When needles look like hay: how to find tissue-specific enhancers in model organism genomes (Q37815869)

23 August 2017

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title

When needles look like hay: how to find tissue-specific enhancers in model organism genomes (English)

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23 August 2017

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1

Maximilian Haeussler

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23 August 2017

Jean-Stéphane Joly

2

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PubMed ID

21130761

23 August 2017

language of work or name

English

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publication date

3 December 2010

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23 August 2017

Developmental Biology

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23 August 2017

350

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23 August 2017

2

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23 August 2017

239-254

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Genomic mapping of Suppressor of Hairy-wing binding sites in Drosophila

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Enhancer-promoter specificity mediated by DPE or TATA core promoter motifs

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cis-Regulatory activity of randomly chosen genomic fragments from the sea urchin.

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Long-range chromatin regulatory interactions in vivo

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Purifying selection maintains highly conserved noncoding sequences in Drosophila.

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RNA profiling of FAC-sorted neurons from the developing zebrafish spinal cord.

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Detecting non-coding selective pressure in coding regions

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Enhancer action in trans is permitted throughout the Drosophila genome

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The core enhancer is essential for proper timing of MyoD activation in limb buds and branchial arches

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Complex cardiac Nkx2-5 gene expression activated by noggin-sensitive enhancers followed by chamber-specific modules

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Mice with targeted disruptions in the paralogous genes hoxa-3 and hoxd-3 reveal synergistic interactions

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The TRA-1A sex determination protein of C. elegans regulates sexually dimorphic cell deaths by repressing the egl-1 cell death activator gene

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Comprehensive characterization of the cis-regulatory code responsible for the spatio-temporal expression of olSix3.2 in the developing medaka forebrain.

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Duplications involving a conserved regulatory element downstream of BMP2 are associated with brachydactyly type A2.

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Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions

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Evolutionary discrimination of mammalian conserved non-genic sequences (CNGs).

7 January 2021

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Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes

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Conserved noncoding sequences are selectively constrained and not mutation cold spots

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Active conservation of noncoding sequences revealed by three-way species comparisons

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Genomic regulatory blocks underlie extensive microsynteny conservation in insects

7 January 2021

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Cooperation of sonic hedgehog enhancers in midline expression.

7 January 2021

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A combinatorial network of evolutionarily conserved myelin basic protein regulatory sequences confers distinct glial-specific phenotypes

7 January 2021

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Housekeeping genes tend to show reduced upstream sequence conservation.

7 January 2021

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The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator

7 January 2021

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Conservation of RET regulatory function from human to zebrafish without sequence similarity

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7 January 2021

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A deletion of the human beta-globin locus activation region causes a major alteration in chromatin structure and replication across the entire beta-globin locus.

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A code for transcription initiation in mammalian genomes

7 January 2021

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7 January 2021

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Automated high-throughput mapping of promoter-enhancer interactions in zebrafish embryos

7 January 2021

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Analysis of combinatorial cis-regulation in synthetic and genomic promoters

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GENSAT: a genomic resource for neuroscience research

7 January 2021

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Regulatory roles of conserved intergenic domains in vertebrate Dlx bigene clusters.

7 January 2021

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Distinct cis-regulatory elements from the Dlx1/Dlx2 locus mark different progenitor cell populations in the ganglionic eminences and different subtypes of adult cortical interneurons

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Highly conserved regulatory elements around the SHH gene may contribute to the maintenance of conserved synteny across human chromosome 7q36.3.

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Finding regulatory DNA motifs using alignment-free evolutionary conservation information

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Visualizing one-dimensional diffusion of proteins along DNA.

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Analysis of vertebrate SCL loci identifies conserved enhancers

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ORegAnno: an open-access community-driven resource for regulatory annotation

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Nuclease hypersensitive sites in chromatin

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7 January 2021

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Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity

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Transcriptional regulatory code of a eukaryotic genome

7 January 2021

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Long Human–Mouse Sequence Alignments Reveal Novel Regulatory Elements: A Reason to Sequence the Mouse Genome

7 January 2021

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A careful look at binding site reorganization in the even-skipped enhancers of Drosophila and sepsids

7 January 2021

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Sepsid even-skipped enhancers are functionally conserved in Drosophila despite lack of sequence conservation

7 January 2021

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Nucleosome dynamics define transcriptional enhancers

7 January 2021

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Histone modifications at human enhancers reflect global cell-type-specific gene expression

7 January 2021

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PCR fusion-based approach to create reporter gene constructs for expression analysis in transgenic C. elegans

7 January 2021

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Regulatory logic of neuronal diversity: terminal selector genes and selector motifs.

7 January 2021

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Shadow enhancers as a source of evolutionary novelty

7 January 2021

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Mutations in paralogous Hox genes result in overlapping homeotic transformations of the axial skeleton: evidence for unique and redundant function

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MOPAT: a graph-based method to predict recurrent cis-regulatory modules from known motifs

7 January 2021

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Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention

7 January 2021

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Cis-regulatory organization of the Pax6 gene in the ascidian Ciona intestinalis

7 January 2021

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Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs

7 January 2021

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A conserved enhancer element that drives FGF4 gene expression in the embryonic myotomes is synergistically activated by GATA and bHLH proteins

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Identification of a prosencephalic-specific enhancer of SALL1: comparative genomic approach using the chick embryo.

7 January 2021

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Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene.

7 January 2021

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Isolation of neuronal chromatin from brain tissue

7 January 2021

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Distal enhancer elements transcribe intergenic RNA in the IL-10 family gene cluster

7 January 2021

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Enhancer timing of Hox gene expression: deletion of the endogenous Hoxc8 early enhancer.

7 January 2021

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Regulation of gene expression via the core promoter and the basal transcriptional machinery.

7 January 2021

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Rational design of a super core promoter that enhances gene expression.

7 January 2021

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The RNA polymerase II core promoter - the gateway to transcription.

7 January 2021

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Motif-blind, genome-wide discovery of cis-regulatory modules in Drosophila and mouse

7 January 2021

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A statistical method for alignment-free comparison of regulatory sequences.

7 January 2021

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Human genome ultraconserved elements are ultraselected

7 January 2021

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Evidence for widespread degradation of gene control regions in hominid genomes

7 January 2021

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Functional constraints and frequency of deleterious mutations in noncoding DNA of rodents

7 January 2021

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A saturation screen for cis-acting regulatory DNA in the Hox genes of Ciona intestinalis

7 January 2021

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Multiple, distant Gata2 enhancers specify temporally and tissue-specific patterning in the developing urogenital system

7 January 2021

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Retroviral enhancer detection insertions in zebrafish combined with comparative genomics reveal genomic regulatory blocks - a fundamental feature of vertebrate genomes

7 January 2021

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Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome

7 January 2021

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Widespread transcription at neuronal activity-regulated enhancers

7 January 2021

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Characterization of the pufferfish Otx2 cis-regulators reveals evolutionarily conserved genetic mechanisms for vertebrate head specification.

7 January 2021

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Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data

7 January 2021

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Modular cis-regulatory organization of developmentally expressed genes: two genes transcribed territorially in the sea urchin embryo, and additional examples.

7 January 2021

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Cis-ruption mechanisms: disruption of cis-regulatory control as a cause of human genetic disease

7 January 2021

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Conserved elements in Pax6 intron 7 involved in (auto)regulation and alternative transcription.

7 January 2021

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Real-time monitoring of functional interactions between upstream and core promoter sequences in living cells of sea urchin embryos

7 January 2021

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Information display by transcriptional enhancers

7 January 2021

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COMIT: identification of noncoding motifs under selection in coding sequences

7 January 2021

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An ultraconserved Hox-Pbx responsive element resides in the coding sequence of Hoxa2 and is active in rhombomere 4.

7 January 2021

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Enhancer-promoter communication at the yellow gene of Drosophila melanogaster: diverse promoters participate in and regulate trans interactions

7 January 2021

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Highly conserved syntenic blocks at the vertebrate Hox loci and conserved regulatory elements within and outside Hox gene clusters

7 January 2021

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A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly

7 January 2021

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Point mutations in a distant sonic hedgehog cis-regulator generate a variable regulatory output responsible for preaxial polydactyly

7 January 2021

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Two Pax2/5/8-binding sites in Engrailed2 are required for proper initiation of endogenous mid-hindbrain expression

7 January 2021

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Chromatin looping and the probability of transcription

7 January 2021

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Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm

7 January 2021

1 reference

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Isolation and characterization of conserved non-coding sequences among rice (Oryza sativa L.) paralogous regions

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Homotypic regulatory clusters in Drosophila.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Interchromosomal interactions and olfactory receptor choice

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Remote control of gene expression

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Genomic identification of regulatory elements by evolutionary sequence comparison and functional analysis

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Adventitious changes in long-range gene expression caused by polymorphic structural variation and promoter competition

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Practical strategies for discovering regulatory DNA sequence motifs

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Cross-regulation in the mouse HoxB complex: the expression of Hoxb2 in rhombomere 4 is regulated by Hoxb1

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Making connections: boundaries and insulators in Drosophila

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Distance preferences in the arrangement of binding motifs and hierarchical levels in organization of transcription regulatory information.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription factor oncogenes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Exploiting position effects and the gypsy retrovirus insulator to engineer precisely expressed transgenes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

STAMP: a web tool for exploring DNA-binding motif similarities

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Transcriptional Regulatory Elements in the Human Genome

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

TRANSFAC: transcriptional regulation, from patterns to profiles

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Ancient duplicated conserved noncoding elements in vertebrates: a genomic and functional analysis

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Dispensability of mammalian DNA

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

An E box in the exon 1 promoter regulates insulin-like growth factor-I expression in differentiating muscle cells

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Promoter specificity mediates the independent regulation of neighboring genes.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Short sequence motifs, overrepresented in mammalian conserved non-coding sequences

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Regulation of the p53 transcriptional response by structurally diverse core promoters

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Systematic human/zebrafish comparative identification of cis-regulatory activity around vertebrate developmental transcription factor genes.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

The regulatory content of intergenic DNA shapes genome architecture

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

UniPROBE: an online database of protein binding microarray data on protein-DNA interactions

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

A Drosophila resource of transgenic RNAi lines for neurogenetics

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Functional noncoding sequences derived from SINEs in the mammalian genome

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Scanning Human Gene Deserts for Long-Range Enhancers

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Comparative genomic analysis as a tool for biological discovery

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Megabase deletions of gene deserts result in viable mice

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Transcription factors mediate long-range enhancer-promoter interactions

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Promoting developmental transcription

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Different core promoters possess distinct regulatory activities in the Drosophila embryo

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Gene expression neighborhoods

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Evolution and functional classification of vertebrate gene deserts

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Locating potential enhancer elements by comparative genomics using the EEL software

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

An Atomic Model of the Interferon-β Enhanceosome

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Increased gamma-globin gene expression in beta-thalassemia intermedia patients correlates with a mutation in 3'HS1

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

ClusterDraw web server: a tool to identify and visualize clusters of binding motifs for transcription factors

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Computational identification of regulatory DNAs underlying animal development

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Conservation patterns in different functional sequence categories of divergent Drosophila species.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Organization of developmental enhancers in the Drosophila embryo

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Analysis of upstream elements in the HuC promoter leads to the establishment of transgenic zebrafish with fluorescent neurons

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Duplication of Stat5-binding sites within the beta-lactoglobulin promoter compromises transcription in vivo

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

In vivo enhancer analysis of human conserved non-coding sequences

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

CTCF: master weaver of the genome

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Identifying cis-regulatory modules by combining comparative and compositional analysis of DNA.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Chicken beta-globin 5'HS4 insulators function to reduce variability in transgenic founder mice

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

In vivo characterization of a vertebrate ultraconserved enhancer

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Close sequence comparisons are sufficient to identify human cis-regulatory elements.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

The amphioxus genome and the evolution of the chordate karyotype

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

E2F in vivo binding specificity: comparison of consensus versus nonconsensus binding sites

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Disruption of an AP-2alpha binding site in an IRF6 enhancer is associated with cleft lip

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

SCORE: a computational approach to the identification of cis-regulatory modules and target genes in whole-genome sequence data. Site clustering over random expectation.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Vertebrate conserved non coding DNA regions have a high persistence length and a short persistence time.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

PASTAA: identifying transcription factors associated with sets of co-regulated genes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Predicting transcription factor affinities to DNA from a biophysical model.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Conservation of Endo16 expression in sea urchins despite evolutionary divergence in both cis and trans-acting components of transcriptional regulation

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Visualization of trans-homolog enhancer-promoter interactions at the Abd-B Hox locus in the Drosophila embryo

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Long-range conserved non-coding SHOX sequences regulate expression in developing chicken limb and are associated with short stature phenotypes in human patients.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Identification and characterization of new long conserved noncoding sequences in vertebrates.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Noncoding RNAs of trithorax response elements recruit Drosophila Ash1 to Ultrabithorax

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

A survey of motif discovery methods in an integrated framework

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

A large fraction of extragenic RNA pol II transcription sites overlap enhancers

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Combining statistical alignment and phylogenetic footprinting to detect regulatory elements.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Synthetic design of strong promoters

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Transcriptional control in the segmentation gene network of Drosophila

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Predicting expression patterns from regulatory sequence in Drosophila segmentation.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Recombineering: a homologous recombination-based method of genetic engineering

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Human-zebrafish non-coding conserved elements act in vivo to regulate transcription

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

DBTGR: a database of tunicate promoters and their regulatory elements

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C).

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Sequence turnover and tandem repeats in cis-regulatory modules in drosophila

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Core promoters: active contributors to combinatorial gene regulation

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Tissue-specific regulatory elements in mammalian promoters

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

A protocol describing the principles of cis-regulatory analysis in the sea urchin

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Epigenetic temporal control of mouse Hox genes in vivo.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Global control regions and regulatory landscapes in vertebrate development and evolution

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

A global control region defines a chromosomal regulatory landscape containing the HoxD cluster

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

The effect of chromosomal position on the expression of the Drosophila xanthine dehydrogenase gene.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Large-Scale Appearance of Ultraconserved Elements in Tetrapod Genomes and Slowdown of the Molecular Clock

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Conserved distances between vertebrate highly conserved elements.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

A novel conserved evx1 enhancer links spinal interneuron morphology and cis-regulation from fish to mammals.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Variable locus length in the human genome leads to ascertainment bias in functional inference for non-coding elements.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

A quantitative approach to the study of cell shapes and interactions during early chordate embryogenesis.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

ESPERR: learning strong and weak signals in genomic sequence alignments to identify functional elements

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Virus induction of human IFN beta gene expression requires the assembly of an enhanceosome

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Assessing computational tools for the discovery of transcription factor binding sites

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Analysis of the distribution of binding sites for a tissue-specific transcription factor in the vertebrate genome

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

An evolutionarily conserved nested gene pair - Mab21 and Lrba/Nbea in metazoan.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

A regulatory module embedded in the coding region of Hoxa2 controls expression in rhombomere 2

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

A toolkit and robust pipeline for the generation of fosmid-based reporter genes in C. elegans

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Functional analysis of chicken Sox2 enhancers highlights an array of diverse regulatory elements that are conserved in mammals.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Proximity among distant regulatory elements at the beta-globin locus requires GATA-1 and FOG-1.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Modeling tissue-specific structural patterns in human and mouse promoters

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Prediction of cis-regulatory elements using binding site matrices--the successes, the failures and the reasons for both

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Defining a genomic radius for long-range enhancer action: duplicated conserved non-coding elements hold the key

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Versatile P[acman] BAC libraries for transgenesis studies in Drosophila melanogaster

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Functional autonomy of distant-acting human enhancers

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

ChIP-seq accurately predicts tissue-specific activity of enhancers

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Enhancer identification through comparative genomics

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Co-regulated expression of HAND2 and DEIN by a bidirectional promoter with asymmetrical activity in neuroblastoma

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

DBTSS: database of transcription start sites, progress report 2008.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Striking nucleotide frequency pattern at the borders of highly conserved vertebrate non-coding sequences

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Experimental validation of predicted mammalian erythroid cis-regulatory modules

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Detection of weakly conserved ancestral mammalian regulatory sequences by primate comparisons

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Functional analysis of the proximal promoter regions of fish rhodopsin and myf-5 genes using transgenesis.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Comparison of Pax1/9 locus reveals 500-Myr-old syntenic block and evolutionary conserved noncoding regions

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Structured RNAs in the ENCODE selected regions of the human genome

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Identification of regulatory regions which confer muscle-specific gene expression.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Applied bioinformatics for the identification of regulatory elements

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Initial sequencing and comparative analysis of the mouse genome

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Genomic cis-regulatory architecture and trans-acting regulators of a single interneuron-specific gene battery in C. elegans.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Multiple conserved regulatory elements with overlapping functions determine Sox10 expression in mouse embryogenesis

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Remote control of gene transcription

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Conserved elements within open reading frames of mammalian Hox genes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Comparative genomics using Fugu reveals insights into regulatory subfunctionalization

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Organization of conserved elements near key developmental regulators in vertebrate genomes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Highly conserved non-coding sequences are associated with vertebrate development

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Evolutionary and functional analysis of the tailless enhancer in Musca domestica and Drosophila melanogaster

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

A family of conserved noncoding elements derived from an ancient transposable element

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

MEIS1 intronic risk haplotype associated with restless legs syndrome affects its mRNA and protein expression levels

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Redundant and unique roles of two enhancer elements in the TCRgamma locus in gene regulation and gammadelta T cell development

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

A comprehensive ChIP-chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Shared long-range regulatory elements coordinate expression of a gene cluster encoding nicotinic receptor heteromeric subtypes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Targeted deletion of a branchial arch-specific enhancer reveals a role of dHAND in craniofacial development.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Next generation tools for high-throughput promoter and expression analysis employing single-copy knock-ins at the Hprt1 locus.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Transgenic analysis of the anterior eye-specific enhancers of the zebrafish gelsolin-like 1 (gsnl1) gene

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Predicting gene expression from sequence: a reexamination

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Genomic cis-regulatory logic: experimental and computational analysis of a sea urchin gene

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Activation of the human PAX6 gene through the exon 1 enhancer by transcription factors SEF and Sp1

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

Combinatorial binding predicts spatio-temporal cis-regulatory activity

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YDBIO.2010.11.026

10.1016/J.YDBIO.2010.11.026

7 January 2021

Identifiers

DOI

1 reference

23 August 2017

1 reference

PubMed ID

21130761