S. Chatterjee and N. Ahituv, Gene Regulatory Elements, Major Drivers of Human Disease. Annual review of genomics and human genetics, 2017.

R. Andersson, A. Sandelin, and C. G. Danko, A unified architecture of transcriptional regulatory elements, Trends in genetics : TIG, vol.31, pp.426-433, 2015.

N. D. Tippens, A. Vihervaara, and J. T. Lis, Enhancer transcription: what, where, when, and why?, Genes Dev, vol.32, pp.1-3, 2018.

G. Li, Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation, Cell, vol.148, pp.84-98, 2012.

R. Andersson, Promoter or enhancer, what's the difference? Deconstruction of established distinctions and presentation of a unifying model, BioEssays : news and reviews in molecular, cellular and developmental biology, vol.37, pp.314-323, 2015.

W. Schaffner and . Enhancers, enhancers-from their discovery to today's universe of transcription enhancers, Biol Chem, vol.396, pp.311-327, 2015.

J. Banerji, S. Rusconi, and W. Schaffner, Expression of a beta-globin gene is enhanced by remote SV40 DNA sequences, Cell, vol.27, pp.299-308, 1981.

D. Santiago-algarra, L. T. Dao, L. Pradel, A. Espana, and S. Spicuglia, Recent advances in high-throughput approaches to dissect enhancer function, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01612096

C. D. Arnold, Genome-wide quantitative enhancer activity maps identified by STARR-seq, Science, vol.339, pp.1074-1077, 2013.

M. A. Zabidi, Enhancer-core-promoter specificity separates developmental and housekeeping gene regulation, Nature, vol.518, pp.556-559, 2015.

T. A. Nguyen, High-throughput functional comparison of promoter and enhancer activities, Genome research, vol.26, pp.1023-1033, 2016.

L. T. Dao, Genome-wide characterization of mammalian promoters with distal enhancer functions, Nature genetics, vol.49, pp.1073-1081, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01595810

Y. Liu, Functional assessment of human enhancer activities using whole-genome STARR-sequencing, Genome Biol, vol.18, 2017.

F. Muerdter, Resolving systematic errors in widely used enhancer activity assays in human cells, Nat Methods, vol.15, pp.141-149, 2018.

T. S. Barakat, Functional dissection of the enhancer repertoire in human embryonic stem cells. bioRxiv, 2017.

X. Wang, High-resolution genome-wide functional dissection of transcriptional regulatory regions in human. bioRxiv, 2017.

J. Ernst, Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions, Nat Biotechnol, vol.34, pp.1180-1190, 2016.

L. Vanhille, High-throughput and quantitative assessment of enhancer activity in mammals by CapStarr-seq, Nat Commun, vol.6, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01614948

M. S. Kowalczyk, Intragenic enhancers act as alternative promoters, Molecular cell, vol.45, pp.447-458, 2012.

J. M. Engreitz, Local regulation of gene expression by lncRNA promoters, transcription and splicing, Nature, 2016.

V. R. Paralkar, Unlinking an lncRNA from Its Associated cis Element, Molecular cell, vol.62, pp.104-110, 2016.

Y. Diao, A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells, Nat Methods, vol.14, pp.629-635, 2017.

N. Rajagopal, High-throughput mapping of regulatory DNA, Nat Biotechnol, vol.34, pp.167-174, 2016.

M. R. Mumbach, Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements, Nature genetics, vol.49, pp.1602-1612, 2017.

N. D. Heintzman and B. Ren, Finding distal regulatory elements in the human genome, Curr Opin Genet Dev, vol.19, pp.541-549, 2009.

L. J. Core, Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers, Nature genetics, vol.46, pp.1311-1320, 2014.

R. Andersson, An atlas of active enhancers across human cell types and tissues, Nature, vol.507, pp.455-461, 2014.

T. Henriques, Widespread transcriptional pausing and elongation control at enhancers, Genes Dev, vol.32, pp.26-41, 2018.

O. Mikhaylichenko, The degree of enhancer or promoter activity is reflected by the levels and directionality of eRNA transcription, Genes Dev, vol.32, pp.42-57, 2018.

B. S. Scruggs, Bidirectional Transcription Arises from Two Distinct Hubs of Transcription Factor Binding and Active Chromatin, Molecular cell, vol.58, pp.1101-1112, 2015.

S. Rennie, Transcription start site analysis reveals widespread divergent transcription in D. melanogaster and core promoter-encoded enhancer activities, Nucleic acids research, 2018.

D. Leung, Integrative analysis of haplotype-resolved epigenomes across human tissues, Nature, vol.518, pp.350-354, 2015.

M. Corrales, Clustering of Drosophila housekeeping promoters facilitates their expression, Genome research, vol.27, pp.1153-1161, 2017.

S. T. Smale and G. Natoli, Transcriptional control of inflammatory responses. Cold Spring Harbor perspectives in biology 6, a016261, 2014.

A. Feuerborn and P. R. Cook, Why the activity of a gene depends on its neighbors, Trends in genetics : TIG, vol.31, pp.483-490, 2015.

D. Hnisz, K. Shrinivas, R. A. Young, A. K. Chakraborty, and P. A. Sharp, A Phase Separation Model for Transcriptional Control, Cell, vol.169, pp.13-23, 2017.

X. Wu and P. A. Sharp, Divergent transcription: a driving force for new gene origination?, Cell, vol.155, pp.990-996, 2013.

C. Arenas-mena, The origins of developmental gene regulation, Evol Dev, vol.19, pp.96-107, 2017.

C. Xie, Hominoid-specific de novo protein-coding genes originating from long non-coding RNAs, PLoS genetics, vol.8, p.1002942, 2012.

C. Y. Mclean, GREAT improves functional interpretation of cis-regulatory regions, Nat Biotechnol, vol.28, pp.495-501, 2010.