Cardiff University, Museum Avenue, P O Box 911, Cardiff CF10 3US, United Kingdom
J Biol Chem 277:11097-106. 2002..In contrast, the cytokine decreased the DNA binding activity of Sp1 without affecting the protein levels. These studies therefore reveal a novel mechanism for IFN-gamma-mediated regulation of macrophage gene transcription... - Interferon-gamma stimulates the expression of the inducible cAMP early repressor in macrophages through the activation of casein kinase 2. A potentially novel pathway for interferon-gamma-mediated inhibition of gene transcriptionJames R Mead
Cardiff School of Biosciences, Cardiff University, Museum Avenue, P O Box 911, Cardiff CF10 3US, United Kingdom
J Biol Chem 278:17741-51. 2003.... - p53 regulates cellular resistance to complement lysis through enhanced expression of CD59Rossen M Donev
Department of Medical Biochemistry and Immunology, School of Medicine, Cardiff University, Cardiff, United Kingdom
Cancer Res 66:2451-8. 2006..Our data suggest that p53 and in vivo positive/negative regulators of p53 could be used to modulate susceptibility of tumor cells to complement lysis in chemotherapy... - BUR kinase selectively regulates H3 K4 trimethylation and H2B ubiquitylation through recruitment of the PAF elongation complexR Nicholas Laribee
Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA
Curr Biol 15:1487-93. 2005..Our data reveal a novel function for the BUR kinase in transcriptional regulation through the selective control of histone modifications... - Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzymeCélia Jeronimo
Laboratory of Gene Transcription and Proteomics Discovery Platform, Institut de Recherches Cliniques de Montreal, Montreal, QC, Canada
Mol Cell 27:262-74. 2007..Our results define a high-density protein interaction network for the mammalian transcription machinery and uncover multiple regulatory factors that target the transcription machinery... - Universal epistasis analysisTimothy R Hughes
Nat Genet 37:457-8. 2005 - The splicing factor Prp43p, a DEAH box ATPase, functions in ribosome biogenesisNina B Leeds
Department of Molecular Genetics and Cell Biology, University of Chicago, 920 E 58th St, Chicago, Illinois 60637, USA
Mol Cell Biol 26:513-22. 2006..The dual function for Prp43p in the cell raises the possibility that ribosome biogenesis and pre-mRNA splicing may be coordinately regulated... - Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferencesMichael F Berger
Division of Genetics, Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
Cell 133:1266-76. 2008..Our results provide an unprecedented level of resolution in the analysis of this simple domain structure and suggest that variation in sequence recognition may be a factor in its functional diversity and evolutionary success...