Seminar: Dr. Michiel de Hoon

FANTOMS: the transcriptome of human primary cells, tissues, and cell lines

Date:
7 November 2014 12:00 hrs. - 13:00 hrs.
Location:
Figdor Lecture Theatre, 8th floor RIMLS Building, Geert Grooteplein 26-28, route 289
Title:
FANTOMS: the transcriptome of human primary cells, tissues, and cell lines
Speaker(s):

Dr. Michiel de Hoon, Human Genome Center, Tokyo University, Japan

Host(s):

Dr. Colin Logie, Dept. of Molecular Biology, RIMLS

07-11-2014 12:00:0007-11-2014 13:00:00Europe/AmsterdamFANTOMS: the transcriptome of human primary cells, tissues, and cell lines Figdor Lecture Theatre, 8th floor RIMLS Building, Geert Grooteplein 26-28, route 289Rimlsrimls@radboudumc.nl

Remarks / more information:

Hoon De , MichielMammals are complex multicellular organisms composed of approximately 400 different cell types. Though all cells (with a few exceptions) in an organism carry the exact same genomic information, their morphology, functionality, developmental pathways, relative numbers, and spatial organization is extraordinarily diverse. The diversity is due to the different transcriptional programs active in each cell type, in particular with regard to the differential usage of promoters and enhancers across cells. Using single molecule sequencing, we mapped human and mouse transcription start sites (TSS0 and measured their expression based upon Cap Analysis of Gene Expression (CAGE) across a broad panel of primary cells, cell lines and tissues, producing a comprehensive atlas of gene expression in mammalian cells. Using the atlas, we identify key transcription factors and promoter proximal motifs used in each primary cell state. Functional annotation of novel transcripts is also provided by systematic testing  of cell, anatomical and disease ontology terms associated with the samples most highly expressing them and functional ontology enrichment analyses. The FANTOMS promoter expression atlas thus provides a comprehensive elucidation and functional annotation of the cell-type-specific transcriptomes in human and mouse with wide applications in biomedical research.

 

Key Publications:

  • A promoter-level mammalian expression atlas. Nature;507:462-70, 2014
  • Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance. Nat Genet. 46: 558-66, 2014
  • Redefinition of the human mast cell transcriptome by deep-CAGE sequencing. Blood, 123: e58-67, 2014

 



<< back to all events