An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement (Q28730815)

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author name string

Esther González-Pérez

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David Tran

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Sonsoles Campuzano

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Jordi Garcia-Fernàndez

De novo genesis of enhancers in vertebrates

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language of work or name

English

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publication date

April 2012

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642-55

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cites work

1 reference

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Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons

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17 March 2017

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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

17 March 2017

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17 March 2017

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Model-based analysis of ChIP-Seq (MACS)

17 March 2017

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The amphioxus genome and the evolution of the chordate karyotype

17 March 2017

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Spliceosomal introns as tools for genomic and evolutionary analysis

17 March 2017

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Genomic regulatory blocks underlie extensive microsynteny conservation in insects

17 March 2017

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PAML 4: phylogenetic analysis by maximum likelihood

17 March 2017

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Survey sequencing and comparative analysis of the elephant shark (Callorhinchus milii) genome

17 March 2017

1 reference

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VISTA Enhancer Browser--a database of tissue-specific human enhancers

17 March 2017

1 reference

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Two rounds of whole genome duplication in the ancestral vertebrate

17 March 2017

1 reference

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

17 March 2017

1 reference

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MAFFT version 5: improvement in accuracy of multiple sequence alignment

17 March 2017

1 reference

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ProtTest: selection of best-fit models of protein evolution

17 March 2017

1 reference

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Highly conserved non-coding sequences are associated with vertebrate development

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

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

17 March 2017

1 reference

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Ultraconserved Elements in the Human Genome

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

The regulatory content of intergenic DNA shapes genome architecture

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

Scanning Human Gene Deserts for Long-Range Enhancers

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood

17 March 2017

1 reference

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MrBayes 3: Bayesian phylogenetic inference under mixed models

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

MRBAYES: Bayesian inference of phylogenetic trees

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

The Iroquois homeodomain proteins are required to specify body wall identity in Drosophila

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

VISTA: computational tools for comparative genomics

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

In vivo enhancer analysis of human conserved non-coding sequences

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

Transphyletic conservation of developmental regulatory state in animal evolution

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

Drosophila araucan and caupolican integrate intrinsic and signalling inputs for the acquisition by muscle progenitors of the lateral transverse fate

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

Contrasting 5' and 3' evolutionary histories and frequent evolutionary convergence in Meis/hth gene structures

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

Identification of cis regulatory features in the embryonic zebrafish genome through large-scale profiling of H3K4me1 and H3K4me3 binding sites

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

Conserved developmental expression of Fezf in chordates and Drosophila and the origin of the Zona Limitans Intrathalamica (ZLI) brain organizer

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

Elephant shark (Callorhinchus milii) provides insights into the evolution of Hox gene clusters in gnathostomes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

Evolution of genome architecture

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

Convergent evolution of clustering of Iroquois homeobox genes across metazoans.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

Ancora: a web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

The random versus fragile breakage models of chromosome evolution: a matter of resolution

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

Antagonistic and cooperative actions of the EGFR and Dpp pathways on the iroquois genes regulate Drosophila mesothorax specification and patterning

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

Ancient noncoding elements conserved in the human genome

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

Evolutionary genomics of the recently duplicated amphioxus Hairy genes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

A functional survey of the enhancer activity of conserved non-coding sequences from vertebrate Iroquois cluster gene deserts.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

Ultraconserved elements in insect genomes: a highly conserved intronic sequence implicated in the control of homothorax mRNA splicing

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

Conservation of regulatory sequences and gene expression patterns in the disintegrating Drosophila Hox gene complex

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

Evolution and functional classification of vertebrate gene deserts

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

Comparative genomics at the vertebrate extremes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

A complementary transposon tool kit for Drosophila melanogaster using P and piggyBac

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

Sequence and expression pattern of ziro7, a novel, divergent zebrafish iroquois homeobox gene.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

The Iroquois family of genes: from body building to neural patterning.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

mirror, a Drosophila homeobox gene in the Iroquois complex, is required for sensory organ and alula formation.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

mirror encodes a novel PBX-class homeoprotein that functions in the definition of the dorsal-ventral border in the Drosophila eye.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

Detecting conserved regulatory elements with the model genome of the Japanese puffer fish, Fugu rubripes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

Proneural clusters of achaete-scute expression and the generation of sensory organs in the Drosophila imaginal wing disc.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

An evolutionarily conserved three-dimensional structure in the vertebrate Irx clusters facilitates enhancer sharing and coregulation.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

Amphioxus whole-mount in situ hybridization.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

Cis-regulation and chromosomal rearrangement of the fgf8 locus after the teleost/tetrapod split.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

Zebrafish enhancer detection (ZED) vector: A new tool to facilitate transgenesis and the functional analysis ofcis-regulatory regions in zebrafish

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

Developmental expression of the three iroquois genes of amphioxus (BfIrxA, BfIrxB, and BfIrxC) with special attention to the gastrula organizer and anteroposterior boundaries in the central nervous system.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

Comprehensive survey and classification of homeobox genes in the genome of amphioxus, Branchiostoma floridae.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

Unexpectedly large number of conserved noncoding regions within the ancestral chordate Hox cluster

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

Gene expansion and retention leads to a diverse tyrosine kinase superfamily in amphioxus

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

Intron loss and gain in Drosophila.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

Odd-skipped genes encode repressors that control kidney development.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

Activation of stem-cell specific genes by HOXA9 and HOXA10 homeodomain proteins in CD34+ human cord blood cells

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

Organization of Iroquois genes in fish

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

The Irx gene family in zebrafish: genomic structure, evolution and initial characterization of irx5b

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

Systematic generation of high-resolution deletion coverage of the Drosophila melanogaster genome

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

A role for iro1 and iro7 in the establishment of an anteroposterior compartment of the ectoderm adjacent to the midbrain-hindbrain boundary.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

PAL: an object-oriented programming library for molecular evolution and phylogenetics.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

Araucan and caupolican, two members of the novel iroquois complex, encode homeoproteins that control proneural and vein-forming genes.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3317147

Expression of the zebrafish Iroquois genes during early nervous system formation and patterning

27 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22234889

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1101/GR.132233.111

1 reference

1 reference

1 reference

PubMed publication ID

22234889

1 reference