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

TY - JOUR

T1 - CAGE-defined promoter regions of the genes implicated in Rett Syndrome

AU - Vitezic, Morana

AU - Bertin, Nicolas

AU - Andersson, Robin

AU - Lipovich, Leonard

AU - Kawaji, Hideya

AU - Lassmann, Timo

AU - Sandelin, Albin Gustav

AU - Heutink, Peter

AU - Goldowitz, Dan

AU - Ha, Thomas

AU - Zhang, Peter

AU - Patrizi, Annarita

AU - Fagiolini, Michela

AU - Forrest, Alistair Rr

AU - Carninci, Piero

AU - Saxena, Alka

PY - 2014/12/24

Y1 - 2014/12/24

N2 - 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.

AB - 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.

U2 - 10.1186/1471-2164-15-1177

DO - 10.1186/1471-2164-15-1177

M3 - Journal article

C2 - 25539566

SN - 1471-2164

VL - 15

JO - BMC Genomics

JF - BMC Genomics

M1 - 1177

ER -