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Research Article

Substantial Histone Reduction Modulates Genomewide Nucleosomal Occupancy and Global Transcriptional Output

  • Barbara Celona,

    Affiliation: San Raffaele University, Milan, Italy

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  • Assaf Weiner,

    Affiliations: School of Computer Science and Engineering, Hebrew University, Jerusalem, Israel, Alexander Silberman Institute of Life Sciences, Hebrew University, Jerusalem, Israel

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  • Francesca Di Felice,

    Affiliation: Dipartimento di Biologia e Biotecnologie, Università di Roma La Sapienza, Rome, Italy

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  • Francesco M. Mancuso,

    Affiliation: IFOM-IEO Campus, Milan, Italy

    Current address: Bioinformatics Unit, Centre for Genomic Regulation (CRG) and UPF, Barcelona, Spain

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  • Elisa Cesarini,

    Affiliation: Dipartimento di Biologia e Biotecnologie, Università di Roma La Sapienza, Rome, Italy

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  • Riccardo L. Rossi,

    Affiliation: Integrative Biology Program, Istituto Nazionale di Genetica Molecolare, Milan, Italy

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  • Lorna Gregory,

    Affiliation: Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom

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  • Dilair Baban,

    Affiliation: Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom

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  • Grazisa Rossetti,

    Affiliation: Integrative Biology Program, Istituto Nazionale di Genetica Molecolare, Milan, Italy

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  • Paolo Grianti,

    Affiliation: Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli Studi di Milano, Milan, Italy

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  • Massimiliano Pagani,

    Affiliation: Integrative Biology Program, Istituto Nazionale di Genetica Molecolare, Milan, Italy

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  • Tiziana Bonaldi,

    Affiliation: IFOM-IEO Campus, Milan, Italy

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  • Jiannis Ragoussis,

    Affiliation: Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom

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  • Nir Friedman,

    Affiliations: School of Computer Science and Engineering, Hebrew University, Jerusalem, Israel, Alexander Silberman Institute of Life Sciences, Hebrew University, Jerusalem, Israel

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  • Giorgio Camilloni,

    Affiliations: Dipartimento di Biologia e Biotecnologie, Università di Roma La Sapienza, Rome, Italy, Istituto di Biologia e Patologia Molecolari, CNR, Rome, Italy

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  • Marco E. Bianchi mail,

    bianchi.marco@hsr.it (MEB); agresti.alessandra@hsr.it (AA)

    Affiliations: San Raffaele University, Milan, Italy, Division of Genetics and Cell Biology, San Raffaele Research Institute, Milan, Italy

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  • Alessandra Agresti mail

    bianchi.marco@hsr.it (MEB); agresti.alessandra@hsr.it (AA)

    Affiliation: Division of Genetics and Cell Biology, San Raffaele Research Institute, Milan, Italy

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  • Published: June 28, 2011
  • DOI: 10.1371/journal.pbio.1001086

About the Authors

Barbara Celona, Marco E. Bianchi
San Raffaele University, Milan, Italy
Assaf Weiner, Nir Friedman
School of Computer Science and Engineering, Hebrew University, Jerusalem, Israel
Assaf Weiner, Nir Friedman
Alexander Silberman Institute of Life Sciences, Hebrew University, Jerusalem, Israel
Francesca Di Felice, Elisa Cesarini, Giorgio Camilloni
Dipartimento di Biologia e Biotecnologie, Università di Roma La Sapienza, Rome, Italy
Francesco M. Mancuso, Tiziana Bonaldi
IFOM-IEO Campus, Milan, Italy
Riccardo L. Rossi, Grazisa Rossetti, Massimiliano Pagani
Integrative Biology Program, Istituto Nazionale di Genetica Molecolare, Milan, Italy
Lorna Gregory, Dilair Baban, Jiannis Ragoussis
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
Paolo Grianti
Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli Studi di Milano, Milan, Italy
Giorgio Camilloni
Istituto di Biologia e Patologia Molecolari, CNR, Rome, Italy
Marco E. Bianchi, Alessandra Agresti
Division of Genetics and Cell Biology, San Raffaele Research Institute, Milan, Italy

Corresponding Authors

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

The author(s) have made the following declarations about their contributions: Conceived and designed the experiments: BC AW NF MEB AA. Performed the experiments: BC FDF EC PG GR. Analyzed the data: BC AW FMM RLR LG DB MP TB. Contributed reagents/materials/analysis tools: AW MP TB JR GC NF MEB AA. Wrote the paper: BC AW NF MEB AA. BC performed experiments on mammalian cells and mice; AW bioinformatic analyses for nucleosome positioning and modeling; FDF, EC, PG, and BC experiments on yeast; BC and FMM bioinformatics for proteome analysis; BC, RLR, GR, and MP transcriptome analyses of mammalian cells; and LG and DB high-throughput sequencing and transcriptome analyses of yeast cells. BC, MEB, and AA formulated the hypotheses. BC, MP, TB, JR, NF, GC, MEB, and AA analyzed the results (mammalian transcriptomics, MP; proteomics, TB; high throughput sequencing and transcriptome analyses of yeast cells, JR; bioinformatic analyses for nucleosome positioning and modeling, NF; experiments on yeast, GC; experiments on mammalian cells and mice, BC, MEB, and AA). MEB and AA coordinated the whole work.