Regulation of gene expression, Ann. Rev. Biochem, vol.37, pp.411-436, 1968. ,
Genomic and chromatin signals underlying transcription start-site selection, Trends Genet, vol.27, pp.475-485, 2011. ,
Chromatin and DNA sequences in defining promoters for transcription initiation, Biochim Biophys. Acta, vol.1839, pp.118-128, 2014. ,
Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers, Nat. Genet, vol.46, pp.1311-1320, 2014. ,
Core promoters in transcription: old problem, new insights, Trends Biochem Sci, vol.40, pp.165-171, 2015. ,
dThe punctilious RNA polymerase II core promoter, Genes Dev, vol.31, pp.1289-1301, 2017. ,
The core promoter: at the heart of gene expression, Biochim Biophys. Acta, vol.1849, pp.1116-1131, 2015. ,
Understanding nucleosome dynamics and their links to gene expression and DNA replication, Nat. Rev. Mol. Cell Biol, vol.18, pp.548-562, 2017. ,
Bidirectional transcription arises from two distinct hubs of transcription factor binding and active chromatin, Mol. Cell, vol.58, pp.1101-1112, 2015. ,
The RNA polymerase II core promoter, Annu Rev. Biochem, vol.72, pp.449-479, 2003. ,
Genome-wide analysis of mammalian promoter architecture and evolution, Nat. Genet, vol.38, pp.626-635, 2006. ,
Characterization of sua7 mutations defines a domain of TFIIB involved in transcription start site selection in yeast, J. Biol. Chem, vol.269, pp.30569-30573, 1994. ,
Amino acid substitutions in yeast TFIIF confer upstream shifts in transcription initiation and altered interaction with RNA polymerase II, Mol. Cell Biol, vol.24, pp.10975-10985, 2004. ,
Hmo1 directs pre-initiation complex assembly to an appropriate site on its target gene promoters by masking a nucleosome-free region, Nucleic Acids Res, vol.39, pp.4136-4150, 2011. ,
Transcription factor Reb1 is required for proper transcriptional start site usage at the divergently transcribed TFC6-ESC2 locus in Saccharomyces cerevisiae, Gene, vol.594, pp.108-116, 2016. ,
A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genome ,
, Genome Res, vol.19, pp.360-371, 2009.
Genome-wide structure and organization of eukaryotic pre-initiation complexes, Nature, vol.483, pp.295-301, 2012. ,
General Regulatory Factors Control the Fidelity of Transcription by Restricting Non-coding and Ectopic Initiation, Mol. Cell, vol.72, pp.955-969, 2018. ,
Role of the CCAAT-binding protein CBF/ NF-Y in transcription, Trends Biochem Sci, vol.23, pp.174-178, 1998. ,
NF-Y and the transcriptional activation of CCAAT promoters, Crit. Rev. Biochem Mol. Biol, vol.47, pp.29-49, 2012. ,
NF-Y (CBF) regulation in specific cell types and mouse models, Biochim Biophys. Acta, vol.1860, pp.598-603, 2017. ,
Sequence-specific transcription factor NF-Y displays histone-like DNA binding and H2B-like ubiquitination, Cell, vol.152, pp.132-143, 2013. ,
DNA minor groove sensing and widening by the CCAAT-binding complex, Structure, vol.20, pp.1757-1768, 2012. ,
Histone-fold domain protein NF-Y promotes chromatin accessibility for cell type-specific master transcription factors, Mol. Cell, vol.55, pp.708-722, 2014. ,
NF-Y coassociates with FOS at promoters, enhancers, repetitive elements, and inactive chromatin regions, and is stereo-positioned with growth-controlling transcription factors, Genome Res, vol.23, pp.1195-1209, 2013. ,
The DNA-encoded nucleosome organization of a eukaryotic genome, Nature, vol.458, pp.362-366, 2009. ,
Facilitated binding of TATA-binding protein to nucleosomal DNA, Nature, vol.370, pp.481-485, 1994. ,
CCAAT binding NF-Y-TBP interactions: NF-YB and NF-YC require short domains adjacent to their histone fold motifs for association with TBP basic residues, Nucleic Acids Res, vol.25, pp.2174-2181, 1997. ,
Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters, Science, vol.322, pp.1845-1848, 2008. ,
Divergent transcription from active promoters, Science, vol.322, pp.1849-1851, 2008. ,
RNA exosome depletion reveals transcription upstream of active human promoters, Science, vol.322, pp.1851-1854, 2008. ,
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes, Genome Res, vol.15, pp.1034-1050, 2005. ,
Transcription and translation in a package deal: the TISU paradigm, Gene, vol.491, pp.1-4, 2012. ,
Genomewide analysis in vivo of translation with nucleotide resolution using ribosome profiling, Science, vol.324, pp.218-223, 2009. ,
Dynamic profiling of the protein life cycle in response to pathogens, Science, vol.347, p.1259038, 2015. ,
Impact of alternative splicing on the human proteome, Cell Rep, vol.20, pp.1229-1241, 2017. ,
The regulatory potential of upstream open reading frames in eukaryotic gene expression, Wiley Inter. Rev. RNA, vol.5, pp.765-778, 2014. ,
Upstream ORFs are prevalent translational repressors in vertebrates, EMBO J, vol.35, pp.706-723, 2016. ,
Pervasive, coordinated protein-level changes driven by transcript isoform switching during meiosis, Cell, vol.172, pp.910-923, 2018. ,
Kinetochore inactivation by expression of a repressive mRNA, Elife, vol.6, p.27417, 2017. ,
Transcription of a 5' extended mRNA isoform directs dynamic chromatin changes and interference of a downstream promoter, Elife, vol.6, p.27420, 2017. ,
Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape, Nat. Biotechnol, vol.32, pp.171-178, 2014. ,
Establishing chromatin regulatory landscape during mouse preimplantation development, Cell, vol.165, pp.1375-1388, 2016. ,
Embryonic epigenetic reprogramming by a pioneer transcription factor in plants, Nature, vol.551, pp.124-128, 2017. ,
The NF-YB/NF-YC structure gives insight into DNA binding and transcription regulation by CCAAT factor NF-Y, J. Biol. Chem, vol.278, pp.1336-1345, 2003. ,
NF-Y binding to twin CCAAT boxes: role of Q-rich domains and histone fold helices, J. Mol. Biol, vol.285, pp.1441-1455, 1999. ,
CBF/NF-Y functions both in nucleosomal disruption and transcription activation of the chromatinassembled topoisomerase IIalpha promoter. Transcription activation by CBF/ NF-Y in chromatin is dependent on the promoter structure, J. Biol. Chem, vol.276, pp.40621-40630, 2001. ,
Interactions of the CCAAT-binding trimer NF-Y with nucleosomes, J. Biol. Chem, vol.274, pp.1326-1333, 1999. ,
The histone-fold protein complex CHRAC-15/17 enhances nucleosome sliding and assembly mediated by ACF, Mol. Cell, vol.13, pp.265-277, 2004. ,
NF-Y recruitment of TFIID, multiple interactions with histone fold TAF(II)s, J. Biol. Chem, vol.277, pp.5841-5848, 2002. ,
Conserved major histocompatibility complex class II boxes-X and Y-are transcriptional control elements and specifically bind nuclear proteins, Proc. Natl Acad. Sci. USA, vol.84, pp.6249-6253, 1987. ,
Transcription initiation patterns indicate divergent strategies for gene regulation at the chromatin level, PLoS Genet, vol.7, p.1001274, 2011. ,
Antagonistic controls of chromatin and mRNA start site selection by Tup family corepressors and the CCAAT-binding factor, Mol. Cell Biol, vol.35, pp.847-855, 2015. ,
A genomic code for nucleosome positioning, Nature, vol.442, pp.772-778, 2006. ,
Dual functions of codons in the genetic code, Crit. Rev. Biochem. Mol. Biol, vol.45, pp.257-265, 2010. ,
Leucine-tRNA initiates at CUG start codons for protein synthesis and presentation by MHC class I, Science, vol.336, pp.1719-1723, 2012. ,
Molecular biology. A new start for protein synthesis, Science, vol.336, pp.1645-1646, 2012. ,
Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans, Proc. Natl Acad. Sci. USA, vol.106, pp.7507-7512, 2009. ,
Regulation of fungal gene expression via short open reading frames in the mRNA 5'untranslated region, Mol. Microbiol, vol.49, pp.859-867, 2003. ,
Intragenic enhancers attenuate host gene expression, Mol. Cell, vol.68, p.6, 2017. ,
Methylation of histone H3 at Lys-9 is an early mark on the X chromosome during X inactivation, Cell, vol.107, pp.727-738, 2001. ,
Pausing of RNA polymerase II regulates mammalian developmental potential through control of signaling networks, Mol. Cell, vol.58, pp.311-322, 2015. ,
Ultrafast and memoryefficient alignment of short DNA sequences to the human genome, Genome Biol, vol.10, p.25, 2009. ,
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions, Genome Biol, vol.14, p.36, 2013. ,
Differential gene and transcript expression analysis of RNAseq experiments with TopHat and Cufflinks, Nat. Protoc, vol.7, pp.562-578, 2012. ,
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol, vol.15, p.550, 2014. ,
Salmon provides accurate, fast, and bias-aware transcript expression estimates using dual-phase inference, Nat Methods, vol.14, pp.417-419, 2017. ,
Global analysis of short RNAs reveals widespread promoterproximal stalling and arrest of Pol II in Drosophila, Science, vol.327, pp.335-338, 2010. ,
Stable pausing by RNA polymerase II provides an opportunity to target and integrate regulatory signals, Mol. Cell, vol.52, pp.517-528, 2013. ,
Cutadapt removes adapter sequences from high-throughput sequencing reads, EMBnet Journal, vol.17, pp.10-12, 2011. ,
Differential expression analysis for sequence count data, Genome Biol, vol.11, p.106, 2010. ,
STAR: ultrafast universal RNA-seq aligner, Bioinformatics, vol.29, pp.15-21, 2013. ,
MEME SUITE: tools for motif discovery and searching, Nucleic Acids Res, vol.37, pp.202-208, 2009. ,
Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs, Nat. Protoc, vol.6, pp.1860-1869, 2011. ,
JASPAR 2016: a major expansion and update of the openaccess database of transcription factor binding profiles, Nucleic Acids Res, vol.44, pp.110-115, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01281181
Detection of nonneutral substitution rates on mammalian phylogenies, Genome Res, vol.20, pp.110-121, 2010. ,