Comparative sequence analysis reveals an intricate network among REST, CREB and miRNA in mediating neuronal gene expression.

Abstract:

BACKGROUND:Two distinct classes of regulators have been implicated in regulating neuronal gene expression and mediating neuronal identity: transcription factors such as REST/NRSF (RE1 silencing transcription factor) and CREB (cAMP response element-binding protein), and microRNAs (miRNAs). How these two classes of regulators act together to mediate neuronal gene expression is unclear. RESULTS:Using comparative sequence analysis, here we report the identification of 895 sites (NRSE) as the putative targets of REST. A set of the identified NRSE sites is present in the vicinity of the miRNA genes that are specifically expressed in brain-related tissues, suggesting the transcriptional regulation of these miRNAs by REST. We have further identified target genes of these miRNAs, and discovered that REST and its cofactor complex are targets of multiple brain-related miRNAs including miR-124a, miR-9 and miR-132. Given the role of both REST and miRNA as repressors, these findings point to a double-negative feedback loop between REST and the miRNAs in stabilizing and maintaining neuronal gene expression. Additionally, we find that the brain-related miRNA genes are highly enriched with evolutionarily conserved cAMP response elements (CRE) in their regulatory regions, implicating the role of CREB in the positive regulation of these miRNAs. CONCLUSION:The expression of neuronal genes and neuronal identity are controlled by multiple factors, including transcriptional regulation through REST and post-transcriptional modification by several brain-related miRNAs. We demonstrate that these different levels of regulation are coordinated through extensive feedbacks, and propose a network among REST, CREB proteins and the brain-related miRNAs as a robust program for mediating neuronal gene expression.

journal_name

Genome Biol

journal_title

Genome biology

authors

Wu J,Xie X

doi

10.1186/gb-2006-7-9-r85

subject

Has Abstract

pub_date

2006-01-01 00:00:00

pages

R85

issue

9

eissn

1474-7596

issn

1474-760X

pii

gb-2006-7-9-r85

journal_volume

7

pub_type

杂志文章
  • Prediction of synergistic transcription factors by function conservation.

    abstract:BACKGROUND:Previous methods employed for the identification of synergistic transcription factors (TFs) are based on either TF enrichment from co-regulated genes or phylogenetic footprinting. Despite the success of these methods, both have limitations. RESULTS:We propose a new strategy to identify synergistic TFs by fu...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2007-8-12-r257

    authors: Hu Z,Hu B,Collins JF

    更新日期:2007-01-01 00:00:00

  • Common gene expression strategies revealed by genome-wide analysis in yeast.

    abstract:BACKGROUND:Gene expression is a two-step synthesis process that ends with the necessary amount of each protein required to perform its function. Since the protein is the final product, the main focus of gene regulation should be centered on it. However, because mRNA is an intermediate step and the amounts of both mRNA ...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2007-8-10-r222

    authors: García-Martínez J,González-Candelas F,Pérez-Ortín JE

    更新日期:2007-01-01 00:00:00

  • A versatile reporter system for CRISPR-mediated chromosomal rearrangements.

    abstract::Although chromosomal deletions and inversions are important in cancer, conventional methods for detecting DNA rearrangements require laborious indirect assays. Here we develop fluorescent reporters to rapidly quantify CRISPR/Cas9-mediated deletions and inversions. We find that inversion depends on the non-homologous e...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-015-0680-7

    authors: Li Y,Park AI,Mou H,Colpan C,Bizhanova A,Akama-Garren E,Joshi N,Hendrickson EA,Feldser D,Yin H,Anderson DG,Jacks T,Weng Z,Xue W

    更新日期:2015-05-28 00:00:00

  • Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma.

    abstract:BACKGROUND:Mycoparasitism, a lifestyle where one fungus is parasitic on another fungus, has special relevance when the prey is a plant pathogen, providing a strategy for biological control of pests for plant protection. Probably, the most studied biocontrol agents are species of the genus Hypocrea/Trichoderma. RESULTS...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2011-12-4-r40

    authors: Kubicek CP,Herrera-Estrella A,Seidl-Seiboth V,Martinez DA,Druzhinina IS,Thon M,Zeilinger S,Casas-Flores S,Horwitz BA,Mukherjee PK,Mukherjee M,Kredics L,Alcaraz LD,Aerts A,Antal Z,Atanasova L,Cervantes-Badillo MG,Challac

    更新日期:2011-01-01 00:00:00

  • Evidence from comparative genomics for a complete sexual cycle in the 'asexual' pathogenic yeast Candida glabrata.

    abstract:BACKGROUND:Candida glabrata is a pathogenic yeast of increasing medical concern. It has been regarded as asexual since it was first described in 1917, yet phylogenetic analyses have revealed that it is more closely related to sexual yeasts than other Candida species. We show here that the C. glabrata genome contains ma...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2003-4-2-r10

    authors: Wong S,Fares MA,Zimmermann W,Butler G,Wolfe KH

    更新日期:2003-01-01 00:00:00

  • A novel protein encoded by circular SMO RNA is essential for Hedgehog signaling activation and glioblastoma tumorigenicity.

    abstract:BACKGROUND:Aberrant activation of the Hedgehog pathway drives tumorigenesis of many cancers, including glioblastoma. However, the sensitization mechanism of the G protein-coupled-like receptor smoothened (SMO), a key component of Hedgehog signaling, remains largely unknown. RESULTS:In this study, we describe a novel p...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-020-02250-6

    authors: Wu X,Xiao S,Zhang M,Yang L,Zhong J,Li B,Li F,Xia X,Li X,Zhou H,Liu D,Huang N,Yang X,Xiao F,Zhang N

    更新日期:2021-01-14 00:00:00

  • Alternative splicing links histone modifications to stem cell fate decision.

    abstract:BACKGROUND:Understanding the embryonic stem cell (ESC) fate decision between self-renewal and proper differentiation is important for developmental biology and regenerative medicine. Attention has focused on mechanisms involving histone modifications, alternative pre-messenger RNA splicing, and cell-cycle progression. ...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-018-1512-3

    authors: Xu Y,Zhao W,Olson SD,Prabhakara KS,Zhou X

    更新日期:2018-09-14 00:00:00

  • iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations.

    abstract:BACKGROUND:Bacillus subtilis is an organism of interest because of its extensive industrial applications, its similarity to pathogenic organisms, and its role as the model organism for Gram-positive, sporulating bacteria. In this work, we introduce a new genome-scale metabolic model of B. subtilis 168 called iBsu1103. ...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2009-10-6-r69

    authors: Henry CS,Zinner JF,Cohoon MP,Stevens RL

    更新日期:2009-01-01 00:00:00

  • Permutation-validated principal components analysis of microarray data.

    abstract:BACKGROUND:In microarray data analysis, the comparison of gene-expression profiles with respect to different conditions and the selection of biologically interesting genes are crucial tasks. Multivariate statistical methods have been applied to analyze these large datasets. Less work has been published concerning the a...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2002-3-4-research0019

    authors: Landgrebe J,Wurst W,Welzl G

    更新日期:2002-01-01 00:00:00

  • Histone modifications: from genome-wide maps to functional insights.

    abstract::A large number of histone modifications has been implicated in the regulation of gene expression. Together, these modifications have the potential to form a complex combinatorial regulatory code. Genome-wide mapping approaches provide new opportunities to decipher this code, but they may suffer from systematic biases....

    journal_title:Genome biology

    pub_type: 杂志文章,评审

    doi:10.1186/gb-2005-6-6-113

    authors: van Leeuwen F,van Steensel B

    更新日期:2005-01-01 00:00:00

  • Molecular archeology of L1 insertions in the human genome.

    abstract:BACKGROUND:As the rough draft of the human genome sequence nears a finished product and other genome-sequencing projects accumulate sequence data exponentially, bioinformatics is emerging as an important tool for studies of transposon biology. In particular, L1 elements exhibit a variety of sequence structures after in...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2002-3-10-research0052

    authors: Szak ST,Pickeral OK,Makalowski W,Boguski MS,Landsman D,Boeke JD

    更新日期:2002-09-19 00:00:00

  • Long mRNAs coding for yeast mitochondrial proteins of prokaryotic origin preferentially localize to the vicinity of mitochondria.

    abstract:BACKGROUND:Subcellular messenger RNA localization is important in most eukaryotic cells, even in unicellular organisms like yeast for which this process has been underestimated. Microarrays are rarely used to study subcellular mRNA localization at whole-genome level, but can be adapted to that purpose. This work focuse...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2003-4-7-r44

    authors: Sylvestre J,Vialette S,Corral Debrinski M,Jacq C

    更新日期:2003-01-01 00:00:00

  • External signals shape the epigenome.

    abstract::A new study shows how a single cytokine, interleukin-4, regulates hematopoietic lineage choice by activating the JAK3-STAT6 pathway, which causes dendritic-cell-specific DNA demethylation. ...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-016-0884-5

    authors: Lennartsson A

    更新日期:2016-02-01 00:00:00

  • A systems view of Drosophila segmentation.

    abstract::High-throughput technologies have enabled the systematic identification and characterization of most, or possibly all, of the components governing segmentation in the fruit fly Drosophila. What have we learned? ...

    journal_title:Genome biology

    pub_type: 杂志文章,评审

    doi:10.1186/gb-2008-9-2-207

    authors: Levine M

    更新日期:2008-01-01 00:00:00

  • Accuracy and quality of massively parallel DNA pyrosequencing.

    abstract:BACKGROUND:Massively parallel pyrosequencing systems have increased the efficiency of DNA sequencing, although the published per-base accuracy of a Roche GS20 is only 96%. In genome projects, highly redundant consensus assemblies can compensate for sequencing errors. In contrast, studies of microbial diversity that cat...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2007-8-7-r143

    authors: Huse SM,Huber JA,Morrison HG,Sogin ML,Welch DM

    更新日期:2007-01-01 00:00:00

  • A cell surface interaction network of neural leucine-rich repeat receptors.

    abstract:BACKGROUND:The vast number of precise intercellular connections within vertebrate nervous systems is only partly explained by the comparatively few known extracellular guidance cues. Large families of neural orphan receptor proteins have been identified and are likely to contribute to these recognition processes but du...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2009-10-9-r99

    authors: Söllner C,Wright GJ

    更新日期:2009-01-01 00:00:00

  • What does biologically meaningful mean? A perspective on gene regulatory network validation.

    abstract::Gene regulatory networks (GRNs) are rapidly being delineated, but their quality and biological meaning are often questioned. Here, I argue that biological meaning is challenging to define and discuss reasons why GRN validation should be interpreted cautiously. ...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2011-12-4-109

    authors: Walhout AJ

    更新日期:2011-01-01 00:00:00

  • Constitutive patterns of gene expression regulated by RNA-binding proteins.

    abstract:BACKGROUND:RNA-binding proteins regulate a number of cellular processes, including synthesis, folding, translocation, assembly and clearance of RNAs. Recent studies have reported that an unexpectedly large number of proteins are able to interact with RNA, but the partners of many RNA-binding proteins are still uncharac...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2014-15-1-r13

    authors: Cirillo D,Marchese D,Agostini F,Livi CM,Botta-Orfila T,Tartaglia GG

    更新日期:2014-01-02 00:00:00

  • The sequence of human chromosome 21 and implications for research into Down syndrome.

    abstract::The recent completion of the DNA sequence of human chromosome 21 has provided the first look at the 225 genes that are candidates for involvement in Down syndrome (trisomy 21). A broad functional classification of these genes, their expression data and evolutionary conservation, and comparison with the gene content of...

    journal_title:Genome biology

    pub_type: 杂志文章,评审

    doi:10.1186/gb-2000-1-2-reviews0002

    authors: Gardiner K,Davisson M

    更新日期:2000-01-01 00:00:00

  • Reduced intrinsic DNA curvature leads to increased mutation rate.

    abstract:BACKGROUND:Mutation rates vary across the genome. Many trans factors that influence mutation rates have been identified, as have specific sequence motifs at the 1-7-bp scale, but cis elements remain poorly characterized. The lack of understanding regarding why different sequences have different mutation rates hampers o...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-018-1525-y

    authors: Duan C,Huan Q,Chen X,Wu S,Carey LB,He X,Qian W

    更新日期:2018-09-14 00:00:00

  • Identifying repeat domains in large genomes.

    abstract::We present a graph-based method for the analysis of repeat families in a repeat library. We build a repeat domain graph that decomposes a repeat library into repeat domains, short subsequences shared by multiple repeat families, and reveals the mosaic structure of repeat families. Our method recovers documented mosaic...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2006-7-1-r7

    authors: Zhi D,Raphael BJ,Price AL,Tang H,Pevzner PA

    更新日期:2006-01-01 00:00:00

  • Genome-wide mutagenesis of Zea mays L. using RescueMu transposons.

    abstract::Derived from the maize Mu1 transposon, RescueMu provides strategies for maize gene discovery and mutant phenotypic analysis. 9.92 Mb of gene-enriched sequences next to RescueMu insertion sites were co-assembled with expressed sequence tags and analyzed. Multiple plasmid recoveries identified probable germinal insertio...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2004-5-10-r82

    authors: Fernandes J,Dong Q,Schneider B,Morrow DJ,Nan GL,Brendel V,Walbot V

    更新日期:2004-01-01 00:00:00

  • Dating branches on the tree of life using DNA.

    abstract::The use of DNA sequences to estimate the timing of evolutionary events is increasingly popular, although it is fraught with practical difficulties. But the exponential growth of relevant information and improved methods of analysis are providing increasingly reliable sequence-derived dates, and it may become possible ...

    journal_title:Genome biology

    pub_type: 杂志文章,评审

    doi:10.1186/gb-2001-3-1-reviews0001

    authors: Wray GA

    更新日期:2002-01-01 00:00:00

  • Where is genomics going next?

    abstract::We polled the Editorial Board of Genome Biology to ask where they see genomics going in the next few years. Here are some of their responses. ...

    journal_title:Genome biology

    pub_type: 社论,面试

    doi:10.1186/s13059-019-1626-2

    authors: Cheifet B

    更新日期:2019-01-22 00:00:00

  • Whole genome DNA sequencing provides an atlas of somatic mutagenesis in healthy human cells and identifies a tumor-prone cell type.

    abstract:BACKGROUND:The lifelong accumulation of somatic mutations underlies age-related phenotypes and cancer. Mutagenic forces are thought to shape the genome of aging cells in a tissue-specific way. Whole genome analyses of somatic mutation patterns, based on both types and genomic distribution of variants, can shed light on...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-019-1892-z

    authors: Franco I,Helgadottir HT,Moggio A,Larsson M,Vrtačnik P,Johansson A,Norgren N,Lundin P,Mas-Ponte D,Nordström J,Lundgren T,Stenvinkel P,Wennberg L,Supek F,Eriksson M

    更新日期:2019-12-18 00:00:00

  • RASTA-Bacteria: a web-based tool for identifying toxin-antitoxin loci in prokaryotes.

    abstract::Toxin/antitoxin (TA) systems, viewed as essential regulators of growth arrest and programmed cell death, are widespread among prokaryotes, but remain sparsely annotated. We present RASTA-Bacteria, an automated method allowing quick and reliable identification of TA loci in sequenced prokaryotic genomes, whether they a...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2007-8-8-r155

    authors: Sevin EW,Barloy-Hubler F

    更新日期:2007-01-01 00:00:00

  • In silico meets in vivo.

    abstract::A report of the 6th Georgia Tech-Oak Ridge National Lab International Conference on Bioinformatics 'In silico Biology: Gene Discovery and Systems Genomics', Atlanta, USA, 15-17 November, 2007. ...

    journal_title:Genome biology

    pub_type:

    doi:10.1186/gb-2008-9-2-302

    authors: Weng Z,Guigó R

    更新日期:2008-01-01 00:00:00

  • Full genome re-sequencing reveals a novel circadian clock mutation in Arabidopsis.

    abstract::Map based cloning in Arabidopsis thaliana can be a difficult and time-consuming process, specifically if the phenotype is subtle and scoring labour intensive. Here, we have re-sequenced the 120-Mb genome of a novel Arabidopsis clock mutant early bird (ebi-1) in Wassilewskija (Ws-2). We demonstrate the utility of seque...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2011-12-3-r28

    authors: Ashelford K,Eriksson ME,Allen CM,D'Amore R,Johansson M,Gould P,Kay S,Millar AJ,Hall N,Hall A

    更新日期:2011-01-01 00:00:00

  • Normalization of boutique two-color microarrays with a high proportion of differentially expressed probes.

    abstract::Normalization is critical for removing systematic variation from microarray data. For two-color microarray platforms, intensity-dependent lowess normalization is commonly used to correct relative gene expression values for biases. Here we outline a normalization method for use when the assumptions of lowess normalizat...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2007-8-1-r2

    authors: Oshlack A,Emslie D,Corcoran LM,Smyth GK

    更新日期:2007-01-01 00:00:00

  • Multiple RNA-protein interactions in Drosophila dosage compensation.

    abstract::From worms to humans, recognizing and modifying a specific chromosome is essential for dosage compensation, the mechanism by which equal X-linked gene expression in males and females is achieved. Recent molecular genetic and biochemical studies have provided new insights into how regulatory factors in Drosophila are r...

    journal_title:Genome biology

    pub_type: 杂志文章,评审

    doi:10.1186/gb-2000-1-6-reviews1030

    authors: Amrein H

    更新日期:2000-01-01 00:00:00