title: Next-generation insights into regulatory T cells: expression profiling and FoxP3 occupancy in Human.
abstract: Regulatory T-cells (Treg) play an essential role in the negative regulation of immune answers by developing an attenuated cytokine response that allows suppressing proliferation and effector function of T-cells (CD4(+) Th). The transcription factor FoxP3 is responsible for the regulation of many genes involved in the Treg gene signature. Its ablation leads to severe immune deficiencies in human and mice. Recent developments in sequencing technologies have revolutionized the possibilities to gain insights into transcription factor binding by ChiP-seq and into transcriptome analysis by mRNA-seq. We combine FoxP3 ChiP-seq and mRNA-seq in order to understand the transcriptional differences between primary human CD4(+) T helper and regulatory T-cells, as well as to study the role of FoxP3 in generating those differences. We show, that mRNA-seq allows analyzing the transcriptomal landscape of T-cells including the expression of specific splice variants at much greater depth than previous approaches, whereas 50% of transcriptional regulation events have not been described before by using diverse array technologies. We discovered splicing patterns like the expression of a kinase-dead isoform of IRAK1 upon T-cell activation. The immunoproteasome is up-regulated in both Treg and CD4(+) Th cells upon activation, whereas the 'standard' proteasome is up-regulated in Tregs only upon activation.
authors: Department of Pulmonary Research, Group Genomics, Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorferstraße 67, 88397 Biberach an der Riß, Germany.
authors: Fabian
authors: F
authors: Birzele
authors: Tanja
authors: T
authors: Fauti
authors: Heiko
authors: H
authors: Stahl
authors: Martin C
authors: MC
authors: Lenter
authors: Eric
authors: E
authors: Simon
authors: Dagmar
authors: D
authors: Knebel
authors: Andreas
authors: A
authors: Weith
authors: Tobias
authors: T
authors: Hildebrandt
authors: Detlev
authors: D
authors: Mennerich
mesh_terms: D017398:Alternative Splicing; D000818:Animals; D001665:Binding Sites; D047369:Chromatin Immunoprecipitation; D051858:Forkhead Transcription Factors / Q000378:metabolism*; D020869:Gene Expression Profiling; D006801:Humans; D051379:Mice; D012333:RNA, Messenger / Q000737:chemistry / Q000378:metabolism; D017422:Sequence Analysis, DNA; D017423:Sequence Analysis, RNA; D006377:T-Lymphocytes, Helper-Inducer / Q000276:immunology*; D050378:T-Lymphocytes, Regulatory / Q000276:immunology*; D059467:Transcriptome
chemical_list: C418974:FOXP3 protein, human; D051858:Forkhead Transcription Factors; D012333:RNA, Messenger