Format

Send to

Choose Destination
BMC Genomics. 2014 Dec 24;15:1177. doi: 10.1186/1471-2164-15-1177.

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

Author information

1
Omics Science Center, RIKEN Yokohama Institute, Omics Science Center (OSC), 1-17-22 Suehiro cho, Tsurumi ku, Yokohama, Japan. mvitezic@gmail.com.
2
Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden. mvitezic@gmail.com.
3
The Bioinformatics Center, Department of Biology and Biotech Research and Innovation Center, University of Copenhagen, Copenhagen, Denmark. mvitezic@gmail.com.
4
Omics Science Center, RIKEN Yokohama Institute, Omics Science Center (OSC), 1-17-22 Suehiro cho, Tsurumi ku, Yokohama, Japan. nicolas.bertin@gmail.com.
5
Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies, Yokohama, Japan. nicolas.bertin@gmail.com.
6
Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore. nicolas.bertin@gmail.com.
7
The Bioinformatics Center, Department of Biology and Biotech Research and Innovation Center, University of Copenhagen, Copenhagen, Denmark. robin@binf.ku.dk.
8
Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA. LLipovich@med.wayne.edu.
9
Department of Neurology, School of Medicine, Wayne State University, Detroit, MI, USA. LLipovich@med.wayne.edu.
10
Omics Science Center, RIKEN Yokohama Institute, Omics Science Center (OSC), 1-17-22 Suehiro cho, Tsurumi ku, Yokohama, Japan. kawaji@gsc.riken.jp.
11
Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies, Yokohama, Japan. kawaji@gsc.riken.jp.
12
RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), Wako, Japan. kawaji@gsc.riken.jp.
13
Omics Science Center, RIKEN Yokohama Institute, Omics Science Center (OSC), 1-17-22 Suehiro cho, Tsurumi ku, Yokohama, Japan. timo.lassmann@telethonkids.org.au.
14
Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies, Yokohama, Japan. timo.lassmann@telethonkids.org.au.
15
Telethon Kids Institute, The University of Western Australia, Perth, Australia. timo.lassmann@telethonkids.org.au.
16
The Bioinformatics Center, Department of Biology and Biotech Research and Innovation Center, University of Copenhagen, Copenhagen, Denmark. albin@binf.ku.dk.
17
Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies, Yokohama, Japan. peter.heutink@dzne.de.
18
German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany. peter.heutink@dzne.de.
19
Eberhard Karls University, Tübingen, Germany. peter.heutink@dzne.de.
20
Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Dept of Medical Genetics, University of British Columbia, Vancouver, Canada. dang@cmmt.ubc.ca.
21
Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Dept of Medical Genetics, University of British Columbia, Vancouver, Canada. tjha@cmmt.ubc.ca.
22
Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Dept of Medical Genetics, University of British Columbia, Vancouver, Canada. pzhang@cmmt.ubc.ca.
23
FM Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA. annarita.patrizi@childrens.harvard.edu.
24
FM Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA. michela.fagiolini@childrens.harvard.edu.
25
Omics Science Center, RIKEN Yokohama Institute, Omics Science Center (OSC), 1-17-22 Suehiro cho, Tsurumi ku, Yokohama, Japan. forrest@gsc.riken.jp.
26
Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies, Yokohama, Japan. forrest@gsc.riken.jp.
27
Omics Science Center, RIKEN Yokohama Institute, Omics Science Center (OSC), 1-17-22 Suehiro cho, Tsurumi ku, Yokohama, Japan. carninci@riken.jp.
28
Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies, Yokohama, Japan. carninci@riken.jp.
29
Omics Science Center, RIKEN Yokohama Institute, Omics Science Center (OSC), 1-17-22 Suehiro cho, Tsurumi ku, Yokohama, Japan. alka.saxena@gstt.nhs.uk.
30
Biomedical Research Centre at Guy's and St Thomas' Trust, Genomics Core Facility, Guy's Hospital, London, UK. alka.saxena@gstt.nhs.uk.

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.

PMID:
25539566
PMCID:
PMC4522966
DOI:
10.1186/1471-2164-15-1177
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for BioMed Central Icon for PubMed Central
Loading ...
Support Center