Literature DB >> 24153303

Topology of mammalian developmental enhancers and their regulatory landscapes.

Wouter de Laat1, Denis Duboule.   

Abstract

How a complex animal can arise from a fertilized egg is one of the oldest and most fascinating questions of biology, the answer to which is encoded in the genome. Body shape and organ development, and their integration into a functional organism all depend on the precise expression of genes in space and time. The orchestration of transcription relies mostly on surrounding control sequences such as enhancers, millions of which form complex regulatory landscapes in the non-coding genome. Recent research shows that high-order chromosome structures make an important contribution to enhancer functionality by triggering their physical interactions with target genes.

Entities:  

Mesh:

Substances:

Year:  2013        PMID: 24153303     DOI: 10.1038/nature12753

Source DB:  PubMed          Journal:  Nature        ISSN: 0028-0836            Impact factor:   49.962


  74 in total

1.  Looping and interaction between hypersensitive sites in the active beta-globin locus.

Authors:  Bas Tolhuis; Robert Jan Palstra; Erik Splinter; Frank Grosveld; Wouter de Laat
Journal:  Mol Cell       Date:  2002-12       Impact factor: 17.970

Review 2.  Evolvability.

Authors:  M Kirschner; J Gerhart
Journal:  Proc Natl Acad Sci U S A       Date:  1998-07-21       Impact factor: 11.205

Review 3.  Gene expression in time and space: additive vs hierarchical organization of cis-regulatory regions.

Authors:  Robert K Maeda; François Karch
Journal:  Curr Opin Genet Dev       Date:  2011-02-23       Impact factor: 5.578

Review 4.  The evolution of 'bricolage'.

Authors:  D Duboule; A S Wilkins
Journal:  Trends Genet       Date:  1998-02       Impact factor: 11.639

5.  Long-range chromatin regulatory interactions in vivo.

Authors:  David Carter; Lyubomira Chakalova; Cameron S Osborne; Yan-feng Dai; Peter Fraser
Journal:  Nat Genet       Date:  2002-11-11       Impact factor: 38.330

6.  A switch between topological domains underlies HoxD genes collinearity in mouse limbs.

Authors:  Guillaume Andrey; Thomas Montavon; Bénédicte Mascrez; Federico Gonzalez; Daan Noordermeer; Marion Leleu; Didier Trono; François Spitz; Denis Duboule
Journal:  Science       Date:  2013-06-07       Impact factor: 47.728

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

Authors:  François Spitz; Federico Gonzalez; Denis Duboule
Journal:  Cell       Date:  2003-05-02       Impact factor: 41.582

8.  Mouse limb deformity mutations disrupt a global control region within the large regulatory landscape required for Gremlin expression.

Authors:  Aimée Zuniga; Odyssé Michos; François Spitz; Anna-Pavlina G Haramis; Lia Panman; Antonella Galli; Kristina Vintersten; Christian Klasen; William Mansfield; Sylwia Kuc; Denis Duboule; Rosanna Dono; Rolf Zeller
Journal:  Genes Dev       Date:  2004-06-15       Impact factor: 11.361

Review 9.  Long-range control of gene expression: emerging mechanisms and disruption in disease.

Authors:  Dirk A Kleinjan; Veronica van Heyningen
Journal:  Am J Hum Genet       Date:  2004-11-17       Impact factor: 11.025

10.  Species-specific transcription in mice carrying human chromosome 21.

Authors:  Michael D Wilson; Nuno L Barbosa-Morais; Dominic Schmidt; Caitlin M Conboy; Lesley Vanes; Victor L J Tybulewicz; Elizabeth M C Fisher; Simon Tavaré; Duncan T Odom
Journal:  Science       Date:  2008-09-11       Impact factor: 47.728

View more
  212 in total

1.  Nanoscale spatial organization of the HoxD gene cluster in distinct transcriptional states.

Authors:  Pierre J Fabre; Alexander Benke; Elisabeth Joye; Thi Hanh Nguyen Huynh; Suliana Manley; Denis Duboule
Journal:  Proc Natl Acad Sci U S A       Date:  2015-10-26       Impact factor: 11.205

2.  A single three-dimensional chromatin compartment in amphioxus indicates a stepwise evolution of vertebrate Hox bimodal regulation.

Authors:  Rafael D Acemel; Juan J Tena; Ibai Irastorza-Azcarate; Ferdinand Marlétaz; Carlos Gómez-Marín; Elisa de la Calle-Mustienes; Stéphanie Bertrand; Sergio G Diaz; Daniel Aldea; Jean-Marc Aury; Sophie Mangenot; Peter W H Holland; Damien P Devos; Ignacio Maeso; Hector Escrivá; José Luis Gómez-Skarmeta
Journal:  Nat Genet       Date:  2016-02-01       Impact factor: 38.330

3.  CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function.

Authors:  Ya Guo; Quan Xu; Daniele Canzio; Jia Shou; Jinhuan Li; David U Gorkin; Inkyung Jung; Haiyang Wu; Yanan Zhai; Yuanxiao Tang; Yichao Lu; Yonghu Wu; Zhilian Jia; Wei Li; Michael Q Zhang; Bing Ren; Adrian R Krainer; Tom Maniatis; Qiang Wu
Journal:  Cell       Date:  2015-08-13       Impact factor: 41.582

4.  The LDB1 Complex Co-opts CTCF for Erythroid Lineage-Specific Long-Range Enhancer Interactions.

Authors:  Jongjoo Lee; Ivan Krivega; Ryan K Dale; Ann Dean
Journal:  Cell Rep       Date:  2017-06-20       Impact factor: 9.423

Review 5.  Vision from next generation sequencing: multi-dimensional genome-wide analysis for producing gene regulatory networks underlying retinal development, aging and disease.

Authors:  Hyun-Jin Yang; Rinki Ratnapriya; Tiziana Cogliati; Jung-Woong Kim; Anand Swaroop
Journal:  Prog Retin Eye Res       Date:  2015-02-07       Impact factor: 21.198

6.  Inference of cell type specific regulatory networks on mammalian lineages.

Authors:  Deborah Chasman; Sushmita Roy
Journal:  Curr Opin Syst Biol       Date:  2017-04-17

Review 7.  Towards a comprehensive catalogue of validated and target-linked human enhancers.

Authors:  Molly Gasperini; Jacob M Tome; Jay Shendure
Journal:  Nat Rev Genet       Date:  2020-01-27       Impact factor: 53.242

8.  OneD: increasing reproducibility of Hi-C samples with abnormal karyotypes.

Authors:  Enrique Vidal; François le Dily; Javier Quilez; Ralph Stadhouders; Yasmina Cuartero; Thomas Graf; Marc A Marti-Renom; Miguel Beato; Guillaume J Filion
Journal:  Nucleic Acids Res       Date:  2018-05-04       Impact factor: 16.971

9.  Disrupting the three-dimensional regulatory topology of the Pitx1 locus results in overtly normal development.

Authors:  Richard Sarro; Acadia A Kocher; Deena Emera; Severin Uebbing; Emily V Dutrow; Scott D Weatherbee; Timothy Nottoli; James P Noonan
Journal:  Development       Date:  2018-04-09       Impact factor: 6.868

Review 10.  The structural and functional roles of CTCF in the regulation of cell type-specific and human disease-associated super-enhancers.

Authors:  Ha Youn Shin
Journal:  Genes Genomics       Date:  2018-11-19       Impact factor: 1.839

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.