A genome wide transcriptional model of the complex response to pre-TCR signalling during thymocyte differentiation

• Published in: Oncotarget Vol. 6; no. 30; pp. 28646 - 28660
• Main Authors: Sahni, Hemant, Ross, Susan, Barbarulo, Alessandro, Solanki, Anisha, Lau, Ching-In, Furmanski, Anna, Saldaña, José Ignacio, Ono, Masahiro, Hubank, Mike, Barenco, Martino, Crompton, Tessa
• Format: Journal Article
• Language: English
• Published: United States Impact Journals LLC 06-10-2015
• Subjects: Animals; Cell Differentiation; Cells, Cultured; Cluster Analysis; Gene Expression Profiling - methods; Gene Expression Regulation, Developmental; Genetic Markers; Genome-Wide Association Study; Genotype; Homeodomain Proteins - genetics; Homeodomain Proteins - immunology; Homeodomain Proteins - metabolism; Mice, Inbred C57BL; Mice, Knockout; Models, Genetic; Oligonucleotide Array Sequence Analysis; Phenotype; Protein Precursors - genetics; Protein Precursors - immunology; Protein Precursors - metabolism; Receptors, Antigen, T-Cell - genetics; Receptors, Antigen, T-Cell - immunology; Receptors, Antigen, T-Cell - metabolism; Research Paper: Immunology; RNA - genetics; RNA - metabolism; RNA Stability; Signal Transduction; Thymocytes - immunology; Thymocytes - metabolism; Time Factors; Transcription Factors - genetics; Transcription Factors - metabolism; Transcription, Genetic; foetal thymic organ cultures; thymus; Immune response; DP; Immunity; Immunology Section; genome wide transcriptional modelling; pre-TCR
• ISSN: 1949-2553; 1949-2553
• DOI: 10.18632/oncotarget.5796

Developing thymocytes require pre-TCR signalling to differentiate from CD4-CD8- double negative to CD4+CD8+ double positive cell. Here we followed the transcriptional response to pre-TCR signalling in a synchronised population of differentiating double negative thymocytes. This time series analysis revealed a complex transcriptional response, in which thousands of genes were up and down-regulated before changes in cell surface phenotype were detected. Genome-wide measurement of RNA degradation of individual genes showed great heterogeneity in the rate of degradation between different genes. We therefore used time course expression and degradation data and a genome wide transcriptional modelling (GWTM) strategy to model the transcriptional response of genes up-regulated on pre-TCR signal transduction. This analysis revealed five major temporally distinct transcriptional activities that up regulate transcription through time, whereas down-regulation of expression occurred in three waves. Our model thus placed known regulators in a temporal perspective, and in addition identified novel candidate regulators of thymocyte differentiation.