P. Carninci, T. Kasukawa, S. Katayama, J. Gough, M. Frith et al., The transcriptional landscape of the mammalian genome, Science, vol.309, pp.1559-63, 2005.

F. Yue, Y. Cheng, A. Breschi, J. Vierstra, W. Wu et al., A comparative encyclopedia of DNA elements in the mouse genome, Nature, vol.46, issue.7527, pp.355-64, 2014.
DOI : 10.1038/nature13992

S. Djebali, C. Davis, A. Merkel, A. Dobin, T. Lassmann et al., Landscape of transcription in human cells, Nature, vol.474, issue.7414, pp.101-109, 2012.
DOI : 10.1038/nature11233
URL : https://hal.archives-ouvertes.fr/hal-01216755

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.1484-1492, 2007.
DOI : 10.1126/science.1138341

J. Harrow, A. Frankish, J. Gonzalez, E. Tapanari, M. Diekhans et al., GENCODE: The reference human genome annotation for The ENCODE Project, Genome Research, vol.22, issue.9, pp.1760-74, 2012.
DOI : 10.1101/gr.135350.111

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.1775-89, 2012.
DOI : 10.1101/gr.132159.111
URL : https://hal.archives-ouvertes.fr/hal-01205054

M. Iyer, Y. Niknafs, R. Malik, U. Singhal, A. Sahu et al., The landscape of long noncoding RNAs in the human transcriptome, Nature Genetics, vol.486, issue.3, pp.199-208, 2015.
DOI : 10.1093/bioinformatics/btr260

T. Mercer, M. Dinger, and J. Mattick, Long non-coding RNAs: insights into functions, Nature Reviews Genetics, vol.72, issue.3, pp.155-164, 2009.
DOI : 10.1038/nrg2521

C. Ponting, P. Oliver, and W. Reik, Evolution and Functions of Long Noncoding RNAs, Cell, vol.136, issue.4, pp.629-670, 2009.
DOI : 10.1016/j.cell.2009.02.006

S. Schmitz, P. Grote, and B. Herrmann, Mechanisms of long noncoding RNA function in development and disease, Cellular and Molecular Life Sciences, vol.72, issue.13, pp.2491-509, 2016.
DOI : 10.1007/s00018-016-2174-5

T. Manolio, F. Collins, N. Cox, D. Goldstein, L. Hindorff et al., Finding the missing heritability of complex diseases, Nature, vol.41, issue.7265, pp.747-53, 2009.
DOI : 10.1038/nature08494

L. Hindorff, P. Sethupathy, H. Junkins, E. Ramos, J. Mehta et al., Potential etiologic and functional implications of genome-wide association loci for human diseases and traits, Proceedings of the National Academy of Sciences, vol.106, issue.23, pp.9362-9369, 2009.
DOI : 10.1073/pnas.0903103106

L. Andersson, A. Archibald, C. Bottema, R. Brauning, S. Burgess et al., Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project, Genome Biology, vol.159, issue.1, p.57, 2015.
DOI : 10.1186/s13059-015-0622-4
URL : https://hal.archives-ouvertes.fr/hal-01194102

L. Koufariotis, Y. Chen, A. Chamberlain, V. Jagt, C. Hayes et al., A catalogue of novel bovine long noncoding RNA across 18 tissues, PLOS ONE, vol.16, issue.6, p.141225, 2015.
DOI : 10.1371/journal.pone.0141225.s008

R. Al-tobasei, B. Paneru, and M. Salem, Genome-wide discovery of long noncoding RNAs in rainbow trout, PLoS One, vol.11, p.148940, 2016.

Y. Zhao, H. Li, S. Fang, Y. Kang, W. Wu et al., NONCODE 2016: an informative and valuable data source of long non-coding RNAs, Nucleic Acids Research, vol.44, issue.D1, pp.203-211, 2016.
DOI : 10.1093/nar/gkv1252

A. Li, J. Zhang, Z. Zhou, L. Wang, Y. Liu et al., ALDB: A Domestic-Animal Long Noncoding RNA Database, PLOS ONE, vol.324, issue.4, p.124003, 2015.
DOI : 10.1371/journal.pone.0124003.s002
URL : http://doi.org/10.1371/journal.pone.0124003

V. Wucher, F. Legeai, B. Hedan, G. Rizk, L. Lagoutte et al., FEELnc: A tool for long non-coding RNAs annotation and its application to the dog transcriptome, p.64436, 2016.

L. Kong, Y. Zhang, Z. Ye, X. Liu, S. Zhao et al., CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine, Nucleic Acids Research, vol.35, issue.Web Server, pp.345-354, 2007.
DOI : 10.1093/nar/gkm391

L. Wang, H. Park, S. Dasari, S. Wang, J. Kocher et al., CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model, Nucleic Acids Research, vol.41, issue.6, p.74, 2013.
DOI : 10.1093/nar/gkt006

H. Baziz, P. Geraert, J. Padilha, and S. Guillaumin, Chronic Heat Exposure Enhances Fat Deposition and Modifies Muscle and Fat Partition in Broiler Carcasses, Poultry Science, vol.75, issue.4, pp.505-518, 1996.
DOI : 10.3382/ps.0750505

E. Bedu, F. Chainier, B. Sibille, R. Meister, G. Dallevet et al., Increased lipogenesis in isolated hepatocytes from cold-acclimated ducklings, American Journal of Physiology - Regulatory, Integrative and Comparative Physiology, vol.283, issue.5, pp.1245-53, 2002.
DOI : 10.1152/ajpregu.00681.2001

R. Rosebrough, B. Russell, and M. Richards, Further studies on short-term adaptations in the expression of lipogenic genes in broilers, Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology, vol.159, issue.1, pp.1-6, 2011.
DOI : 10.1016/j.cbpa.2010.10.032

T. Ravasi, H. Suzuki, K. Pang, S. Katayama, M. Furuno et al., Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome, Genome Research, vol.16, issue.1, pp.11-20, 2006.
DOI : 10.1101/gr.4200206

U. Ørom, T. Derrien, M. Beringer, K. Gumireddy, A. Gardini et al., Long Noncoding RNAs with Enhancer-like Function in Human Cells, Cell, vol.143, issue.1, pp.46-58, 2010.
DOI : 10.1016/j.cell.2010.09.001

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.1915-1942, 2011.
DOI : 10.1101/gad.17446611

A. Rau, M. Gallopin, G. Celeux, and F. Jaffrezic, Data-based filtering for replicated high-throughput transcriptome sequencing experiments, Bioinformatics, vol.29, issue.17, pp.2146-52, 2013.
DOI : 10.1093/bioinformatics/btt350
URL : https://hal.archives-ouvertes.fr/hal-00927025

Y. Wang, S. Xue, X. Liu, H. Liu, T. Hu et al., Analyses of long non-coding RNA and mRNA profiling using RNA sequencing during the pre-implantation phases in pig endometrium. Sci Rep, p.20238, 2016.

C. Billerey, M. Boussaha, D. Esquerré, E. Rebours, A. Djari et al., Identification of large intergenic non-coding RNAs in bovine muscle using next-generation transcriptomic sequencing, BMC Genomics, vol.15, issue.1, p.499, 2014.
DOI : 10.1186/1471-2164-15-499
URL : https://hal.archives-ouvertes.fr/hal-01011303

L. Sun, H. Luo, D. Bu, G. Zhao, K. Yu et al., Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts, Nucleic Acids Research, vol.41, issue.17, p.166, 2013.
DOI : 10.1093/nar/gkt646
URL : http://doi.org/10.1093/nar/gkt646

L. Li, S. Eichten, R. Shimizu, K. Petsch, C. Yeh et al., Genome-wide discovery and characterization of maize long non-coding RNAs, Genome Biology, vol.15, issue.2, p.40, 2014.
DOI : 10.1023/A:1014893521186

H. Hezroni, D. Koppstein, M. Schwartz, A. Avrutin, D. Bartel et al., Principles of Long Noncoding RNA Evolution Derived from Direct Comparison of Transcriptomes in 17 Species, Cell Reports, vol.11, issue.7, pp.1110-1132, 2015.
DOI : 10.1016/j.celrep.2015.04.023

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.1537-50, 2011.
DOI : 10.1016/j.cell.2011.11.055

S. Mohammadin, P. Edger, J. Pires, and M. Schranz, Positionally-conserved but sequence-diverged: identification of long non-coding RNAs in the Brassicaceae and Cleomaceae, BMC Plant Biology, vol.36, issue.Web Server issu, p.217, 2015.
DOI : 10.1186/s12870-015-0603-5

D. Huang, B. Sherman, and R. Lempicki, Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists, Nucleic Acids Research, vol.37, issue.1, pp.1-13, 2009.
DOI : 10.1093/nar/gkn923

M. Cantile, A. Procino, D. Armiento, M. Cindolo, L. Cillo et al., HOX gene network is involved in the transcriptional regulation of in vivo human adipogenesis, Journal of Cellular Physiology, vol.194, issue.2, pp.225-261, 2003.
DOI : 10.1002/jcp.10210

S. Dankel, D. Fadnes, A. Stavrum, C. Stansberg, R. Holdhus et al., Switch from Stress Response to Homeobox Transcription Factors in Adipose Tissue After Profound Fat Loss, PLoS ONE, vol.145, issue.6, p.11033, 2010.
DOI : 10.1371/journal.pone.0011033.s013

U. Ørom and R. Shiekhattar, Long Noncoding RNAs Usher In a New Era in the Biology of Enhancers, Cell, vol.154, issue.6, pp.1190-1193, 2013.
DOI : 10.1016/j.cell.2013.08.028

J. Ponjavic, P. Oliver, G. Lunter, and C. Ponting, Genomic and Transcriptional Co-Localization of Protein-Coding and Long Non-Coding RNA Pairs in the Developing Brain, PLoS Genetics, vol.23, issue.8, p.1000617, 2009.
DOI : 10.1371/journal.pgen.1000617.s011

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.1845-1853, 2008.
DOI : 10.1126/science.1162228
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2833333

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, pp.62-68, 2004.
DOI : 10.1101/gr.1982804

N. Adachi and M. Lieber, Bidirectional Gene Organization, Cell, vol.109, issue.7, pp.807-816, 2002.
DOI : 10.1016/S0092-8674(02)00758-4
URL : http://doi.org/10.1016/s0092-8674(02)00758-4

A. Seila, L. Core, J. Lis, and P. Sharp, Divergent transcription: A new feature of active promoters, Cell Cycle, vol.8, issue.16, pp.2557-64, 2009.
DOI : 10.4161/cc.8.16.9305

I. Cajigas, D. Leib, J. Cochrane, H. Luo, K. Swyter et al., lncRNA/BRG1/DLX1 interactions reveal RNA-dependent inhibition of chromatin remodeling, Development, vol.142, issue.15, pp.2641-52, 2015.
DOI : 10.1242/dev.126318
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4529037

P. Latos, F. Pauler, M. Koerner, H. Senergin, Q. Hudson et al., Airn Transcriptional Overlap, But Not Its lncRNA Products, Induces Imprinted Igf2r Silencing, Science, vol.338, issue.6113, pp.1469-72, 2012.
DOI : 10.1126/science.1228110

N. Wei, Y. Wang, R. Xu, G. Wang, Y. Xiong et al., antisense lncRNA against its mRNA translation promotes adipogenesis in porcine preadipocytes, Animal Genetics, vol.42, issue.2, pp.133-173, 2015.
DOI : 10.1111/age.12275

K. Li, Y. Blum, A. Verma, Z. Liu, K. Pramanik et al., A noncoding antisense RNA in tie-1 locus regulates tie-1 function in vivo, Blood, vol.115, issue.1, pp.133-142, 2010.
DOI : 10.1182/blood-2009-09-242180

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.454-461, 2012.
DOI : 10.1038/nature11508

S. Zucchelli, D. Cotella, H. Takahashi, C. Carrieri, L. Cimatti et al., SINEUPs: A new class of natural and synthetic antisense long non-coding RNAs that activate translation, RNA Biology, vol.28, issue.8, pp.771-780, 2015.
DOI : 10.1093/nar/gkv125

V. Tripathi, J. Ellis, Z. Shen, D. Song, Q. Pan et al., The Nuclear-Retained Noncoding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor Phosphorylation, Molecular Cell, vol.39, issue.6, pp.925-963, 2010.
DOI : 10.1016/j.molcel.2010.08.011

Y. Xue, G. Ma, Z. Zhang, Q. Hua, H. Chu et al., A novel antisense long noncoding RNA regulates the expression of MDC1 in bladder cancer, Oncotarget, vol.1, issue.1, pp.484-93, 2015.
DOI : 10.18632/oncotarget.2861

Z. Chen, Progress and prospects of long noncoding RNAs in lipid homeostasis, Molecular Metabolism, vol.5, issue.3, pp.164-70, 2016.
DOI : 10.1016/j.molmet.2015.12.003

P. Li, X. Ruan, L. Yang, K. Kiesewetter, Y. Zhao et al., A Liver-Enriched Long Non-Coding RNA, lncLSTR, Regulates Systemic Lipid Metabolism in Mice, Cell Metabolism, vol.21, issue.3, pp.455-67, 2015.
DOI : 10.1016/j.cmet.2015.02.004

M. Cui, Z. Xiao, Y. Wang, M. Zheng, T. Song et al., Long Noncoding RNA HULC Modulates Abnormal Lipid Metabolism in Hepatoma Cells through an miR-9-Mediated RXRA Signaling Pathway, Cancer Research, vol.75, issue.5, pp.846-57, 2015.
DOI : 10.1158/0008-5472.CAN-14-1192

P. Halley, B. Kadakkuzha, M. Faghihi, M. Magistri, Z. Zeier et al., Regulation of the Apolipoprotein Gene Cluster by a Long Noncoding RNA, Cell Reports, vol.6, issue.1, pp.222-252, 2014.
DOI : 10.1016/j.celrep.2013.12.015

F. Inagaki, M. Tanaka, N. Inagaki, T. Yagai, Y. Sato et al., Nephronectin is upregulated in acute and chronic hepatitis and aggravates liver injury by recruiting CD4 positive cells, Biochemical and Biophysical Research Communications, vol.430, issue.2, pp.751-757, 2013.
DOI : 10.1016/j.bbrc.2012.11.076

A. Marques and C. Ponting, Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness, Genome Biology, vol.10, issue.11, p.124, 2009.
DOI : 10.1186/gb-2009-10-11-r124

R. Chodroff, L. Goodstadt, T. Sirey, P. Oliver, K. Davies et al., Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes The evolution of lncRNA repertoires and expression patterns in tetrapods, Genome Biol. Nature, vol.11505, pp.635-675, 2010.

A. Nitsche, D. Rose, M. Fasold, K. Reiche, and P. Stadler, Comparison of splice sites reveals that long noncoding RNAs are evolutionarily well conserved, RNA, vol.21, issue.5, pp.801-813, 2015.
DOI : 10.1261/rna.046342.114

A. Dobin, C. Davis, F. Schlesinger, J. Drenkow, C. Zaleski et al., STAR: ultrafast universal RNA-seq aligner, Bioinformatics, vol.29, issue.1, pp.15-21, 2013.
DOI : 10.1093/bioinformatics/bts635
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530905

H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan et al., The Sequence Alignment/Map format and SAMtools, Bioinformatics, vol.25, issue.16, pp.2078-2087, 2009.
DOI : 10.1093/bioinformatics/btp352
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723002

M. Pertea, G. Pertea, C. Antonescu, T. Chang, J. Mendell et al., StringTie enables improved reconstruction of a transcriptome from RNA-seq reads, Nature Biotechnology, vol.16, issue.3, pp.290-295, 2015.
DOI : 10.1038/nbt.3122

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.511-516, 2010.
DOI : 10.1038/nbt.1621
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3146043

Y. Liao, G. Smyth, and W. Shi, featureCounts: an efficient general purpose program for assigning sequence reads to genomic features, Bioinformatics, vol.30, issue.7, pp.923-953, 2014.
DOI : 10.1093/bioinformatics/btt656

A. Quinlan and I. Hall, BEDTools: a flexible suite of utilities for comparing genomic features, Bioinformatics, vol.26, issue.6, pp.841-843, 2010.
DOI : 10.1093/bioinformatics/btq033

S. Altschul, W. Gish, W. Miller, E. Myers, and D. Lipman, Basic local alignment search tool, Journal of Molecular Biology, vol.215, issue.3, pp.403-413, 1990.
DOI : 10.1016/S0022-2836(05)80360-2

R. Kinsella, A. Kahari, S. Haider, J. Zamora, G. Proctor et al., Ensembl BioMarts: a hub for data retrieval across taxonomic space, Database, vol.2011, issue.0, p.30, 2011.
DOI : 10.1093/database/bar030
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3170168

J. Bullard, E. Purdom, K. Hansen, and S. Dudoit, Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments, BMC Bioinformatics, vol.11, issue.1, p.94, 2010.
DOI : 10.1186/1471-2105-11-94

L. Tsoi, M. Iyer, P. Stuart, W. Swindell, J. Gudjonsson et al., Analysis of long non-coding RNAs highlights tissue-specific expression patterns and epigenetic profiles in normal and psoriatic skin, Genome Biology, vol.16, issue.1, p.24, 2015.
DOI : 10.1038/jid.2010.313

Y. Benjamini and Y. Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, J R Stat Soc, vol.57, pp.289-300, 1995.

P. Roux, S. Boitard, Y. Blum, B. Parks, A. Montagner et al., as New Candidate Genes for Adiposity Regulation, G3: Genes|Genomes|Genetics, vol.5, issue.4, pp.517-546, 2015.
DOI : 10.1534/g3.115.016865
URL : https://hal.archives-ouvertes.fr/hal-01194040

M. Robinson and A. Oshlack, A scaling normalization method for differential expression analysis of RNA-seq data, Genome Biology, vol.11, issue.3, p.25, 2010.
DOI : 10.1186/gb-2010-11-3-r25