Extended Data Fig. 3: Identification of determinates that regulate LySR activation.
From: A lysosomal surveillance response to stress extends healthspan
a, The top five enriched motifs for promoters of the 760 up-regulated genes upon vha-6 RNAi, but not upon vha-16 or vha-19 RNAi, by using Hypergeometric optimization of motif enrichment (HOMER) and ranked based on the P values. P. Value was derived from HOMER (one-sided hypergeometric test). b, The similarity of the Rank 1 motif as found in (a) to the putative binding motifs of all known transcription factors in C. elegans. All transcription factors with a similarity score above 0.500 were shown. The GATA transcription factor members were highlighted in bold. c, RNAi of other GATA transcription factor members, or pqm-1, did not affect the GFP expression of cpr-5p::gfp worms induced by vha-6 RNAi. RNAi targeting vha-6 occupied 40%, RNAi targeting GATA transcription factor members, or pqm-1, occupied 60%. d, GFP induction induced by vha-6 RNAi in cpr-5p::gfp worms is not blocked by the knockout of hlh-30 or atfs-1. e,f, Genotyping results for the wild-type, hlh-30(tm1978) (e) and atfs-1(tm4525) (f) strains in a cpr-5p::gfp-NLS background as indicated in (d). g, The indicated autophagy defective mutants have a normal induction of representative lysosomal proteases in response to vha-6 RNAi. qRT-PCR analysis (n = 4 biologically independent samples) of wild-type (N2) or autophagy defect mutants treated with control or vha-6 RNAi (****P < 0.0001). h, ChIP-qPCR (n = 4 biologically independent samples) analyses of the indicated genes in elt-2p::elt-2::gfp-flag worms treated with control or vha-6 RNAi, and/or elt-2 RNAi. ChIP was performed by using IgG control or anti-Flag M2 beads (****P < 0.0001; for hsp-4, P = 0.6641 (N.S., IgG VS ev), P = 0.8960 (N.S., IgG VS vha-6), P > 0.9999 (N.S., IgG VS elt-2), P = 0.9688 (N.S., IgG VS elt-2 + vha-6); for hsp-3, P = 0.5232 (N.S., IgG VS ev), P > 0.9999 (N.S., IgG VS vha-6), P = 0.7291 (N.S., IgG VS elt-2), P = 0.8456 (N.S., IgG VS elt-2 + vha-6); for hsp-16.2, P = 0.8197 (N.S., IgG VS ev), P > 0.9999 (N.S., IgG VS vha-6), P = 0.6324 (N.S., IgG VS elt-2), P = 0.2148 (N.S., IgG VS elt-2 + vha-6); for sod-3, P = 0.9950 (N.S., IgG VS ev), P = 0.9985 (N.S., IgG VS vha-6), P = 0.4144 (N.S., IgG VS elt-2), P = 0.8408 (N.S., IgG VS elt-2 + vha-6); for act-1, P = 0.9714 (N.S., IgG VS ev), P = 0.5075 (N.S., IgG VS vha-6), P = 0.3890 (N.S., IgG VS elt-2), P = 0.8057 (N.S., IgG VS elt-2 + vha-6); for act-3, P = 0.9976 (N.S., IgG VS ev), P > 0.9999 (N.S., IgG VS vha-6), P = 0.8545 (N.S., IgG VS elt-2), P = 0.8580 (N.S., IgG VS elt-2 + vha-6); for ges-1, P = 0.1858 (N.S., ev VS vha-6); for elo-6, P = 0.7980 (N.S., ev VS vha-6), ***P = 0.0003 (vha-6 VS elt-2), ***P = 0.0005 (vha-6 VS elt-2 + vha-6)). Scale bar, 0.3 mm. Error bars denote SEM. Statistical analysis was performed by two-tailed unpaired Student’s t-test (g) or ANOVA followed by Tukey post-hoc test (h) (N.S., not significant).
