Limits...
An atlas of mouse CD4(+) T cell transcriptomes.

Stubbington MJ, Mahata B, Svensson V, Deonarine A, Nissen JK, Betz AG, Teichmann SA - Biol. Direct (2015)

Bottom Line: During an immune response Th cells mature from a naive state into one of several effector subtypes that exhibit distinct functions.To facilitate its use by others, we have made the data available in an easily accessible online resource at www.th-express.org .This article was reviewed by Wayne Hancock, Christine Wells and Erik van Nimwegen.

View Article: PubMed Central - PubMed

Affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. mstubb@ebi.ac.uk.

ABSTRACT

Background: CD4(+) T cells are key regulators of the adaptive immune system and can be divided into T helper (Th) cells and regulatory T (Treg) cells. During an immune response Th cells mature from a naive state into one of several effector subtypes that exhibit distinct functions. The transcriptional mechanisms that underlie the specific functional identity of CD4(+) T cells are not fully understood.

Results: To assist investigations into the transcriptional identity and regulatory processes of these cells we performed mRNA-sequencing on three murine T helper subtypes (Th1, Th2 and Th17) as well as on splenic Treg cells and induced Treg (iTreg) cells. Our integrated analysis of this dataset revealed the gene expression changes associated with these related but distinct cellular identities. Each cell subtype differentially expresses a wealth of 'subtype upregulated' genes, some of which are well known whilst others promise new insights into signalling processes and transcriptional regulation. We show that hundreds of genes are regulated purely by alternative splicing to extend our knowledge of the role of post-transcriptional regulation in cell differentiation.

Conclusions: This CD4(+) transcriptome atlas provides a valuable resource for the study of CD4(+) T cell populations. To facilitate its use by others, we have made the data available in an easily accessible online resource at www.th-express.org .

Reviewers: This article was reviewed by Wayne Hancock, Christine Wells and Erik van Nimwegen.

No MeSH data available.


Related in: MedlinePlus

Varying expression of splicing factors in the CD4+subtypes. Expression levels of genes known to encode proteins involved in pre-mRNA splicing are presented as Z-scores. Colours to the left of the rows indicate the subtype that SU genes were assigned to as follows. Naive, red; Th1, blue; Th2, green, Th17, purple, Treg, orange; iTreg, yellow. The list of splicing factors was taken from Chen et al. [68] and mouse orthologues of human genes were found by searching the Mouse Genome Database [82].
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4384382&req=5

Fig13: Varying expression of splicing factors in the CD4+subtypes. Expression levels of genes known to encode proteins involved in pre-mRNA splicing are presented as Z-scores. Colours to the left of the rows indicate the subtype that SU genes were assigned to as follows. Naive, red; Th1, blue; Th2, green, Th17, purple, Treg, orange; iTreg, yellow. The list of splicing factors was taken from Chen et al. [68] and mouse orthologues of human genes were found by searching the Mouse Genome Database [82].

Mentions: To find a possible explanation for the observed splicing changes between subtypes we analysed the differential expression of genes encoding protein factors involved in the regulation of alternative splicing [57]. The expression of these genes varies between subtypes and seven of them are classed as SU genes (FigureĀ 13).Figure 13


An atlas of mouse CD4(+) T cell transcriptomes.

Stubbington MJ, Mahata B, Svensson V, Deonarine A, Nissen JK, Betz AG, Teichmann SA - Biol. Direct (2015)

Varying expression of splicing factors in the CD4+subtypes. Expression levels of genes known to encode proteins involved in pre-mRNA splicing are presented as Z-scores. Colours to the left of the rows indicate the subtype that SU genes were assigned to as follows. Naive, red; Th1, blue; Th2, green, Th17, purple, Treg, orange; iTreg, yellow. The list of splicing factors was taken from Chen et al. [68] and mouse orthologues of human genes were found by searching the Mouse Genome Database [82].
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4384382&req=5

Fig13: Varying expression of splicing factors in the CD4+subtypes. Expression levels of genes known to encode proteins involved in pre-mRNA splicing are presented as Z-scores. Colours to the left of the rows indicate the subtype that SU genes were assigned to as follows. Naive, red; Th1, blue; Th2, green, Th17, purple, Treg, orange; iTreg, yellow. The list of splicing factors was taken from Chen et al. [68] and mouse orthologues of human genes were found by searching the Mouse Genome Database [82].
Mentions: To find a possible explanation for the observed splicing changes between subtypes we analysed the differential expression of genes encoding protein factors involved in the regulation of alternative splicing [57]. The expression of these genes varies between subtypes and seven of them are classed as SU genes (FigureĀ 13).Figure 13

Bottom Line: During an immune response Th cells mature from a naive state into one of several effector subtypes that exhibit distinct functions.To facilitate its use by others, we have made the data available in an easily accessible online resource at www.th-express.org .This article was reviewed by Wayne Hancock, Christine Wells and Erik van Nimwegen.

View Article: PubMed Central - PubMed

Affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. mstubb@ebi.ac.uk.

ABSTRACT

Background: CD4(+) T cells are key regulators of the adaptive immune system and can be divided into T helper (Th) cells and regulatory T (Treg) cells. During an immune response Th cells mature from a naive state into one of several effector subtypes that exhibit distinct functions. The transcriptional mechanisms that underlie the specific functional identity of CD4(+) T cells are not fully understood.

Results: To assist investigations into the transcriptional identity and regulatory processes of these cells we performed mRNA-sequencing on three murine T helper subtypes (Th1, Th2 and Th17) as well as on splenic Treg cells and induced Treg (iTreg) cells. Our integrated analysis of this dataset revealed the gene expression changes associated with these related but distinct cellular identities. Each cell subtype differentially expresses a wealth of 'subtype upregulated' genes, some of which are well known whilst others promise new insights into signalling processes and transcriptional regulation. We show that hundreds of genes are regulated purely by alternative splicing to extend our knowledge of the role of post-transcriptional regulation in cell differentiation.

Conclusions: This CD4(+) transcriptome atlas provides a valuable resource for the study of CD4(+) T cell populations. To facilitate its use by others, we have made the data available in an easily accessible online resource at www.th-express.org .

Reviewers: This article was reviewed by Wayne Hancock, Christine Wells and Erik van Nimwegen.

No MeSH data available.


Related in: MedlinePlus