V. Vinci and G. Byng, Strain Improvement by Nonrecombinant Methods, pp.103-113, 1999.

C. Kubicek, M. Mikus, A. Schuster, M. Schmoll, and B. Seiboth, Metabolic engineering strategies for the improvement of cellulase production by Hypocrea jecorina, Biotechnology for Biofuels, vol.2, issue.1, p.19, 2009.
DOI : 10.1186/1754-6834-2-19

R. Peterson and H. Nevalainen, Trichoderma reesei RUT-C30 - thirty years of strain improvement, Microbiology, vol.158, issue.1, pp.58-68, 2011.
DOI : 10.1099/mic.0.054031-0

A. Stricker, R. Mach, D. Graaff, and L. , Regulation of transcription of cellulases- and hemicellulases-encoding genes in Aspergillus niger and Hypocrea jecorina (Trichoderma reesei), Applied Microbiology and Biotechnology, vol.270, issue.Pt 3, pp.211-220, 2008.
DOI : 10.1007/s00253-007-1322-0

A. Stricker, K. Grosstessner-hain, W. Rleitner, E. Mach, and R. , Xyr1 (Xylanase Regulator 1) Regulates both the Hydrolytic Enzyme System and D-Xylose Metabolism in Hypocrea jecorina, Eukaryotic Cell, vol.5, issue.12, pp.2128-2137, 2006.
DOI : 10.1128/EC.00211-06

A. Mach-aigner, M. Pucher, M. Steiger, G. Bauer, S. Preis et al., Transcriptional Regulation of xyr1, Encoding the Main Regulator of the Xylanolytic and Cellulolytic Enzyme System in Hypocrea jecorina, Applied and Environmental Microbiology, vol.74, issue.21, pp.6554-6562, 2008.
DOI : 10.1128/AEM.01143-08

V. Seidl, C. Gamauf, I. Druzhinina, B. Seiboth, L. Hartl et al., The Hypocrea jecorina (Trichoderma reesei) hypercellulolytic mutant RUT C30 lacks a 85 kb (29 gene-encoding) region of the wild-type genome, BMC Genomics, vol.9, issue.1, p.327, 2008.
DOI : 10.1186/1471-2164-9-327

T. Portnoy, A. Margeot, R. Linke, L. Atanasova, E. Fekete et al., The CRE1 carbon catabolite repressor of the fungus Trichoderma reesei: a master regulator of carbon assimilation, BMC Genomics, vol.6, issue.1, p.269, 2011.
DOI : 10.1089/106652799318274
URL : https://hal.archives-ouvertes.fr/inserm-00663944

T. Nakari-setala, M. Paloheimo, J. Kallio, J. Vehmaanpera, M. Penttila et al., Genetic Modification of Carbon Catabolite Repression in Trichoderma reesei for Improved Protein Production, Applied and Environmental Microbiology, vol.75, issue.14, p.4853, 2009.
DOI : 10.1128/AEM.00282-09

M. Ilm-?-n and C. Thrane, The glucose repressor gene cre1 of Trichoderma: isolation and expression of a full-length and a truncated mutant form, Mol Gen Genet, vol.251, pp.451-460, 1996.

A. Saloheimo and N. Aro, Isolation of the ace1 Gene Encoding a Cys2-His2 Transcription Factor Involved in Regulation of Activity of the Cellulase Promoter cbh1 of Trichoderma reesei, Journal of Biological Chemistry, vol.275, issue.8, pp.5817-5825, 2000.
DOI : 10.1074/jbc.275.8.5817

N. Aro and A. Saloheimo, ACEII, a Novel Transcriptional Activator Involved in Regulation of Cellulase and Xylanase Genes of Trichoderma reesei, Journal of Biological Chemistry, vol.276, issue.26, pp.24309-24314, 2001.
DOI : 10.1074/jbc.M003624200

B. Seiboth, R. Karimi, P. Phatale, R. Linke, L. Hartl et al., The putative protein methyltransferase LAE1 controls cellulase gene expression in Trichoderma reesei, Molecular Microbiology, vol.20, issue.6, pp.1150-1164, 2012.
DOI : 10.1111/j.1365-2958.2012.08083.x

J. Denton and J. Kelly, Disruption of Trichoderma reesei cre2, encoding an ubiquitin C-terminal hydrolase, results in increased cellulase activity, BMC Biotechnology, vol.11, issue.1, pp.11-103, 2011.
DOI : 10.1016/0378-1119(87)90110-7

H. ?-kkinen, M. Valkonen, M. Westerholm-parvinen, A. Aro, N. Arvas et al., Screening of candidate regulators for cellulase and hemicellulase production in Trichoderma reesei and identification of a factor essential for cellulase production, Biotechnol Biofuels, vol.7, p.14, 2014.

T. Pakula, K. Salonen, and J. Uusitalo, The effect of specific growth rate on protein synthesis and secretion in the filamentous fungus Trichoderma reesei, Microbiology, vol.151, issue.1, pp.151135-143, 2005.
DOI : 10.1099/mic.0.27458-0

I. Herpo-?-l-gimbert, A. Margeot, A. Dolla, G. Jan, . Moll-?-d et al., Comparative secretome analyses of two Trichoderma reesei RUT-C30 and CL847 hypersecretory strains, Biotechnology for Biofuels, vol.1, issue.1, p.18, 2008.
DOI : 10.1186/1754-6834-1-18

D. Martinez, R. Berka, B. Henrissat, M. Saloheimo, M. Arvas et al., Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina), Nature Biotechnology, vol.307, issue.5, pp.553-560, 2008.
DOI : 10.1038/nbt1403

L. Crom, S. Schackwitz, W. Pennacchio, L. Magnuson, J. Culley et al., Tracking the roots of cellulase hyperproduction by the fungus Trichoderma reesei using massively parallel DNA sequencing, Proceedings of the National Academy of Sciences, vol.106, issue.38, pp.16151-16156, 2009.
DOI : 10.1073/pnas.0905848106

H. Koike, A. Aerts, K. Labutti, I. Grigoriev, and S. Baker, Strains, Industrial Biotechnology, vol.9, issue.6, pp.352-367, 2013.
DOI : 10.1089/ind.2013.0015

M. Nitta, T. Furukawa, Y. Shida, K. Mori, S. Kuhara et al., A new Zn(II)2Cys6-type transcription factor BglR regulates ??-glucosidase expression in Trichoderma reesei, Fungal Genetics and Biology, vol.49, issue.5, pp.388-397, 2012.
DOI : 10.1016/j.fgb.2012.02.009

J. Porciuncula, T. Furukawa, Y. Shida, K. Mori, S. Kuhara et al., Identification of major facilitator transporters involved in cellulase production during lactose culture of Trichoderma reesei PC, pp.3-7

M. Vitikainen, M. Arvas, T. Pakula, M. Oja, . Penttil-?-m et al., Array comparative genomic hybridization analysis of Trichoderma reesei strains with enhanced cellulase production properties, BMC Genomics, vol.11, issue.1, p.441, 2010.
DOI : 10.1186/1471-2164-11-441

C. Ivanova, B. , J. Seiboth, B. Kubicek, and C. , Systems Analysis of Lactose Metabolism in Trichoderma reesei Identifies a Lactose Permease That Is Essential for Cellulase Induction, PLoS ONE, vol.57, issue.5, p.62631, 2013.
DOI : 10.1371/journal.pone.0062631.s006

R. Bischof, L. Fourtis, A. Limbeck, C. Gamauf, B. Seiboth et al., Comparative analysis of the Trichoderma reesei transcriptome during growth on the cellulase inducing substrates wheat straw and lactose, Biotechnology for Biofuels, vol.6, issue.1, p.127, 2013.
DOI : 10.1007/BF00500103

D. Santos, C. Pedersoli, W. , A. ?. To, A. Steindorff et al., Fa? a VM: Comparative metabolism of cellulose, sophorose and glucose in Trichoderma reesei using high-throughput genomic and proteomic analyses, Biotechnol Biofuels, vol.7, issue.1, 2014.

E. Jourdier, L. Poughon, C. Larroche, F. Monot, B. Chaabane et al., A new stoichiometric miniaturization strategy for screening of industrial microbial strains: application to cellulase hyper-producing Trichoderma reesei strains, Microbial Cell Factories, vol.11, issue.1, p.70, 2012.
DOI : 10.1016/0141-0229(88)90012-9

E. Jourdier, C. Cohen, L. Poughon, C. Larroche, F. Monot et al., Cellulase activity mapping of Trichoderma reesei cultivated in sugar mixtures under fed-batch conditions, Biotechnology for Biofuels, vol.6, issue.1, p.79, 2013.
DOI : 10.1186/1754-6834-6-79
URL : https://hal.archives-ouvertes.fr/hal-00905448

M. Bradford, A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding, Analytical Biochemistry, vol.72, issue.1-2, pp.248-254, 1976.
DOI : 10.1016/0003-2697(76)90527-3

A. Gusakov, T. Shulga, A. Chekushina, and A. Sinitsyn, Comparison of Three Protein Assays for Purified Cellulases and Hemicellulases from Fungi, Open Journal of Analytical Chemistry Research, vol.1, issue.1, pp.1-4, 2013.
DOI : 10.12966/ojacr.05.01.2013

O. Lowry, N. Rosebrough, A. Farr, and R. Randall, Protein measurement with the Folin phenol reagent, J Biol Chem, vol.193, pp.265-275, 1951.

T. Portnoy, A. Margeot, V. Seidl-seiboth, L. Crom, S. et al., Differential Regulation of the Cellulase Transcription Factors XYR1, ACE2, and ACE1 in Trichoderma reesei Strains Producing High and Low Levels of Cellulase, Eukaryotic Cell, vol.10, issue.2, pp.262-271, 2011.
DOI : 10.1128/EC.00208-10

G. Hemsworth, G. Davies, and P. Walton, Recent insights into copper-containing lytic polysaccharide mono-oxygenases, Current Opinion in Structural Biology, vol.23, issue.5, pp.660-668, 2013.
DOI : 10.1016/j.sbi.2013.05.006

B. Seiboth, L. Hartl, N. Salovuori, K. Lanthaler, G. Robson et al., Role of the bga1-Encoded Extracellular ??-Galactosidase of Hypocrea jecorina in Cellulase Induction by Lactose, Applied and Environmental Microbiology, vol.71, issue.2
DOI : 10.1128/AEM.71.2.851-857.2005

M. Arvas, N. Haiminen, B. Smit, J. Rautio, M. Vitikainen et al., Detecting novel genes with sparse arrays, Gene, vol.467, issue.1-2, pp.41-51, 2010.
DOI : 10.1016/j.gene.2010.07.009

P. Foreman, D. Brown, L. Dankmeyer, R. Dean, S. Diener et al., Transcriptional Regulation of Biomass-degrading Enzymes in the Filamentous Fungus Trichoderma reesei, Journal of Biological Chemistry, vol.278, issue.34, pp.31988-31997, 2003.
DOI : 10.1074/jbc.M304750200

N. Boase and J. Kelly, A role for creD, a carbon catabolite repression gene from Aspergillus nidulans, in ubiquitination, Molecular Microbiology, vol.21, issue.3, pp.929-940, 2004.
DOI : 10.1111/j.1365-2958.2004.04172.x

E. Fekete, B. Seiboth, C. Kubicek, A. Szentirmai, and L. Karaffa, Lack of aldose 1-epimerase in Hypocrea jecorina (anamorph Trichoderma reesei): A key to cellulase gene expression on lactose, Proceedings of the National Academy of Sciences, vol.105, issue.20, pp.7141-7146, 2008.
DOI : 10.1073/pnas.0802789105

D. Ivanen, N. Rongjina, S. Shishlyannikov, G. Litviakova, L. Isaeva-ivanova et al., Novel precipitated fluorescent substrates for the screening of cellulolytic microorganisms, Journal of Microbiological Methods, vol.76, issue.3, pp.295-300, 2009.
DOI : 10.1016/j.mimet.2008.12.008

W. Zhang, Y. Kou, J. Xu, Y. Cao, G. Zhao et al., Two Major Facilitator Superfamily Sugar Transporters from Trichoderma reesei and Their Roles in Induction of Cellulase Biosynthesis, Journal of Biological Chemistry, vol.288, issue.46, pp.32861-32872, 2013.
DOI : 10.1074/jbc.M113.505826

M. Warzywoda, E. Larbre, and J. Pourqui, Production and characterization of cellulolytic enzymes from Trichoderma reesei grown on various carbon sources, Bioresource Technology, vol.39, issue.2, pp.125-130, 1992.
DOI : 10.1016/0960-8524(92)90130-P

B. Montenecourt and D. Eveleigh, Preparation of mutants of Trichoderma reesei with enhanced cellulase production, Appl Environ Microbiol, vol.34, pp.777-782, 1977.

D. Eveleigh and B. Montenecourt, Increasing Yields of Extracellular Enzymes, Adv Appl Microbiol, vol.23, p.74, 1979.
DOI : 10.1016/S0065-2164(08)70146-1

L. Ries, N. Belshaw, M. Ilm-?-n, . Penttil, . Me et al., The role of CRE1 in nucleosome positioning within the cbh1 promoter and coding regions of Trichoderma reesei, Applied Microbiology and Biotechnology, vol.18, issue.Corrigendum, pp.749-762, 2014.
DOI : 10.1007/s00253-013-5354-3

T. Mello-de-sousa, R. Gorsche, A. Rassinger, M. Fonseca, R. Mach et al., A truncated form of the Carbon catabolite repressor 1 increases cellulase production in Trichoderma reesei, Biotechnology for Biofuels, vol.25, issue.1, p.129, 2014.
DOI : 10.1186/s13068-014-0129-3

F. Kazi, J. Fortman, R. Anex, D. Hsu, A. Aden et al., Techno-economic comparison of process technologies for biochemical ethanol production from corn stover, Fuel, vol.89, pp.20-28, 2010.
DOI : 10.1016/j.fuel.2010.01.001

T. Ghose, Measurement of cellulase activities, Pure and Applied Chemistry, vol.59, issue.2, pp.257-268, 1987.
DOI : 10.1351/pac198759020257

L. Jourdren, A. Duclos, C. Brion, and T. Portnoy, Teolenn: an efficient and customizable workflow to design high-quality probes for microarray experiments, Nucleic Acids Research, vol.38, issue.10, p.117, 2010.
DOI : 10.1093/nar/gkq110

S. Lemoine, F. Combes, N. Servant, L. Crom, and S. , Goulphar: rapid access and expertise for standard two-color microarray normalization methods, BMC Bioinformatics, vol.7, issue.1, p.467, 2006.
DOI : 10.1186/1471-2105-7-467
URL : https://hal.archives-ouvertes.fr/inserm-00122139

G. Smyth, Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments, Statistical Applications in Genetics and Molecular Biology, vol.3, issue.1, p.3, 2004.
DOI : 10.2202/1544-6115.1027

L. Jourdren, M. Bernard, M. Dillies, L. Crom, and S. , Eoulsan: a cloud computing-based framework facilitating high throughput sequencing analyses, Bioinformatics, vol.28, issue.11, pp.1542-1543, 2012.
DOI : 10.1093/bioinformatics/bts165

B. Langmead, C. Trapnell, M. Pop, and S. Salzberg, Ultrafast and memoryefficient alignment of short DNA sequences to the human genome

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.2078-2079, 2009.
DOI : 10.1093/bioinformatics/btp352

A. Mortazavi, B. Williams, K. Mccue, L. Schaeffer, and B. Wold, Mapping and quantifying mammalian transcriptomes by RNA-Seq, Nature Methods, vol.14, issue.7, pp.621-628, 2008.
DOI : 10.1038/nmeth.1226

J. Vaquerizas, L. Conde, P. Yankilevich, A. Cabez-?-n, P. Minguez et al., GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data, Nucleic Acids Research, vol.33, issue.Web Server, pp.33-616, 2005.
DOI : 10.1093/nar/gki500

E. Howe, K. Holton, S. Nair, D. Schlauch, R. Sinha et al., MeV: MultiExperiment Viewer, Biomedical Informatics for Cancer Research, pp.267-277
DOI : 10.1007/978-1-4419-5714-6_15

A. Ruepp, A. Zollner, D. Maier, K. Albermann, J. Hani et al., The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes, Nucleic Acids Research, vol.32, issue.18, pp.5539-5545, 2004.
DOI : 10.1093/nar/gkh894