The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update, Nucleic Acids Research, vol.44, issue.W1, pp.3-10, 2016. ,
DOI : 10.1093/nar/gkw343
URL : https://hal.archives-ouvertes.fr/hal-01360125
Crosstalk between Components of Circadian and Metabolic Cycles in Mammals, Cell Metabolism, vol.13, issue.2, pp.125-137, 2011. ,
DOI : 10.1016/j.cmet.2011.01.006
Long-term variations of AP-1 composition after CRH stimulation: consequence on POMC gene regulation, Molecular and Cellular Endocrinology, vol.175, issue.1-2, pp.93-100, 2001. ,
DOI : 10.1016/S0303-7207(01)00393-8
Evidence for an internal and functional circadian clock in rat pituitary cells, Molecular and Cellular Endocrinology, vol.382, issue.2, pp.888-898 ,
DOI : 10.1016/j.mce.2013.11.004
URL : https://hal.archives-ouvertes.fr/hal-00966197
Paraspeckles: nuclear bodies built on long noncoding RNA, The Journal of Cell Biology, vol.13, issue.5, pp.637-644, 2009. ,
DOI : 10.1128/MCB.23.18.6618-6630.2003
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2742191
Subnuclear Localization and Dynamics of the Pre-mRNA 3' End Processing Factor Mammalian Cleavage Factor I 68-kDa Subunit, Molecular Biology of the Cell, vol.18, issue.4, pp.1282-1292, 2007. ,
DOI : 10.1091/mbc.E06-09-0846
Gene regulation by SINES and inosines: biological consequences of A-to-I editing of Alu element inverted repeats, Cell Cycle, vol.7, issue.21, pp.3294-3301, 2008. ,
DOI : 10.4161/cc.7.21.6927
Alu element-mediated gene silencing, The EMBO Journal, vol.106, issue.12, pp.1694-170594, 2008. ,
DOI : 10.1038/emboj.2008.94
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2435129
Altered Nuclear Retention of mRNAs Containing Inverted Repeats in Human Embryonic Stem Cells: Functional Role of a Nuclear Noncoding RNA, Molecular Cell, vol.35, issue.4, pp.467-478, 2009. ,
DOI : 10.1016/j.molcel.2009.06.027
An Architectural Role for a Nuclear Noncoding RNA: NEAT1 RNA Is Essential for the Structure of Paraspeckles, Molecular Cell, vol.33, issue.6, pp.717-726, 2009. ,
DOI : 10.1016/j.molcel.2009.01.026
Paraspeckles, Current Biology, vol.12, issue.1, pp.13-25, 2002. ,
DOI : 10.1016/S0960-9822(01)00632-7
URL : http://doi.org/10.1016/s0960-9822(01)00632-7
Chromatin remodeling as a mechanism for circadian prolactin transcription: rhythmic NONO and SFPQ recruitment to HLTF, The FASEB Journal, vol.25, issue.8, pp.2740-275610, 2011. ,
DOI : 10.1096/fj.10-178616
URL : https://hal.archives-ouvertes.fr/hal-00625435
A transcript map for the 2.8-Mb region containing the multiple endocrine neoplasia type 1 locus, Genome Research, vol.7, pp.725-735, 1997. ,
Finding the active genes in deep RNA-seq gene expression studies, BMC Genomics, vol.14, issue.1, pp.778-788, 2013. ,
DOI : 10.1093/nar/gkn488
High-resolution Time Course Analysis of Gene Expression from Pituitary, Cold Spring Harbor Symposia on Quantitative Biology, vol.25, issue.1, pp.381-386, 2007. ,
DOI : 10.1016/S0076-6879(05)93016-4
Analysis of clock-regulated genes in Neurospora reveals widespread posttranscriptional control of metabolic potential, PNAS, vol.11, pp.16995-17002, 2014. ,
A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains, BMC Genomics, vol.8, issue.1, pp.39-49, 2007. ,
DOI : 10.1186/1471-2164-8-39
The impact of sleep deprivation and nighttime light exposure on clock gene expression in humans, Croatian Medical Journal, vol.52, issue.5, pp.594-603, 2011. ,
DOI : 10.3325/cmj.2011.52.594
Transposable elements modulate human RNA abundance and splicing via specific RNA-protein interactions, Genome Biology, vol.29, issue.12, pp.537-547, 2014. ,
DOI : 10.1186/s13059-014-0537-5
URL : http://doi.org/10.1186/s13059-014-0537-5
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions, Genome Biology, vol.14, issue.4, pp.10-1186, 2013. ,
DOI : 10.1186/gb-2009-10-3-r25
Transcriptional Architecture and Chromatin Landscape of the Core Circadian Clock in Mammals, Science, vol.338, issue.6105, pp.349-354, 2012. ,
DOI : 10.1126/science.1226339
Control of somatic tissue differentiation by the long non-coding RNA TINCR, Nature, vol.31, issue.7431, pp.231-235, 1038. ,
DOI : 10.1038/nature11661
Emerging roles for post-transcriptional regulation in circadian clocks, Nature Neuroscience, vol.135, issue.11, 2013. ,
DOI : 10.1038/nrg3141
Improved RNA secondary structure prediction by maximizing expected pair accuracy, RNA, vol.15, issue.10, pp.1805-1813, 2009. ,
DOI : 10.1261/rna.1643609
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2743040
Deep proteome and transcriptome mapping of a human cancer cell line, Molecular Systems Biology, vol.5, issue.1, 2011. ,
DOI : 10.1038/nmeth.1322
Paraspeckle nuclear bodies???useful uselessness?, Cellular and Molecular Life Sciences, vol.20, issue.19, pp.3027-3036, 2012. ,
DOI : 10.1007/s00018-012-0973-x
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3428521
Molecular architecture of the mammalian circadian clock, Trends in Cell Biology, vol.24, issue.2, pp.90-99, 2014. ,
DOI : 10.1016/j.tcb.2013.07.002
Regulating Gene Expression through RNA Nuclear Retention, Cell, vol.123, issue.2, pp.249-263, 2005. ,
DOI : 10.1016/j.cell.2005.08.033
URL : http://doi.org/10.1016/j.cell.2005.08.033
Genome-wide and phase-specific DNAbinding rhythms of BMAL1 control circadian output functions in mouse liver, PLoS Biology, vol.9, 2011. ,
A software solution for recording circadian oscillator features in time-lapse live cell microscopy, Cell Division, vol.5, issue.1, pp.17-27, 2010. ,
DOI : 10.1186/1747-1028-5-17
How to build a paraspeckle, Genome Biology, vol.10, issue.7, 2009. ,
DOI : 10.1186/gb-2009-10-7-227
Capture Hybridization Analysis of RNA Targets (CHART), Current Protocols in Molecular Biology Chapter, vol.108, 2013. ,
DOI : 10.1002/0471142727.mb2125s101
Highly Ordered Spatial Organization of the Structural Long Noncoding NEAT1 RNAs within Paraspeckle Nuclear Bodies, Molecular Biology of the Cell, vol.21, issue.22, pp.4020-4027, 2010. ,
DOI : 10.1091/mbc.E10-08-0690
MEN ??/?? nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles, Genome Research, vol.19, issue.3, pp.347-359, 2009. ,
DOI : 10.1101/gr.087775.108
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
Ribonucleoprotein Complexes That Control Circadian Clocks, International Journal of Molecular Sciences, vol.14, issue.5, pp.9018-9036, 2013. ,
DOI : 10.3390/ijms14059018
URL : http://doi.org/10.3390/ijms14059018
The Long Noncoding RNAs NEAT1 and MALAT1 Bind Active Chromatin Sites, Molecular Cell, vol.55, issue.5, pp.791-802, 2014. ,
DOI : 10.1016/j.molcel.2014.07.012
Gender Disparity of Hepatic Lipid Homoeostasis Regulated by the Circadian Clock, Journal of Biochemistry, vol.145, issue.5, pp.609-623, 2009. ,
DOI : 10.1093/jb/mvp018
Direct Competition between hnRNP C and U2AF65 Protects the Transcriptome from the Exonization of Alu Elements, Cell, vol.152, issue.3, pp.453-466, 2013. ,
DOI : 10.1016/j.cell.2012.12.023