Literature DB >> 29889606

Transcriptional regulation by promoters with enhancer function.

Lan T M Dao1, Salvatore Spicuglia2,3.   

Abstract

Promoters with enhancer activity have been described recently. In this point of view, we will discuss current findings highlighting the commonality of this type of regulatory elements, their genetic and epigenetic characteristics, their potential biological roles in the regulation of gene expression and the underlining molecular mechanisms. ABBREVIATIONS: TSS: transcription start site; IFN: interferon; STARR-seq: Self-Transcribing Active Regulatory Region sequencing; MPRA: Massively Parallel Reporter Assay; ChIP: chromatin immunoprecipitation; CRISPR: Clustered Regularly Interspaced Short Palindromic Repeats; lncRNA: long non-coding RNA.

Entities:  

Keywords:  CRISPR/Cas9; Enhancer; Epromoter; gene regulation; promoter; reporter-assay

Mesh:

Substances:

Year:  2018        PMID: 29889606      PMCID: PMC6150634          DOI: 10.1080/21541264.2018.1486150

Source DB:  PubMed          Journal:  Transcription        ISSN: 2154-1272


  39 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

Review 2.  Transcriptional control of inflammatory responses.

Authors:  Stephen T Smale; Gioacchino Natoli
Journal:  Cold Spring Harb Perspect Biol       Date:  2014-09-11       Impact factor: 10.005

3.  Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements.

Authors:  Maxwell R Mumbach; Ansuman T Satpathy; Evan A Boyle; Chao Dai; Benjamin G Gowen; Seung Woo Cho; Michelle L Nguyen; Adam J Rubin; Jeffrey M Granja; Katelynn R Kazane; Yuning Wei; Trieu Nguyen; Peyton G Greenside; M Ryan Corces; Josh Tycko; Dimitre R Simeonov; Nabeela Suliman; Rui Li; Jin Xu; Ryan A Flynn; Anshul Kundaje; Paul A Khavari; Alexander Marson; Jacob E Corn; Thomas Quertermous; William J Greenleaf; Howard Y Chang
Journal:  Nat Genet       Date:  2017-09-25       Impact factor: 38.330

4.  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

5.  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

Review 6.  Finding distal regulatory elements in the human genome.

Authors:  Nathaniel D Heintzman; Bing Ren
Journal:  Curr Opin Genet Dev       Date:  2009-10-23       Impact factor: 5.578

7.  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

8.  Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions.

Authors:  Jason Ernst; Alexandre Melnikov; Xiaolan Zhang; Li Wang; Peter Rogov; Tarjei S Mikkelsen; Manolis Kellis
Journal:  Nat Biotechnol       Date:  2016-10-03       Impact factor: 54.908

Review 9.  Recent advances in high-throughput approaches to dissect enhancer function.

Authors:  David Santiago-Algarra; Lan T M Dao; Lydie Pradel; Alexandre España; Salvatore Spicuglia
Journal:  F1000Res       Date:  2017-06-19

10.  Transcription start site analysis reveals widespread divergent transcription in D. melanogaster and core promoter-encoded enhancer activities.

Authors:  Sarah Rennie; Maria Dalby; Marta Lloret-Llinares; Stylianos Bakoulis; Christian Dalager Vaagensø; Torben Heick Jensen; Robin Andersson
Journal:  Nucleic Acids Res       Date:  2018-06-20       Impact factor: 16.971

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  15 in total

1.  Functional effects of variation in transcription factor binding highlight long-range gene regulation by epromoters.

Authors:  Joanna Mitchelmore; Nastasiya F Grinberg; Chris Wallace; Mikhail Spivakov
Journal:  Nucleic Acids Res       Date:  2020-04-06       Impact factor: 16.971

2.  Genomics, molecular and evolutionary perspective of NAC transcription factors.

Authors:  Tapan Kumar Mohanta; Dhananjay Yadav; Adil Khan; Abeer Hashem; Baby Tabassum; Abdul Latif Khan; Elsayed Fathi Abd Allah; Ahmed Al-Harrasi
Journal:  PLoS One       Date:  2020-04-10       Impact factor: 3.240

3.  High-resolution targeted 3C interrogation of cis-regulatory element organization at genome-wide scale.

Authors:  Damien J Downes; Robert A Beagrie; Matthew E Gosden; Jelena Telenius; Stephanie J Carpenter; Lea Nussbaum; Sara De Ornellas; Martin Sergeant; Chris Q Eijsbouts; Ron Schwessinger; Jon Kerry; Nigel Roberts; Arun Shivalingam; Afaf El-Sagheer; A Marieke Oudelaar; Tom Brown; Veronica J Buckle; James O J Davies; Jim R Hughes
Journal:  Nat Commun       Date:  2021-01-22       Impact factor: 14.919

4.  DOCK8-expressing T follicular helper cells newly generated beyond self-organized criticality cause systemic lupus erythematosus.

Authors:  Shunichi Shiozawa; Ken Tsumiyama; Yumi Miyazaki; Kenichi Uto; Keiichi Sakurai; Toshie Nakashima; Hiroko Matsuyama; Ai Doi; Miho Tarui; Manabu Izumikawa; Mai Kimura; Yuko Fujita; Chisako Satonaka; Takahiko Horiuchi; Tsukasa Matsubara; Motohiro Oribe; Takashi Yamane; Hidetoshi Kagawa; Quan-Zhen Li; Keiko Mizuno; Yohei Mukai; Kazuhiro Murakami; Takuji Enya; Shota Tsukimoto; Yoshiyuki Hakata; Masaaki Miyazawa; Kazuko Shiozawa
Journal:  iScience       Date:  2021-12-02

5.  Assessing genome-wide dynamic changes in enhancer activity during early mESC differentiation by FAIRE-STARR-seq.

Authors:  Laura V Glaser; Mara Steiger; Alisa Fuchs; Alena van Bömmel; Edda Einfeldt; Ho-Ryun Chung; Martin Vingron; Sebastiaan H Meijsing
Journal:  Nucleic Acids Res       Date:  2021-12-02       Impact factor: 16.971

6.  Parallel characterization of cis-regulatory elements for multiple genes using CRISPRpath.

Authors:  Xingjie Ren; Mengchi Wang; Bingkun Li; Kirsty Jamieson; Lina Zheng; Ian R Jones; Bin Li; Maya Asami Takagi; Jerry Lee; Lenka Maliskova; Tsz Wai Tam; Miao Yu; Rong Hu; Lindsay Lee; Armen Abnousi; Gang Li; Yun Li; Ming Hu; Bing Ren; Wei Wang; Yin Shen
Journal:  Sci Adv       Date:  2021-09-15       Impact factor: 14.957

7.  DECODE: a Deep-learning framework for Condensing enhancers and refining boundaries with large-scale functional assays.

Authors:  Zhanlin Chen; Jing Zhang; Jason Liu; Yi Dai; Donghoon Lee; Martin Renqiang Min; Min Xu; Mark Gerstein
Journal:  Bioinformatics       Date:  2021-07-12       Impact factor: 6.937

8.  iEnhancer-GAN: A Deep Learning Framework in Combination with Word Embedding and Sequence Generative Adversarial Net to Identify Enhancers and Their Strength.

Authors:  Runtao Yang; Feng Wu; Chengjin Zhang; Lina Zhang
Journal:  Int J Mol Sci       Date:  2021-03-30       Impact factor: 5.923

9.  Regulatory regions in natural transposable element insertions drive interindividual differences in response to immune challenges in Drosophila.

Authors:  Anna Ullastres; Miriam Merenciano; Josefa González
Journal:  Genome Biol       Date:  2021-09-14       Impact factor: 13.583

10.  AnnoMiner is a new web-tool to integrate epigenetics, transcription factor occupancy and transcriptomics data to predict transcriptional regulators.

Authors:  Arno Meiler; Fabio Marchiano; Margaux Haering; Manuela Weitkunat; Frank Schnorrer; Bianca H Habermann
Journal:  Sci Rep       Date:  2021-07-29       Impact factor: 4.379

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