A Global Control Region Defines a Chromosomal Regulatory Landscape Containing the HoxD Cluster
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TLDR
A targeted enhancer-trap approach was used to identify a DNA segment capable of directing reporter gene expression in both digits and CNS, following Lnp, Evx2, and Hoxd-specific patterns, and discusses the heuristic value of these results in term of locus specific versus gene-specific regulation.About:
This article is published in Cell.The article was published on 2003-05-02 and is currently open access. It has received 473 citations till now. The article focuses on the topics: Locus (genetics) & Enhancer.read more
Citations
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GREAT improves functional interpretation of cis-regulatory regions
Cory Y. McLean,Dave Bristor,Michael Hiller,Shoa L. Clarke,Bruce T. Schaar,Craig B. Lowe,Aaron M. Wenger,Gill Bejerano +7 more
TL;DR: The Genomic Regions Enrichment of Annotations Tool (GREAT) is developed to analyze the functional significance of cis-regulatory regions identified by localized measurements of DNA binding events across an entire genome.
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Transcription factors: from enhancer binding to developmental control.
TL;DR: Current knowledge of transcription factor function from genomic and genetic studies is reviewed and how different strategies, including extensive cooperative regulation, progressive priming of regulatory elements, and the integration of activities from multiple enhancers, confer specificity and robustness to transcriptional regulation during development are discussed.
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Ultraconserved Elements in the Human Genome
Gill Bejerano,Michael Pheasant,Igor V. Makunin,Stuart Stephen,W. James Kent,John S. Mattick,David Haussler +6 more
TL;DR: There are 481 segments longer than 200 base pairs that are absolutely conserved between orthologous regions of the human, rat, and mouse genomes, which represent a class of genetic elements whose functions and evolutionary origins are yet to be determined, but which are more highly conserving between these species than are proteins.
Journal ArticleDOI
Highly conserved non-coding sequences are associated with vertebrate development.
Adam Woolfe,Martin Goodson,Debbie K. Goode,Phil Snell,Gayle K. McEwen,Tanya Vavouri,Sarah Smith,Phil North,Heather Callaway,Krys Kelly,Klaudia Walter,Irina I. Abnizova,Walter R. Gilks,Yvonne J. K. Edwards,Julie E. Cooke,Greg Elgar +15 more
TL;DR: A whole-genome comparison between humans and the pufferfish, Fugu rubripes, is used to identify nearly 1,400 highly conserved non-coding sequences, which are likely to form part of the genomic circuitry that uniquely defines vertebrate development.
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Long-range control of gene expression: emerging mechanisms and disruption in disease.
TL;DR: Functional studies have shown many of these conserved sites to be transcriptional regulatory elements that sometimes reside inside unrelated neighboring genes, such sequence-conserved elements generally harbor sites for tissue-specific DNA-binding proteins.
References
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Basic Local Alignment Search Tool
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
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Sonic Hedgehog Mediates the Polarizing Activity of the ZPA
TL;DR: A vertebrate gene related to the Drosophila segment polarity gene hedgehog, which is expressed specifically in the ZPA and in other regions of the embryo, that is capable of polarizing limbs in grafting experiments is isolated.
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Whole-Genome Shotgun Assembly and Analysis of the Genome of Fugu rubripes
Samuel Aparicio,Jarrod Chapman,Elia Stupka,Nik Putnam,Jer Ming Chia,Paramvir S. Dehal,Alan Christoffels,Sam Rash,Shawn Hoon,Arian F.A. Smit,Maarten D. Sollewijn Gelpke,Jared C. Roach,Tania Oh,Isaac Ho,Marie Wong,Chris Detter,Frans Verhoef,Paul Predki,Alice Tay,Susan Lucas,Paul G. Richardson,Sarah Smith,Melody S. Clark,Yvonne J. K. Edwards,Norman A. Doggett,Andrey Zharkikh,Sean V. Tavtigian,Dmitry Pruss,Mary Barnstead,Cheryl Evans,Holly Baden,Justin Powell,Gustavo Glusman,Lee Rowen,Leroy Hood,Y. H. Tan,Greg Elgar,Trevor Hawkins,Byrappa Venkatesh,Daniel S. Rokhsar,Sydney Brenner +40 more
TL;DR: The Fugu rubripes genome has been sequenced to over 95% coverage, and more than 80% of the assembly is in multigene-sized scaffolds as discussed by the authors.
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A highly efficient Escherichia coli-based chromosome engineering system adapted for recombinogenic targeting and subcloning of BAC DNA.
E-Chiang Lee,Daiguan Yu,J. Martinez de Velasco,Lino Tessarollo,Deborah A. Swing,Donald L. Court,Nancy A. Jenkins,Neal G. Copeland +7 more
TL;DR: The ability to modify or subclone large fragments of genomic DNA with precision should facilitate many kinds of genomic experiments that were difficult or impossible to perform previously and aid in studies of gene function in the postgenomic era.