NDLI: Comparative genomics modeling of the NRSF/REST repressor network: from single conserved sites to genome-wide repertoire.

Please wait, while we are loading the content...

Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice.

Genomic organization of the Drosophila telomere retrotransposable elements.

Identifying gene regulatory elements by genomic microarray mapping of DNaseI hypersensitive sites.

Large-scale intron conservation and order-of-magnitude variation in intron loss/gain rates in apicomplexan evolution.

Mapping of the juxtacentromeric heterochromatin-euchromatin frontier of human chromosome 21.

Year: 2006 Volume: 16 Issue: 9

Year: 2006 Volume: 16 Issue: 8

Year: 2006 Volume: 16 Issue: 7

Year: 2006 Volume: 16 Issue: 6

Year: 2006 Volume: 16 Issue: 5

Year: 2006 Volume: 16 Issue: 4

Year: 2006 Volume: 16 Issue: 3

Year: 2006 Volume: 16 Issue: 2

Year: 2006 Volume: 16 Issue: 1

Year: 2005 Volume: 15

Year: 2004 Volume: 14

Year: 2003 Volume: 13

Year: 2002 Volume: 12

Year: 2001 Volume: 11

Year: 2000 Volume: 10

Year: 1999 Volume: 9

Year: 1998 Volume: 8

Year: 1997 Volume: 7

Comparative genomics modeling of the NRSF/REST repressor network: from single conserved sites to genome-wide repertoire.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Mortazavi, Ali Leeper Thompson, Evonne Chen Garcia, Sarah T. Myers, Richard M. Wold, Barbara
Description	Country affiliation: United States Author Affiliation: Mortazavi A ( Division of Biology, California Institute of Technology, Pasadena, California 91125, USA.)
Abstract	We constructed and applied an open source informatic framework called Cistematic in an effort to predict the target gene repertoire for transcription factors with large binding sites. Cistematic uses two different evolutionary conservation-filtering algorithms in conjunction with several analysis modules. Beginning with a single conserved and biologically tested site for the neuronal repressor NRSF/REST, Cistematic generated a refined PSFM (position specific frequency matrix) based on conserved site occurrences in mouse, human, and dog genomes. Predictions from this model were validated by chromatin immunoprecipitation (ChIP) followed by quantitative PCR. The combination of transfection assays and ChIP enrichment data provided an objective basis for setting a threshold for membership and rank-ordering a final gene cohort model consisting of 842 high-confidence sites in the human genome associated with 733 genes. Statistically significant enrichment of NRSE-associated genes was found for neuron-specific Gene Ontology (GO) terms and neuronal mRNA expression profiles. A more extensive evolutionary survey showed that NRSE sites matching the PSFM model exist in roughly similar numbers in all fully sequenced vertebrate genomes but are notably absent from invertebrate and protochordate genomes, as is NRSF itself. Some NRSF/REST sites reside in repeats, which suggests a mechanism for both ancient and modern dispersal of NRSEs through vertebrate genomes. Multiple predicted sites are located near neuronal microRNA and splicing-factor genes, and these tested positive for NRSF/REST occupancy in vivo. The resulting network model integrates post-transcriptional and translational controllers, including candidate feedback loops on NRSF and its corepressor, CoREST.
File Format	HTM / HTML
ISSN	10889051
e-ISSN	15495469
Journal	Genome Research
Issue Number	10
Volume Number	16
Language	English
Publisher	Cold Spring Harbor Laboratory Press
Publisher Date	2006-10-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Discipline Genetics Discipline Genomics Dna-binding Proteins Genetics Gene Expression Profiling Genomics Models, Genetic Nerve Tissue Proteins Repressor Proteins Animals Chromatin Immunoprecipitation Co-repressor Proteins Conserved Sequence Metabolism Jurkat Cells Mice Molecular Sequence Data Species Specificity Transcription Factors Comparative Study Research Support, N.i.h., Extramural Research Support, Non-u.s. Gov't Research Support, U.s. Gov't, Non-p.h.s.
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

Comparative genomics modeling of the NRSF/REST repressor network: From single conserved sites to genome-wide repertoire

Functional diversity for REST (NRSF) is defined by in vivo binding affinity hierarchies at the DNA sequence level.

Genome-wide analysis of repressor element 1 silencing transcription factor/neuron-restrictive silencing factor (REST/NRSF) target genes.

Identification of functional transcription factor binding sites using closely related Saccharomyces species.

Discovery and assessment of conserved Pax6 target genes and enhancers.

Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis.

The genomic landscape of cohesin-associated chromatin interactions.

Comparative motif discovery combined with comparative transcriptomics yields accurate targetome and enhancer predictions.

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

Comparative genomics modeling of the NRSF/REST repressor network: from single conserved sites to genome-wide repertoire.

Similar Documents

Comparative genomics modeling of the NRSF/REST repressor network: From single conserved sites to genome-wide repertoire

Functional diversity for REST (NRSF) is defined by in vivo binding affinity hierarchies at the DNA sequence level.

Genome-wide analysis of repressor element 1 silencing transcription factor/neuron-restrictive silencing factor (REST/NRSF) target genes.

Identification of functional transcription factor binding sites using closely related Saccharomyces species.

Discovery and assessment of conserved Pax6 target genes and enhancers.

Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis.

The genomic landscape of cohesin-associated chromatin interactions.

Comparative motif discovery combined with comparative transcriptomics yields accurate targetome and enhancer predictions.

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

Comparative genomics modeling of the NRSF/REST repressor network: from single conserved sites to genome-wide repertoire.