Literature DB >> 28656981

Promoting transcription over long distances.

Rui R Catarino1, Christoph Neumayr1, Alexander Stark1.   

Abstract

Promoters and enhancers have long been regarded as distinct elements, a notion that has been challenged more recently. Two new studies now identify promoters that function as long-range enhancers in vivo to regulate the transcription of distal genes.

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Year:  2017        PMID： 28656981     DOI： 10.1038/ng.3904

Source DB:  PubMed          Journal:  Nat Genet        ISSN： 1061-4036            Impact factor:   38.330


  15 in total

1.  Genome-wide characterization of mammalian promoters with distal enhancer functions.

Authors:  Lan T M Dao; Ariel O Galindo-Albarrán; Jaime A Castro-Mondragon; Charlotte Andrieu-Soler; Alejandra Medina-Rivera; Charbel Souaid; Guillaume Charbonnier; Aurélien Griffon; Laurent Vanhille; Tharshana Stephen; Jaafar Alomairi; David Martin; Magali Torres; Nicolas Fernandez; Eric Soler; Jacques van Helden; Denis Puthier; Salvatore Spicuglia
Journal:  Nat Genet       Date:  2017-06-05       Impact factor: 38.330

2.  Genome-wide quantitative enhancer activity maps identified by STARR-seq.

Authors:  Cosmas D Arnold; Daniel Gerlach; Christoph Stelzer; Łukasz M Boryń; Martina Rath; Alexander Stark
Journal:  Science       Date:  2013-01-17       Impact factor: 47.728

3.  Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers.

Authors:  Leighton J Core; André L Martins; Charles G Danko; Colin T Waters; Adam Siepel; John T Lis
Journal:  Nat Genet       Date:  2014-11-10       Impact factor: 38.330

4.  Local regulation of gene expression by lncRNA promoters, transcription and splicing.

Authors:  Jesse M Engreitz; Jenna E Haines; Elizabeth M Perez; Glen Munson; Jenny Chen; Michael Kane; Patrick E McDonel; Mitchell Guttman; Eric S Lander
Journal:  Nature       Date:  2016-10-26       Impact factor: 49.962

5.  An atlas of active enhancers across human cell types and tissues.

Authors:  Robin Andersson; Claudia Gebhard; Michael Rehli; Albin Sandelin; Irene Miguel-Escalada; Ilka Hoof; Jette Bornholdt; Mette Boyd; Yun Chen; Xiaobei Zhao; Christian Schmidl; Takahiro Suzuki; Evgenia Ntini; Erik Arner; Eivind Valen; Kang Li; Lucia Schwarzfischer; Dagmar Glatz; Johanna Raithel; Berit Lilje; Nicolas Rapin; Frederik Otzen Bagger; Mette Jørgensen; Peter Refsing Andersen; Nicolas Bertin; Owen Rackham; A Maxwell Burroughs; J Kenneth Baillie; Yuri Ishizu; Yuri Shimizu; Erina Furuhata; Shiori Maeda; Yutaka Negishi; Christopher J Mungall; Terrence F Meehan; Timo Lassmann; Masayoshi Itoh; Hideya Kawaji; Naoto Kondo; Jun Kawai; Andreas Lennartsson; Carsten O Daub; Peter Heutink; David A Hume; Torben Heick Jensen; Harukazu Suzuki; Yoshihide Hayashizaki; Ferenc Müller; Alistair R R Forrest; Piero Carninci
Journal:  Nature       Date:  2014-03-27       Impact factor: 49.962

6.  Intragenic enhancers act as alternative promoters.

Authors:  Monika S Kowalczyk; Jim R Hughes; David Garrick; Magnus D Lynch; Jacqueline A Sharpe; Jacqueline A Sloane-Stanley; Simon J McGowan; Marco De Gobbi; Mona Hosseini; Douglas Vernimmen; Jill M Brown; Nicola E Gray; Licio Collavin; Richard J Gibbons; Jonathan Flint; Stephen Taylor; Veronica J Buckle; Thomas A Milne; William G Wood; Douglas R Higgs
Journal:  Mol Cell       Date:  2012-01-19       Impact factor: 17.970

7.  Enhancer-core-promoter specificity separates developmental and housekeeping gene regulation.

Authors:  Muhammad A Zabidi; Cosmas D Arnold; Katharina Schernhuber; Michaela Pagani; Martina Rath; Olga Frank; Alexander Stark
Journal:  Nature       Date:  2014-12-15       Impact factor: 49.962

8.  Coding exons function as tissue-specific enhancers of nearby genes.

Authors:  Ramon Y Birnbaum; E Josephine Clowney; Orly Agamy; Mee J Kim; Jingjing Zhao; Takayuki Yamanaka; Zachary Pappalardo; Shoa L Clarke; Aaron M Wenger; Loan Nguyen; Fiorella Gurrieri; David B Everman; Charles E Schwartz; Ohad S Birk; Gill Bejerano; Stavros Lomvardas; Nadav Ahituv
Journal:  Genome Res       Date:  2012-03-22       Impact factor: 9.043

9.  A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells.

Authors:  Yarui Diao; Rongxin Fang; Bin Li; Zhipeng Meng; Juntao Yu; Yunjiang Qiu; Kimberly C Lin; Hui Huang; Tristin Liu; Ryan J Marina; Inkyung Jung; Yin Shen; Kun-Liang Guan; Bing Ren
Journal:  Nat Methods       Date:  2017-04-17       Impact factor: 28.547

10.  Clustering of Drosophila housekeeping promoters facilitates their expression.

Authors:  Marc Corrales; Aránzazu Rosado; Ruggero Cortini; Joris van Arensbergen; Bas van Steensel; Guillaume J Filion
Journal:  Genome Res       Date:  2017-04-18       Impact factor: 9.043
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  7 in total

Review 1.  Eukaryotic core promoters and the functional basis of transcription initiation.

Authors:  Vanja Haberle; Alexander Stark
Journal:  Nat Rev Mol Cell Biol       Date:  2018-10       Impact factor: 94.444

Review 2.  The spatial organization of transcriptional control.

Authors:  Antonina Hafner; Alistair Boettiger
Journal:  Nat Rev Genet       Date:  2022-09-14       Impact factor: 59.581

3.  Integrative Functional Annotation of 52 Genetic Loci Influencing Myocardial Mass Identifies Candidate Regulatory Variants and Target Genes.

Authors:  Daiane Hemerich; Jiayi Pei; Magdalena Harakalova; Jessica van Setten; Sander Boymans; Bas J Boukens; Igor R Efimov; Michelle Michels; Jolanda van der Velden; Aryan Vink; Caroline Cheng; Pim van der Harst; Jason H Moore; Michal Mokry; Vinicius Tragante; Folkert W Asselbergs
Journal:  Circ Genom Precis Med       Date:  2019-02

Review 4.  Assessing sufficiency and necessity of enhancer activities for gene expression and the mechanisms of transcription activation.

Authors:  Rui R Catarino; Alexander Stark
Journal:  Genes Dev       Date:  2018-02-01       Impact factor: 11.361

5.  Targeted Forward Genetics: Population-Scale Analyses of Allele Replacements Spanning Thousands of Base Pairs in Fission Yeast.

Authors:  Aaron J Storey; Hsin-Ping Wang; Reine U Protacio; Mari K Davidson; Wayne P Wahls
Journal:  G3 (Bethesda)       Date:  2019-12-03       Impact factor: 3.154

6.  Epromoters function as a hub to recruit key transcription factors required for the inflammatory response.

Authors:  David Santiago-Algarra; Charbel Souaid; Himanshu Singh; Lan T M Dao; Saadat Hussain; Alejandra Medina-Rivera; Lucia Ramirez-Navarro; Jaime A Castro-Mondragon; Nori Sadouni; Guillaume Charbonnier; Salvatore Spicuglia
Journal:  Nat Commun       Date:  2021-11-18       Impact factor: 14.919

Review 7.  Three-dimensional genome architecture and emerging technologies: looping in disease.

Authors:  Arpit Mishra; R David Hawkins
Journal:  Genome Med       Date:  2017-09-30       Impact factor: 11.117
  7 in total

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