library_construction_protocol: It was performed as described elsewhere (Cobo, Cheng, et al. 2022; Cobo, Tanaka, et al. 2022). Briefly, BMDM were lysed in Trizol (ThermoFisher, #15596026) and RNA was isolation and DNase treatment were carried out using RNA MicroPrep kit (Zymoresearch, #11-33MB). RNA-Seq library preparation  It was performed as described elsewhere (Cobo, Cheng, et al. 2022; Cobo, Tanaka, et al. 2022). Briefly, BMDM were lysed in Trizol (ThermoFisher, #15596026) and RNA was isolation and DNase treatment were carried out using RNA MicroPrep kit (Zymoresearch, #11-33MB). 500 ng-1 μg of RNA was incubated with Oligo d(T) magnetic beads (NEB, #S1419S) to enrich for poly-A tailed transcripts and then fragmented by incubating for 9 min at 94º in 2X Superscript III first-strand buffer containing 10 mM DTT (Invitrogen, #P2325). Reverse transcription (RT) of fragmented RNA was performed at 25ºC for 10 min followed by 50ºC for 50 min. RT product was purified with RNAClean XP (Beckman Coulter, #A63987) and the solution of RNA-cDNA complexes was then added to a mix containing 1.5 μl of 10X Blue Buffer (Enzymatics, #B0110-L), 1.1 μl of dUTP mix (10 mM dATP, dCTP, dGTP and 20 mM dUTP), 0.2 μl of 5 U/ml RNAseH (Enzymatics, #Y9220L), 1 μl of 10 U/ml DNA polymerase I (Enzymatics, #P7050L), 0.15 μl of 1% Tween 20 and 1.05 μl of nuclease free water; and incubated at 16ºC overnight. Next day, the resulting DNA was purified using 28 μl of SpeedbBead Magnetic Carboxylate (GE Health- care, #651521050 50250) diluted in 20%PEG8000:2.5M NaCl to a final 13% PEG concentration. After two washes owith 80% etOH, air dry and eluted, the purified DNA was end-repaired by blunting followed by A-tailing and adapter ligation using NOVA (BIOO-NextFlex adapters. Libraries were amplified by PCR for 13 cycles using Solexa 1GA and Solexa 1GB primers (AATGATACGGCGACCACCGA and CAAGCAGAAGACGGCATACGA, respectively), purified using 1 μl of SpeedbBead Magnetic Carboxylate. Eluted libraries were quantified using a Qubit dsDNA HS Assay Kit and sequenced on NovaSeq SP100 (Illumina, San Diego, California).  ChIP-Seq library preparation  Chromatin immunoprecipitation (ChIP) was performed as described elsewhere (Seidman et al. 2020; Gosselin et al. 2017). Briefly, MDM or BMDM were fixed with 1% formaldehyde for H3K27ac, H3K4me3 and H3K79me3 or doubly fixed with 3 mM Disuccinimidyl-glutarate -DSG- (Proteochem, #C1104) in PBS for 30 min at room temperature and then with 1% formaldehyde (ThermoFisher, #28906) for 10 min at room temperature for TFEB, TFEC, BHLHE40, BHLHE41, DOT1L and DNMT3A. Fixation was then quenched upon adding glycine to final concentration of 125 mM. Cells were then washed with 0.01%Triton X-100:PBS, scraped and pelleted by centrifugation at 3000 rpm for 10 min at 4ºC and snap frozen for storage at -80ºC. For ChIP experiments, fixed cells were thawed and permeabilised in 1 mL of chilled buffer containing 10 mM HEPES/KOH pH7.9, 85 mM KCl, 1 mM EDTA, 0.2% IGEPAL CA-630 (Sigma-Aldrich, #I8896), 1X protease inhibitor cocktail (Sigma, #11836145001) and 1 mM PMSF for 10 min on ice. After that cells were spun down and lysed in 130 μl of either LB3 lysis buffer containing 10 mM Tris/HCl pH 7.5, 100 mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine, 1 X protease inhibitor cocktail for H3K27ac, H3K4me3 and H3K79me3 or lysis buffer containing 20 mM Tris/HCl pH7.5, 1 mM EDTA, 0.5 mM EGTA, 0.1% SDS, 0.4% Sodium Deoxycholate, 1% NP-40, 0.5 mM DTT, 1x protease inhibitor cocktail and 1 mM PMSF. Chromatin was sheared by sonication in a 96 microTUBE Rack (Covaris, #500282) using a Covaris E220 for 25 cycles with the following settings: time, 60 s; duty, 5.0; PIP, 140; cycles, 200; amplitude, 0.0; velocity, 0.0. Sonicated lysates were spun down at 10,000 rpm for 10 min at 4ºC and one percent of the sonicated lysate was kept as ChIP input for analysis. In all buffers, DTT, protease inhibitor and PMSF were added freshly. Sonicated lysates were incubated with a mix consisting of Protein G Dynabeads (Invitrogen, #10003D) and TFEB antibody cocktail (Abcam, #ab2636 plus CST, #37785), TFE3 antibody cocktail (Abcam, #196681 plus Abcam, #93808), BHLHE40 (Novus Biologicals, #NBP100-1800), DOT1L (CST, #D1W4Z), DNMT3A cocktail (Abcam, #ab2850 plus Diagenode, #C15410085), H3K27ac (ActiveMotifs, #AB_2793305), H3K4me3 (Millipore, #04-745), or H3K79me3 (Diagenode, #C15410068),  was added to the sonicated material and incubated overnight on a rotator at 4ºC. Next day, immunocomplexes were placed on a magnet and bead complexes were washed with 100 μl of chilled buffers. For H3K27ac, H3K4me3 and H3K79me3 ChIP, beads were washed four times each with wash buffer I containing 20 mM Tris/HCl pH 7.5, 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA, wash buffer III containing 10 mM Tris/HCl pH 7.4, 250 mM LiCl, 1% Triton X-100, 0.7% Na-Deoxycholate, 1 mM EDTA and twice with ice-cold TET containing 10 mM Tris/HClpH7.5, 1 mM EDTA, 0.2% Tween-20. For TFEB, TFEC, BHLHE40, BHLHE41, DOT1L and DNMT3A ChIP beads were washed as it follows: 3 times lysis buffer, 6 times with wash buffer containing 10 mM Tris/HCl pH7.5, 250 mM LiCl, 1 mM EDTA, 0.7% Na-Deoxycholate and 1% NP-40 alternative; 3 times with TET buffer containing 10 mM Tris/HCl pH 8.0, 1 mM EDTA, 0.2% Tween 20; and 1 time with IDTE buffer containing 10 mM Tris/HCl pH 8.0 and 0.1 mM EDTA. Bead complexes were resuspended in 25 mL of TT buffer containing 10 mM Tris/HCl pH 8.0, 0.05% Tween 20. ChIP libraries for sequencing were prepared on beads using NEBNext Ultra II Library kit (NEB, #E7645L) by reducing 50% the reaction volume as previously described (Heinz et al. 2015; Sakai et al. 2019). Reverse crosslinking was performed by adding 33.5 μl of a mix containing 4 μl 10% SDS, 3 μl 0.5 M EDTA, 1.6 μl 0.2M EGTA, 1 μl 10 mg/ml Proteinase K (Biolabs, #P8107 S), 1 μl 10 mg/ml RNase A, 4.5 μl 5M NaCl and 18.4 μl nuclease free water and incubating at 55C for 1h followed by 75ºC for 30 min. After removing the dynabeads, libraries were cleaned by adding  2 μl of SpeadBeads in 124 μl of 20% PEG 8000/ 1.5M NaCl and washed twice with 100 μl of 80% etOH, air dry and eluted in 13 μl of buffer containing 10 mM Tris/HCl pH 8.0 and 0.05% Tween 20. Libraries were amplified by PC for 14 cycles using NEBNext Ultra II PCR master mix using Solexa 1GA and Solexa 1GB primers. After that, libraries were size selected 200-500 bp upon running in 10% TBE acrylamide gels (ThermoFisher, #EC62752BOX) and sequenced using a NovaSeq SP100.