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CAGE-defined promoter regions of the genes implicated in Rett Syndrome.

Vitezic M, Bertin N, Andersson R, Lipovich L, Kawaji H, Lassmann T, Sandelin A, Heutink P, Goldowitz D, Ha T, Zhang P, Patrizi A, Fagiolini M, Forrest AR, Carninci P, Saxena A, FANTOM Consorti - BMC Genomics (2014)

Bottom Line: We show that FOXG1 expression is poorly correlated with the expression of MECP2 and CDKL5.We identify promoter shapes for each TSS, the predicted location of enhancers for each gene and the common transcription factors likely to regulate the three genes.Our data imply Polycomb Repressive Complex 2 (PRC2) mediated silencing of Foxg1 in cerebellum.

View Article: PubMed Central - PubMed

Affiliation: Omics Science Center, RIKEN Yokohama Institute, Omics Science Center (OSC), 1-17-22 Suehiro cho, Tsurumi ku, Yokohama, Japan. mvitezic@gmail.com.

ABSTRACT

Background: Mutations in three functionally diverse genes cause Rett Syndrome. Although the functions of Forkhead box G1 (FOXG1), Methyl CpG binding protein 2 (MECP2) and Cyclin-dependent kinase-like 5 (CDKL5) have been studied individually, not much is known about their relation to each other with respect to expression levels and regulatory regions. Here we analyzed data from hundreds of mouse and human samples included in the FANTOM5 project, to identify transcript initiation sites, expression levels, expression correlations and regulatory regions of the three genes.

Results: Our investigations reveal the predominantly used transcription start sites (TSSs) for each gene including novel transcription start sites for FOXG1. We show that FOXG1 expression is poorly correlated with the expression of MECP2 and CDKL5. We identify promoter shapes for each TSS, the predicted location of enhancers for each gene and the common transcription factors likely to regulate the three genes. Our data imply Polycomb Repressive Complex 2 (PRC2) mediated silencing of Foxg1 in cerebellum.

Conclusions: Our analyses provide a comprehensive picture of the regulatory regions of the three genes involved in Rett Syndrome.

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Related in: MedlinePlus

Expression levels of the identified TSS for the three genes. Dot plots showing the expression level of each promoter in TPM values in all brain regions, and selected other samples (based on expression level). The novel promoter pA@Foxg1 is the most highly expressed Foxg1 TSS in mouse primary cells and brain tissue (a), with the highest expression in cortical neurons (1018 TPM) and neonate hippocampus (435 TPM). Among mouse cells, we find high levels of p1@ Foxg1 expressed in hippocampal neurons and fibroblast cell line. In human samples (panel b) the highest expression of FOXG1 is seen from p1@FOXG1 in fetal temporal lobe (292 TPM), among primary cells in neurons (149 TPM) and among cell lines in medulloblastoma cell line (184 TPM). For mouse Mecp2, the highest expression of p1@Mecp2 is in striatal neurons (77 TPM) and cerebellar granule cells (70 TPM) and among mouse tissues (panel c) the maximum expression is seen in neonate corpus striatum (65 TPM) and adult cerebellum (52 TPM). For human, the highest expression of p1@MECP2 is found in cancer cell lines including breast carcinoma cell line (119 TPM) (panel d). In human brain the highest expression of p1@MECP2 is found in the temporal lobe (63 TPM). The two promoters of Cdkl5 in mouse are co-expressed with highest expression in adult cortex in the brain and raphe neurons among primary cells (panel e). In humans (panel f) the two promoters are expressed differentially with transcripts arising from p1 over-represented. p1@CDKL5 expression is highest in the newborn medial frontal gyrus and in neurons. In human cancer cell lines, CDKL5 is generally expressed at low levels (less than 10 TPM) from either of the promoters (p1 > p2), with a few exceptions (Additional file 1: Table S1, Additional file 3: Figure S1f).
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Fig1: Expression levels of the identified TSS for the three genes. Dot plots showing the expression level of each promoter in TPM values in all brain regions, and selected other samples (based on expression level). The novel promoter pA@Foxg1 is the most highly expressed Foxg1 TSS in mouse primary cells and brain tissue (a), with the highest expression in cortical neurons (1018 TPM) and neonate hippocampus (435 TPM). Among mouse cells, we find high levels of p1@ Foxg1 expressed in hippocampal neurons and fibroblast cell line. In human samples (panel b) the highest expression of FOXG1 is seen from p1@FOXG1 in fetal temporal lobe (292 TPM), among primary cells in neurons (149 TPM) and among cell lines in medulloblastoma cell line (184 TPM). For mouse Mecp2, the highest expression of p1@Mecp2 is in striatal neurons (77 TPM) and cerebellar granule cells (70 TPM) and among mouse tissues (panel c) the maximum expression is seen in neonate corpus striatum (65 TPM) and adult cerebellum (52 TPM). For human, the highest expression of p1@MECP2 is found in cancer cell lines including breast carcinoma cell line (119 TPM) (panel d). In human brain the highest expression of p1@MECP2 is found in the temporal lobe (63 TPM). The two promoters of Cdkl5 in mouse are co-expressed with highest expression in adult cortex in the brain and raphe neurons among primary cells (panel e). In humans (panel f) the two promoters are expressed differentially with transcripts arising from p1 over-represented. p1@CDKL5 expression is highest in the newborn medial frontal gyrus and in neurons. In human cancer cell lines, CDKL5 is generally expressed at low levels (less than 10 TPM) from either of the promoters (p1 > p2), with a few exceptions (Additional file 1: Table S1, Additional file 3: Figure S1f).

Mentions: Analyses of TSS from 1193 human samples and 457 mouse samples comprised of tissues, primary cells and cell lines (only one mouse cell line was investigated in FANTOM5) identified 8 TSSs for human FOXG1 and 6 TSSs for mouse Foxg1 (Additional file 2: Table S2). FOXG1 expression above 1 TPM was found in 23% (231) and 30% (140) of human and mouse samples respectively, suggesting that the expression of this gene was limited to selected tissues (Additional file 1: Table S1). Transcription start sites were defined as novel if they were found at a distance of over 500 bp from the known RefSeq TSSs. Our data show 3 TSSs in mouse highly expressed in brain sub-regions and cells, two of which are novel. The expression levels of different TSSs of FOXG1 were variable in human and mouse samples, with the highest expression seen in specific regions of the brain (Figures 1a, b, Additional file 3: Figures S1a,b). The top three initiation sites were located at (in order of their expression levels) chr12:50484904..50484950,+; (pA@Foxg1, novel promoter, located more than 1000 bases downstream of the RefSeq annotated TSSs) chr12:50483639..50483654,+; (p1@Foxg1, 200 bp upstream of the two annotated Foxg1 TSSs) and chr12:50485112..50485144,+;(pB@Foxg1, novel promoter, 1200 bp downstream from the annotated RefSeq initiation sites) (Figure 2a). Expression of mouse Foxg1 was also restricted to brain tissue and brain related cells, but surprisingly the two novel TSSs of mouse Foxg1 were also found highly expressed in the single mouse cell line sequenced in the FANTOM5 project (fibroblast cell line) suggesting that other than the brain, fibroblast cell lines may be useful for in vitro analysis of Foxg1 in mouse (Figure 1a).Figure 1


CAGE-defined promoter regions of the genes implicated in Rett Syndrome.

Vitezic M, Bertin N, Andersson R, Lipovich L, Kawaji H, Lassmann T, Sandelin A, Heutink P, Goldowitz D, Ha T, Zhang P, Patrizi A, Fagiolini M, Forrest AR, Carninci P, Saxena A, FANTOM Consorti - BMC Genomics (2014)

Expression levels of the identified TSS for the three genes. Dot plots showing the expression level of each promoter in TPM values in all brain regions, and selected other samples (based on expression level). The novel promoter pA@Foxg1 is the most highly expressed Foxg1 TSS in mouse primary cells and brain tissue (a), with the highest expression in cortical neurons (1018 TPM) and neonate hippocampus (435 TPM). Among mouse cells, we find high levels of p1@ Foxg1 expressed in hippocampal neurons and fibroblast cell line. In human samples (panel b) the highest expression of FOXG1 is seen from p1@FOXG1 in fetal temporal lobe (292 TPM), among primary cells in neurons (149 TPM) and among cell lines in medulloblastoma cell line (184 TPM). For mouse Mecp2, the highest expression of p1@Mecp2 is in striatal neurons (77 TPM) and cerebellar granule cells (70 TPM) and among mouse tissues (panel c) the maximum expression is seen in neonate corpus striatum (65 TPM) and adult cerebellum (52 TPM). For human, the highest expression of p1@MECP2 is found in cancer cell lines including breast carcinoma cell line (119 TPM) (panel d). In human brain the highest expression of p1@MECP2 is found in the temporal lobe (63 TPM). The two promoters of Cdkl5 in mouse are co-expressed with highest expression in adult cortex in the brain and raphe neurons among primary cells (panel e). In humans (panel f) the two promoters are expressed differentially with transcripts arising from p1 over-represented. p1@CDKL5 expression is highest in the newborn medial frontal gyrus and in neurons. In human cancer cell lines, CDKL5 is generally expressed at low levels (less than 10 TPM) from either of the promoters (p1 > p2), with a few exceptions (Additional file 1: Table S1, Additional file 3: Figure S1f).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4522966&req=5

Fig1: Expression levels of the identified TSS for the three genes. Dot plots showing the expression level of each promoter in TPM values in all brain regions, and selected other samples (based on expression level). The novel promoter pA@Foxg1 is the most highly expressed Foxg1 TSS in mouse primary cells and brain tissue (a), with the highest expression in cortical neurons (1018 TPM) and neonate hippocampus (435 TPM). Among mouse cells, we find high levels of p1@ Foxg1 expressed in hippocampal neurons and fibroblast cell line. In human samples (panel b) the highest expression of FOXG1 is seen from p1@FOXG1 in fetal temporal lobe (292 TPM), among primary cells in neurons (149 TPM) and among cell lines in medulloblastoma cell line (184 TPM). For mouse Mecp2, the highest expression of p1@Mecp2 is in striatal neurons (77 TPM) and cerebellar granule cells (70 TPM) and among mouse tissues (panel c) the maximum expression is seen in neonate corpus striatum (65 TPM) and adult cerebellum (52 TPM). For human, the highest expression of p1@MECP2 is found in cancer cell lines including breast carcinoma cell line (119 TPM) (panel d). In human brain the highest expression of p1@MECP2 is found in the temporal lobe (63 TPM). The two promoters of Cdkl5 in mouse are co-expressed with highest expression in adult cortex in the brain and raphe neurons among primary cells (panel e). In humans (panel f) the two promoters are expressed differentially with transcripts arising from p1 over-represented. p1@CDKL5 expression is highest in the newborn medial frontal gyrus and in neurons. In human cancer cell lines, CDKL5 is generally expressed at low levels (less than 10 TPM) from either of the promoters (p1 > p2), with a few exceptions (Additional file 1: Table S1, Additional file 3: Figure S1f).
Mentions: Analyses of TSS from 1193 human samples and 457 mouse samples comprised of tissues, primary cells and cell lines (only one mouse cell line was investigated in FANTOM5) identified 8 TSSs for human FOXG1 and 6 TSSs for mouse Foxg1 (Additional file 2: Table S2). FOXG1 expression above 1 TPM was found in 23% (231) and 30% (140) of human and mouse samples respectively, suggesting that the expression of this gene was limited to selected tissues (Additional file 1: Table S1). Transcription start sites were defined as novel if they were found at a distance of over 500 bp from the known RefSeq TSSs. Our data show 3 TSSs in mouse highly expressed in brain sub-regions and cells, two of which are novel. The expression levels of different TSSs of FOXG1 were variable in human and mouse samples, with the highest expression seen in specific regions of the brain (Figures 1a, b, Additional file 3: Figures S1a,b). The top three initiation sites were located at (in order of their expression levels) chr12:50484904..50484950,+; (pA@Foxg1, novel promoter, located more than 1000 bases downstream of the RefSeq annotated TSSs) chr12:50483639..50483654,+; (p1@Foxg1, 200 bp upstream of the two annotated Foxg1 TSSs) and chr12:50485112..50485144,+;(pB@Foxg1, novel promoter, 1200 bp downstream from the annotated RefSeq initiation sites) (Figure 2a). Expression of mouse Foxg1 was also restricted to brain tissue and brain related cells, but surprisingly the two novel TSSs of mouse Foxg1 were also found highly expressed in the single mouse cell line sequenced in the FANTOM5 project (fibroblast cell line) suggesting that other than the brain, fibroblast cell lines may be useful for in vitro analysis of Foxg1 in mouse (Figure 1a).Figure 1

Bottom Line: We show that FOXG1 expression is poorly correlated with the expression of MECP2 and CDKL5.We identify promoter shapes for each TSS, the predicted location of enhancers for each gene and the common transcription factors likely to regulate the three genes.Our data imply Polycomb Repressive Complex 2 (PRC2) mediated silencing of Foxg1 in cerebellum.

View Article: PubMed Central - PubMed

Affiliation: Omics Science Center, RIKEN Yokohama Institute, Omics Science Center (OSC), 1-17-22 Suehiro cho, Tsurumi ku, Yokohama, Japan. mvitezic@gmail.com.

ABSTRACT

Background: Mutations in three functionally diverse genes cause Rett Syndrome. Although the functions of Forkhead box G1 (FOXG1), Methyl CpG binding protein 2 (MECP2) and Cyclin-dependent kinase-like 5 (CDKL5) have been studied individually, not much is known about their relation to each other with respect to expression levels and regulatory regions. Here we analyzed data from hundreds of mouse and human samples included in the FANTOM5 project, to identify transcript initiation sites, expression levels, expression correlations and regulatory regions of the three genes.

Results: Our investigations reveal the predominantly used transcription start sites (TSSs) for each gene including novel transcription start sites for FOXG1. We show that FOXG1 expression is poorly correlated with the expression of MECP2 and CDKL5. We identify promoter shapes for each TSS, the predicted location of enhancers for each gene and the common transcription factors likely to regulate the three genes. Our data imply Polycomb Repressive Complex 2 (PRC2) mediated silencing of Foxg1 in cerebellum.

Conclusions: Our analyses provide a comprehensive picture of the regulatory regions of the three genes involved in Rett Syndrome.

Show MeSH
Related in: MedlinePlus