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Literature DB >> 26100358

Recent advances in functional assays of transcriptional enhancers.

Courtney C Babbitt¹, Michele Markstein², Jesse M Gray³.

Abstract

In this special edition of Genomics, we present reviews of the current state of the field in identifying and functionally understanding transcriptional enhancers in cells and developing tissues. Typically several enhancers coordinate the expression of an individual target gene, each controlling that gene's expression in specific cell types at specific times. Until recently, identifying each gene's enhancers had been challenging because enhancers do not occupy prescribed locations relative to their target genes. Recently there have been powerful advances in DNA sequencing and other technologies that make it possible to identify the majority of enhancers in virtually any cell type of interest. The reviews in this edition of Genomics highlight some of these new and powerful approaches.

Entities: Chemical Disease Gene Species

Keywords: Cis-regulatory elements; Enhancers; FIREWACh; MPRA; STARR-Seq; TRIP

Mesh：

Year: 2015 PMID： 26100358 PMCID： PMC4556128 DOI： 10.1016/j.ygeno.2015.06.002

Source DB: PubMed Journal: Genomics ISSN： 0888-7543 Impact factor: 5.736

11 in total

1. Histone H3K27ac separates active from poised enhancers and predicts developmental state.

Authors: Menno P Creyghton; Albert W Cheng; G Grant Welstead; Tristan Kooistra; Bryce W Carey; Eveline J Steine; Jacob Hanna; Michael A Lodato; Garrett M Frampton; Phillip A Sharp; Laurie A Boyer; Richard A Young; Rudolf Jaenisch
Journal: Proc Natl Acad Sci U S A Date: 2010-11-24 Impact factor: 11.205

2. DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays.

Authors: Gregory E Crawford; Sean Davis; Peter C Scacheri; Gabriel Renaud; Mohamad J Halawi; Michael R Erdos; Roland Green; Paul S Meltzer; Tyra G Wolfsberg; Francis S Collins
Journal: Nat Methods Date: 2006-07 Impact factor: 28.547

3. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome.

Authors: Nathaniel D Heintzman; Rhona K Stuart; Gary Hon; Yutao Fu; Christina W Ching; R David Hawkins; Leah O Barrera; Sara Van Calcar; Chunxu Qu; Keith A Ching; Wei Wang; Zhiping Weng; Roland D Green; Gregory E Crawford; Bing Ren
Journal: Nat Genet Date: 2007-02-04 Impact factor: 38.330

4. 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

5. Using TRIP for genome-wide position effect analysis in cultured cells.

Authors: Waseem Akhtar; Alexey V Pindyurin; Johann de Jong; Ludo Pagie; Jelle Ten Hoeve; Anton Berns; Lodewyk F A Wessels; Bas van Steensel; Maarten van Lohuizen
Journal: Nat Protoc Date: 2014-05-08 Impact factor: 13.491

6. Genome-scale functional characterization of Drosophila developmental enhancers in vivo.

Authors: Evgeny Z Kvon; Tomas Kazmar; Gerald Stampfel; J Omar Yáñez-Cuna; Michaela Pagani; Katharina Schernhuber; Barry J Dickson; Alexander Stark
Journal: Nature Date: 2014-06-01 Impact factor: 49.962

7. Expression of a beta-globin gene is enhanced by remote SV40 DNA sequences.

Authors: J Banerji; S Rusconi; W Schaffner
Journal: Cell Date: 1981-12 Impact factor: 41.582

8. The INTACT method for cell type-specific gene expression and chromatin profiling in Arabidopsis thaliana.

Authors: Roger B Deal; Steven Henikoff
Journal: Nat Protoc Date: 2010-12-16 Impact factor: 13.491

9. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position.

Authors: Jason D Buenrostro; Paul G Giresi; Lisa C Zaba; Howard Y Chang; William J Greenleaf
Journal: Nat Methods Date: 2013-10-06 Impact factor: 28.547

Recent advances in functional assays of transcriptional enhancers.

1. Histone H3K27ac separates active from poised enhancers and predicts developmental state.

2. DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays.

3. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome.

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

5. Using TRIP for genome-wide position effect analysis in cultured cells.

6. Genome-scale functional characterization of Drosophila developmental enhancers in vivo.

7. Expression of a beta-globin gene is enhanced by remote SV40 DNA sequences.

8. The INTACT method for cell type-specific gene expression and chromatin profiling in Arabidopsis thaliana.

9. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position.

10. Hi-C: a method to study the three-dimensional architecture of genomes.

Review 1. Enhancer redundancy in development and disease.

Review 2. Genome-wide identification of enhancer elements in the placenta.

3. Primate optogenetics: Progress and prognosis.

4. Charting the cis-regulome of activated B cells by coupling structural and functional genomics.

5. A Library Screening Strategy Combining the Concepts of MS Binding Assays and Affinity Selection Mass Spectrometry.