Michiel Hoon

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David Seamon

Kansas State University

John Sutton

Macquarie University

M. A. Katritzky

The Open University

Benjamin Bonavida

UCLA David Geffen School of Medicine

Jeremy Ravi Mumford

Brown University

Ahmet Corak

Marmara University

Smita Sorte

All India Institute of Medical Sciences

Trinitat Cambras

Universitat de Barcelona

Jasper Heinsbroek

Medical University of South Carolina

Sade Spencer

Medical University of South Carolina

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Papers by Michiel Hoon

Discovery of Transcription Factors Novel to Mouse Cerebellar Granule Cell Development Through Laser-Capture Microdissection

Cerebellum (London, England), Jan 6, 2018

Laser-capture microdissection was used to isolate external germinal layer tissue from three devel... more Laser-capture microdissection was used to isolate external germinal layer tissue from three developmental periods of mouse cerebellar development: embryonic days 13, 15, and 18. The cerebellar granule cell-enriched mRNA library was generated with next-generation sequencing using the Helicos technology. Our objective was to discover transcriptional regulators that could be important for the development of cerebellar granule cells-the most numerous neuron in the central nervous system. Through differential expression analysis, we have identified 82 differentially expressed transcription factors (TFs) from a total of 1311 differentially expressed genes. In addition, with TF-binding sequence analysis, we have identified 46 TF candidates that could be key regulators responsible for the variation in the granule cell transcriptome between developmental stages. Altogether, we identified 125 potential TFs (82 from differential expression analysis, 46 from motif analysis with 3 overlaps in th...

Open source clustering software

Bioinformatics, 2004

1Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Mina... more

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Site-specific DICER and DROSHA RNA products control the DNA-damage response

Nature, 2012

Non-coding RNAs (ncRNAs) are involved in an increasing number of cellular events 1. Some ncRNAs a... more Non-coding RNAs (ncRNAs) are involved in an increasing number of cellular events 1. Some ncRNAs are processed by DICER and DROSHA ribonucleases to give rise to small doublestranded RNAs involved in RNA interference (RNAi) 2. The DNA-damage response (DDR) is a signaling pathway that originates from the DNA lesion and arrests cell proliferation 3. So far, DICER or DROSHA RNA products have not been reported to control DDR activation. Here we show that DICER and DROSHA, but not downstream elements of the RNAi pathway, are necessary to activate DDR upon oncogene-induced genotoxic stress and exogenous DNA damage, as studied also by DDR foci formation in mammalian cells and zebrafish and by checkpoint assays. DDR foci are sensitive to RNase A treatment, and DICER-and DROSHA-dependent RNA products are required to restore DDR foci in treated cells. Through RNA deep sequencing and studies of DDR activation at an inducible unique DNA double-strand break (DSB), we demonstrate that DDR foci formation requires site-specific DICER-and DROSHA-dependent small RNAs, named DDRNAs, which act in a MRE11-RAD50-NBS1 (MRN) complex-dependent manner. Chemically synthesized or in vitro-generated by DICER cleavage, DDRNAs are sufficient to restore DDR in RNase A-treated cells, also in the absence of other cellular RNAs. Our results describe an unanticipated direct role of a novel class of ncRNAs in the control of DDR activation at sites of DNA damage.

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Redefining the transcriptional regulatory dynamics of classically and alternatively activated macrophages by deepCAGE transcriptomics

Nucleic acids research, Jan 27, 2015

Classically or alternatively activated macrophages (M1 and M2, respectively) play distinct and im... more Classically or alternatively activated macrophages (M1 and M2, respectively) play distinct and important roles for microbiocidal activity, regulation of inflammation and tissue homeostasis. Despite this, their transcriptional regulatory dynamics are poorly understood. Using promoter-level expression profiling by non-biased deepCAGE we have studied the transcriptional dynamics of classically and alternatively activated macrophages. Transcription factor (TF) binding motif activity analysis revealed four motifs, NFKB1_REL_RELA, IRF1,2, IRF7 and TBP that are commonly activated but have distinct activity dynamics in M1 and M2 activation. We observe matching changes in the expression profiles of the corresponding TFs and show that only a restricted set of TFs change expression. There is an overall drastic and transient up-regulation in M1 and a weaker and more sustainable up-regulation in M2. Novel TFs, such as Thap6, Maff, (M1) and Hivep1, Nfil3, Prdm1, (M2) among others, were suggested ...

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A promoter-level mammalian expression atlas

by Piero Carninci and Michiel Hoon

Nature, 2014

Regulated transcription controls the diversity, developmental pathways and spatial organization o... more Regulated transcription controls the diversity, developmental pathways and spatial organization of the hundreds of cell types that make up a mammal. Using single-molecule cDNA sequencing, we mapped transcription start sites (TSSs) and their usage in human and mouse primary cells, cell lines and tissues to produce a comprehensive overview of mammalian gene expression across the human body. We find that few genes are truly…

Discovery of Transcription Factors Novel to Mouse Cerebellar Granule Cell Development Through Laser-Capture Microdissection

Cerebellum (London, England), Jan 6, 2018