P. Kapranov, A. Willingham, and T. Gingeras, Genome-wide transcription and the implications for genomic organization, Nature Reviews Genetics, vol.12, issue.6, pp.413-423, 2007.
DOI : 10.1038/nrg2083

M. Guttman and J. Rinn, Modular regulatory principles of large non-coding RNAs, Nature, vol.136, issue.7385, pp.339-346, 2012.
DOI : 10.1038/nature10887

T. Derrien, R. Johnson, G. Bussotti, A. Tanzer, S. Djebali et al., The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression, Genome Research, vol.22, issue.9, pp.1775-1789, 2012.
DOI : 10.1101/gr.132159.111
URL : https://hal.archives-ouvertes.fr/hal-01205054

E. Birney, J. Stamatoyannopoulos, A. Dutta, R. Guigo, T. Gingeras et al., Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project, Nature, vol.12, issue.7146, pp.799-816, 2007.
DOI : 10.1038/nature05874

M. Tisseur, M. Kwapisz, and A. Morillon, Pervasive transcription ??? Lessons from yeast, Biochimie, vol.93, issue.11, pp.1889-1896, 2011.
DOI : 10.1016/j.biochi.2011.07.001

M. Clark, P. Amaral, F. Schlesinger, M. Dinger, R. Taft et al., The Reality of Pervasive Transcription, PLoS Biology, vol.25, issue.7, pp.1000625-1001102, 2011.
DOI : 10.1371/journal.pbio.1000625.s008

M. Magistri, M. Faghihi, S. Laurent, G. Iii, and C. Wahlestedt, Regulation of chromatin structure by long noncoding RNAs: focus on natural antisense transcripts, Trends in Genetics, vol.28, issue.8, pp.389-396, 2012.
DOI : 10.1016/j.tig.2012.03.013

S. Katayama, Y. Tomaru, T. Kasukawa, K. Waki, M. Nakanishi et al., Antisense transcription in the mammalian transcriptome, Science, vol.309, pp.1564-1566, 2005.

C. Carrieri, L. Cimatti, M. Biagioli, A. Beugnet, S. Zucchelli et al., Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat, Nature, vol.12, issue.7424, pp.491454-457
DOI : 10.1038/nature11508

W. Wei, V. Pelechano, A. Jarvelin, and L. Steinmetz, Functional consequences of bidirectional promoters, Trends in Genetics, vol.27, issue.7, pp.267-276, 2011.
DOI : 10.1016/j.tig.2011.04.002

L. Core, J. Waterfall, and J. Lis, Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters, Science, vol.322, issue.5909, pp.1845-1848, 2008.
DOI : 10.1126/science.1162228

A. Seila, J. Calabrese, S. Levine, G. Yeo, P. Rahl et al., Divergent Transcription from Active Promoters, Science, vol.322, issue.5909, pp.1849-1851, 2008.
DOI : 10.1126/science.1162253

P. Kapranov, J. Cheng, S. Dike, D. Nix, R. Duttagupta et al., RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription, Science, vol.316, issue.5830, pp.1484-1488, 2007.
DOI : 10.1126/science.1138341

F. Wyers, M. Rougemaille, G. Badis, J. Rousselle, M. Dufour et al., Cryptic Pol II Transcripts Are Degraded by a Nuclear Quality Control Pathway Involving a New Poly(A) Polymerase, Cell, vol.121, issue.5, pp.725-737, 2005.
DOI : 10.1016/j.cell.2005.04.030

P. Preker, K. Almvig, M. Christensen, E. Valen, C. Mapendano et al., PROMoter uPstream Transcripts share characteristics with mRNAs and are produced upstream of all three major types of mammalian promoters, Nucleic Acids Research, vol.39, issue.16, pp.7179-7193, 2011.
DOI : 10.1093/nar/gkr370

P. Preker, J. Nielsen, S. Kammler, S. Lykke-andersen, M. Christensen et al., RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters, Science, vol.322, issue.5909, pp.1851-1854, 2008.
DOI : 10.1126/science.1164096

H. Neil, C. Malabat, Y. Aubenton-carafa, Z. Xu, L. Steinmetz et al., Widespread bidirectional promoters are the major source of cryptic transcripts in yeast, Nature, vol.320, issue.7232, pp.1038-1042, 2009.
DOI : 10.1038/nature07747

M. Guttman, M. Garber, J. Levin, J. Donaghey, J. Robinson et al., Ab initio reconstruction of cell type???specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs, Nature Biotechnology, vol.10, issue.5, pp.503-510, 2010.
DOI : 10.1038/nbt.1633

M. Cabili, C. Trapnell, L. Goff, M. Koziol, B. Tazon-vega et al., Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses, Genes & Development, vol.25, issue.18, pp.1915-1927, 2011.
DOI : 10.1101/gad.17446611

A. Sigova, A. Mullen, B. Molinie, S. Gupta, D. Orlando et al., Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells, Proceedings of the National Academy of Sciences, vol.110, issue.8, pp.1102876-2881
DOI : 10.1073/pnas.1221904110

J. Levin, M. Yassour, X. Adiconis, C. Nusbaum, D. Thompson et al., Comprehensive comparative analysis of strand-specific RNA sequencing methods, Nature Methods, vol.5, issue.9, pp.709-715, 2010.
DOI : 10.1038/nmeth.1491

R. Thiagarajan, N. Cloonan, B. Gardiner, T. Mercer, G. Kolle et al., Refining transcriptional programs in kidney development by integration of deep RNA-sequencing and array-based spatial profiling, BMC Genomics, vol.282, issue.1, p.441, 2011.
DOI : 10.1074/jbc.M609578200

C. Trapnell, A. Roberts, L. Goff, G. Pertea, D. Kim et al., Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks, Nature Protocols, vol.7, issue.3, pp.562-578, 2012.
DOI : 10.1038/nbt0710-691

C. Trapnell, B. Williams, G. Pertea, A. Mortazavi, G. Kwan et al., Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation, Nature Biotechnology, vol.25, issue.5, pp.511-515, 2010.
DOI : 10.1038/nbt.1621

M. Lin, I. Jungreis, and M. Kellis, PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions, Bioinformatics, vol.27, issue.13, pp.275-282, 2011.
DOI : 10.1093/bioinformatics/btr209

D. Bhatt, A. Pandya-jones, A. Tong, I. Barozzi, M. Lissner et al., Transcript Dynamics of Proinflammatory Genes Revealed by Sequence Analysis of Subcellular RNA Fractions, Cell, vol.150, issue.2, pp.279-290, 2012.
DOI : 10.1016/j.cell.2012.05.043

E. Rothenberg, J. Moore, and M. Yui, Launching the T-cell-lineage developmental programme, Nature Reviews Immunology, vol.8, issue.1, pp.9-21, 2008.
DOI : 10.1038/nri2232

J. Chen, E. Bardes, B. Aronow, and A. Jegga, ToppGene Suite for gene list enrichment analysis and candidate gene prioritization, Nucleic Acids Research, vol.37, issue.Web Server, pp.305-311, 2009.
DOI : 10.1093/nar/gkp427

Y. Shen, F. Yue, D. Mccleary, Z. Ye, L. Edsall et al., A map of the cis-regulatory sequences in the mouse genome, Nature, vol.6, issue.7409, pp.488116-120
DOI : 10.1038/nature11243

A. Hayday and D. Pennington, Key factors in the organized chaos of early T cell development, Nature Immunology, vol.44, issue.2, pp.137-144, 2007.
DOI : 10.1126/science.1123497

F. Koch, R. Fenouil, M. Gut, P. Cauchy, T. Albert et al., Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters, Nature Structural & Molecular Biology, vol.2, issue.8, pp.956-963, 2011.
DOI : 10.1093/nar/gkn304
URL : https://hal.archives-ouvertes.fr/hal-00609674

J. Zhang, A. Mortazavi, B. Williams, B. Wold, and E. Rothenberg, Dynamic Transformations of Genome-wide Epigenetic Marking and Transcriptional Control Establish T Cell Identity, Cell, vol.149, issue.2, pp.467-482, 2012.
DOI : 10.1016/j.cell.2012.01.056

A. Akalin, D. Fredman, E. Arner, X. Dong, J. Bryne et al., Transcriptional features of genomic regulatory blocks, Genome Biology, vol.10, issue.4, p.38, 2009.
DOI : 10.1186/gb-2009-10-4-r38

B. Lenhard, A. Sandelin, and P. Carninci, Metazoan promoters: emerging characteristics and insights into transcriptional regulation, Nature Reviews Genetics, vol.107, pp.233-245, 2012.
DOI : 10.1038/nrg3163

V. Zhou, A. Goren, and B. Bernstein, Charting histone modifications and the functional organization of mammalian genomes, Nature Reviews Genetics, vol.28, issue.1, pp.7-18, 2011.
DOI : 10.1038/nrg2905

T. Mikkelsen, M. Ku, D. Jaffe, I. B. Lieberman, E. Giannoukos et al., Genome-wide maps of chromatin state in pluripotent and lineage-committed cells, Nature, vol.99, issue.7153, pp.553-560, 2007.
DOI : 10.1038/nature06008

B. Bernstein, T. Mikkelsen, X. Xie, M. Kamal, D. Huebert et al., A Bivalent Chromatin Structure Marks Key Developmental Genes in Embryonic Stem Cells, Cell, vol.125, issue.2, pp.315-326, 2006.
DOI : 10.1016/j.cell.2006.02.041

G. Wei, B. Abraham, R. Yagi, R. Jothi, K. Cui et al., Genome-wide Analyses of Transcription Factor GATA3-Mediated Gene Regulation in Distinct T Cell Types, Immunity, vol.35, issue.2, pp.299-311, 2011.
DOI : 10.1016/j.immuni.2011.08.007

J. Zhang, A. Jackson, T. Naito, M. Dose, J. Seavitt et al., Harnessing of the nucleosome-remodeling-deacetylase complex controls lymphocyte development and prevents leukemogenesis, Nature Immunology, vol.3, issue.1, pp.86-94, 2012.
DOI : 10.1016/j.immuni.2009.09.024

P. Carninci, A. Sandelin, B. Lenhard, S. Katayama, K. Shimokawa et al., Genome-wide analysis of mammalian promoter architecture and evolution, Nature Genetics, vol.33, issue.6, pp.626-635, 2006.
DOI : 10.1089/1066527041410472

P. Ginno, P. Lott, H. Christensen, and I. Korf, R-Loop Formation Is a Distinctive Characteristic of Unmethylated Human CpG Island Promoters, Molecular Cell, vol.45, issue.6, pp.814-825, 2012.
DOI : 10.1016/j.molcel.2012.01.017

. Almadaae, . Wux, . Krizaj, . Burgecb, and . Sharppa, Promoter directionality is controlled by U1 snRNP and polyadenylation signals, Nature, vol.9, issue.7458, pp.360-363, 2013.
DOI : 10.1038/nature12349

E. Ntini, A. Jarvelin, J. Bornholdt, Y. Chen, M. Boyd et al., Polyadenylation site???induced decay of upstream transcripts enforces promoter directionality, Nature Structural & Molecular Biology, vol.38, issue.8, pp.923-928, 2013.
DOI : 10.1038/nsmb.2640

N. Bieberstein, C. Oesterreich, F. Straube, K. Neugebauer, and K. , First Exon Length Controls Active Chromatin Signatures and Transcription, Cell Reports, vol.2, issue.1, pp.62-68, 2012.
DOI : 10.1016/j.celrep.2012.05.019

J. Huff, A. Plocik, C. Guthrie, and K. Yamamoto, Reciprocal intronic and exonic histone modification regions in humans, Nature Structural & Molecular Biology, vol.137, issue.12, pp.1495-1499, 2010.
DOI : 10.1038/nsmb.1924

M. Heidemann, C. Hintermair, K. Voss, and D. Eick, Dynamic phosphorylation patterns of RNA polymerase II CTD during transcription, Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, vol.1829, issue.1, pp.55-62
DOI : 10.1016/j.bbagrm.2012.08.013

J. Nam and D. Bartel, Long non-coding RNAs in C. elegans, Genome Res, vol.2012, issue.2212, pp.2529-2540

R. Fenouil, P. Cauchy, F. Koch, N. Descostes, J. Cabeza et al., CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters, Genome Research, vol.22, issue.12, pp.2399-2408, 2012.
DOI : 10.1101/gr.138776.112

T. Mercer, M. Dinger, S. Sunkin, M. Mehler, and J. Mattick, Specific expression of long noncoding RNAs in the mouse brain, Proceedings of the National Academy of Sciences, vol.105, issue.2, pp.716-721, 2008.
DOI : 10.1073/pnas.0706729105

M. Guttman, I. Amit, M. Garber, C. French, M. Lin et al., Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals, Nature, vol.322, issue.7235, pp.223-227, 2009.
DOI : 10.1038/nature07672

J. Wamstad, J. Alexander, R. Truty, A. Shrikumar, F. Li et al., Dynamic and Coordinated Epigenetic Regulation of Developmental Transitions in the Cardiac Lineage, Cell, vol.151, issue.1, pp.206-220, 2012.
DOI : 10.1016/j.cell.2012.07.035

I. Ulitsky and D. Bartel, lincRNAs: Genomics, Evolution, and Mechanisms, Cell, vol.154, issue.1, pp.26-46, 2013.
DOI : 10.1016/j.cell.2013.06.020

I. Ulitsky, A. Shkumatava, C. Jan, H. Sive, and D. Bartel, Conserved Function of lincRNAs in Vertebrate Embryonic Development despite Rapid Sequence Evolution, Cell, vol.147, issue.7, pp.1537-1550, 2011.
DOI : 10.1016/j.cell.2011.11.055

A. Tanay, O. Donnell, A. Damelin, M. Bestor, and T. , Hyperconserved CpG domains underlie Polycomb-binding sites, Proceedings of the National Academy of Sciences, vol.104, issue.13, pp.5521-5526, 2007.
DOI : 10.1073/pnas.0609746104
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1838490

M. Yang and L. Elnitski, Diversity of core promoter elements comprising human bidirectional promoters, BMC Genomics, vol.9, issue.Suppl 2, p.3, 2008.
DOI : 10.1186/1471-2164-9-S2-S3

N. Trinklein, S. Aldred, S. Hartman, D. Schroeder, R. Otillar et al., An Abundance of Bidirectional Promoters in the Human Genome, Genome Research, vol.14, issue.1
DOI : 10.1101/gr.1982804

X. Li and J. Manley, Cotranscriptional processes and their influence on genome stability, Genes & Development, vol.20, issue.14, pp.1838-1847, 2006.
DOI : 10.1101/gad.1438306

M. Dominguez-sanchez, S. Barroso, B. Gomez-gonzalez, R. Luna, and A. Aguilera, Genome Instability and Transcription Elongation Impairment in Human Cells Depleted of THO/TREX, PLoS Genetics, vol.16, issue.12, p.1002386, 2011.
DOI : 10.1371/journal.pgen.1002386.s009

E. Hage, A. French, S. Beyer, A. Tollervey, and D. , Loss of Topoisomerase I leads to R-loop-mediated transcriptional blocks during ribosomal RNA synthesis, Genes & Development, vol.24, issue.14, pp.1546-1558, 2010.
DOI : 10.1101/gad.573310

C. Tous and A. Aguilera, Impairment of transcription elongation by R-loops in vitro, Biochemical and Biophysical Research Communications, vol.360, issue.2, pp.428-432, 2007.
DOI : 10.1016/j.bbrc.2007.06.098

J. Lee, A. Khan, H. Min, X. Wang, and M. Kim, Identification and characterization of a noncoding RNA at the mouse Pcna locus, Molecules and Cells, vol.7, issue.2, pp.111-116, 2012.
DOI : 10.1007/s10059-012-2164-x

P. Grote, L. Wittler, D. Hendrix, F. Koch, S. Wahrisch et al., The Tissue-Specific lncRNA Fendrr Is an Essential Regulator of Heart and Body Wall Development in the Mouse, Developmental Cell, vol.24, issue.2, pp.206-214, 2013.
DOI : 10.1016/j.devcel.2012.12.012

K. Adelman and J. Lis, Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans, Nature Reviews Genetics, vol.16, issue.10, pp.720-731, 2012.
DOI : 10.1006/jmbi.1995.0517

M. Guenther, S. Levine, L. Boyer, R. Jaenisch, and R. Young, A Chromatin Landmark and Transcription Initiation at Most Promoters in Human Cells, Cell, vol.130, issue.1, pp.77-88, 2007.
DOI : 10.1016/j.cell.2007.05.042

K. Adelman, M. Kennedy, S. Nechaev, D. Gilchrist, G. Muse et al., Immediate mediators of the inflammatory response are poised for gene activation through RNA polymerase II stalling, Proceedings of the National Academy of Sciences, vol.106, issue.43, pp.18207-18212, 2009.
DOI : 10.1073/pnas.0910177106

D. Hargreaves, T. Horng, and R. Medzhitov, Control of Inducible Gene Expression by Signal-Dependent Transcriptional Elongation, Cell, vol.138, issue.1, pp.129-145, 2009.
DOI : 10.1016/j.cell.2009.05.047

F. Koch, F. Jourquin, P. Ferrier, and J. Andrau, Genome-wide RNA polymerase II: not genes only! Trends Biochem Sci, pp.265-273, 2008.
DOI : 10.1016/j.tibs.2008.04.006

Z. Xu, W. Wei, J. Gagneur, S. Clauder-munster, M. Smolik et al., Antisense expression increases gene expression variability and locus interdependency, Molecular Systems Biology, vol.11, issue.1, p.468, 2011.
DOI : 10.1038/msb.2011.1
URL : http://doi.org/10.1038/msb.2011.1

L. Lopez-maury, S. Marguerat, and J. Bahler, Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation, Nature Reviews Genetics, vol.8, issue.8, pp.583-593, 2008.
DOI : 10.1038/nrg2398

A. Arias and P. Hayward, Filtering transcriptional noise during development: concepts and mechanisms, Nature Reviews Genetics, vol.101, issue.1, pp.34-44, 2006.
DOI : 10.1038/nrg1750

Y. Shinkai, G. Rathbun, K. Lam, E. Oltz, V. Stewart et al., RAG-2-deficient mice lack mature lymphocytes owing to inability to initiate V(D)J rearrangement, Cell, vol.68, issue.5, pp.855-867, 1992.
DOI : 10.1016/0092-8674(92)90029-C

A. Pekowska, T. Benoukraf, J. Zacarias-cabeza, M. Belhocine, F. Koch et al., tri-methylation provides an epigenetic signature of active enhancers, EMBO J, vol.30, pp.3-44198, 2011.

A. Quinlan and I. Hall, BEDTools: a flexible suite of utilities for comparing genomic features, Bioinformatics, vol.26, issue.6, pp.841-842, 2010.
DOI : 10.1093/bioinformatics/btq033

A. Su, T. Wiltshire, S. Batalov, H. Lapp, K. Ching et al., A gene atlas of the mouse and human protein-encoding transcriptomes, Proceedings of the National Academy of Sciences, vol.101, issue.16, pp.6062-6067, 2004.
DOI : 10.1073/pnas.0400782101

S. Heinz, C. Benner, N. Spann, E. Bertolino, Y. Lin et al., Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities, Molecular Cell, vol.38, issue.4, pp.576-589, 2010.
DOI : 10.1016/j.molcel.2010.05.004

W. Da-huang, B. Sherman, and R. Lempicki, Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources, Nature Protocols, vol.99, issue.1, pp.44-57, 2009.
DOI : 10.1038/nprot.2008.211

C. Lepoivre, A. Bergon, F. Lopez, N. Perumal, C. Nguyen et al., TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks, BMC Bioinformatics, vol.13, issue.1, p.19, 2012.
DOI : 10.1016/j.cell.2008.04.043
URL : https://hal.archives-ouvertes.fr/inserm-00676438