NDLI: Discovery and assessment of conserved Pax6 target genes and enhancers

Content Provider	PubMed Central
Author	Coutinho, Pedro Pavlou, Sofia Bhatia, Shipra Chalmers, Kevin J. Kleinjan, Dirk A. Heyningen, Veronica Van
Copyright Year	2011
Abstract	The characterization of transcriptional networks (TNs) is essential for understanding complex biological phenomena such as development, disease, and evolution. In this study, we have designed and implemented a procedure that combines in silico target screens with zebrafish and mouse validation, in order to identify cis-elements and genes directly regulated by Pax6. We chose Pax6 as the paradigm because of its crucial roles in organogenesis and human disease. We identified over 600 putative Pax6 binding sites and more than 200 predicted direct target genes, conserved in evolution from zebrafish to human and to mouse. This was accomplished using hidden Markov models (HMMs) generated from experimentally validated Pax6 binding sites. A small sample of genes, expressed in the neural lineage, was chosen from the predictions for RNA in situ validation using zebrafish and mouse models. Validation of DNA binding to some predicted cis-elements was also carried out using chromatin immunoprecipitation (ChIP) and zebrafish reporter transgenic studies. The results show that this combined procedure is a highly efficient tool to investigate the architecture of TNs and constitutes a useful complementary resource to ChIP and expression data sets because of its inherent spatiotemporal independence. We have identified several novel direct targets, including some putative disease genes, among them Foxp2; these will allow further dissection of Pax6 function in development and disease.
Related Links	http://dx.doi.org/10.1101/gr.124115.111
Ending Page	1359
Page Count	11
Starting Page	1349
File Format	PDF
ISSN	10889051
e-ISSN	15495469
Journal	Genome Research
Issue Number	8
Volume Number	21
Language	English
Publisher	Cold Spring Harbor Laboratory Press
Publisher Date	2011-08-01
Access Restriction	Open
Rights Holder	Cold Spring Harbor Laboratory Press
Subject Keyword	Genetics(clinical) Genetics Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Genetics Genetics (clinical)

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Discovery and assessment of conserved Pax6 target genes and enhancers.

Genome-wide prediction of conserved and nonconserved enhancers by histone acetylation patterns

Genome-wide discovery of human heart enhancers

Coding exons function as tissue-specific enhancers of nearby genes

Identification of conserved skeletal enhancers associated with craniosynostosis risk genes

ChIP-seq Identification of Weakly Conserved Heart Enhancers

Native homing endonucleases can target conserved genes in humans and in animal models

Conserved and non-conserved enhancers direct tissue specific transcription in ancient germ layer specific developmental control genes

Sequencing of Pax6 Loci from the Elephant Shark Reveals a Family of Pax6 Genes in Vertebrate Genomes, Forged by Ancient Duplications and Divergences

Discovery and assessment of conserved Pax6 target genes and enhancers

Similar Documents

Discovery and assessment of conserved Pax6 target genes and enhancers.

Genome-wide prediction of conserved and nonconserved enhancers by histone acetylation patterns

Genome-wide discovery of human heart enhancers

Coding exons function as tissue-specific enhancers of nearby genes

Identification of conserved skeletal enhancers associated with craniosynostosis risk genes

ChIP-seq Identification of Weakly Conserved Heart Enhancers

Native homing endonucleases can target conserved genes in humans and in animal models

Conserved and non-conserved enhancers direct tissue specific transcription in ancient germ layer specific developmental control genes

Sequencing of Pax6 Loci from the Elephant Shark Reveals a Family of Pax6 Genes in Vertebrate Genomes, Forged by Ancient Duplications and Divergences

Discovery and assessment of conserved Pax6 target genes and enhancers