## 2 Results
### Analysis of TFs  
The implications of L1L4 disruption appear to significantly impact the network of transcriptional regulators and TFs, many of them known to affect fruit quality traits, including color, texture, flavor, and nutritional content. Detailed information regarding the number of DEGs across TF families in the mutant lines can be found in Supplementary Table S1 and Figure 6A. Interestingly, M7_5 displayed a greater number of TFs (543 DEGs) compared to M29_2 (402 DEGs), potentially due to differences in sensitivity to the mutations produced by the disruption of L1L4. The ERF family exhibited the highest number of DEGs, with an even number of 45 TFs in both mutants, followed by MYBs (44 DEGs in M7_5; 30 in M29_2), bHLHs (43 in M7_5; 29 in M29_2), WRKYs (38 in M7_5; 27 in M29_2), C2H2s (31 in M7_5; 22 in M29_2) and NACs (29 in M7_5; 19 in M29_2). In the case of the NF-Y family, both NF-YA and NF-YB revealed a more stable regulatory role of L1L4 in these subunits, evidenced by the consistent expression patterns in both lines. In contrast, NF-YC exhibited a variable response with two DEGs in M7_5 and none in M29_2, implying a line-specific affinity on this subunit. Overall, the magnitude of _L1L4_ disruption impacted a vast network of TFs, highlighting the complex and crucial role of L1L4 in the gene expression landscape of tomato fruit. Figure 5: DEGs of histone and histone modifiers. (**A**) The Venn diagram displays common and unique histone-related DEGs in the M7_5 and M29_2 mutant lines compared to the WT. (**B**) The heatmap displays histone-related genes in the M7_5 and M29_2 mutant fruits, with red indicating upregulation and blu indicating downregulation compared to the WT. The values represent the fold change in gene expression. (**C**) The cartoon illustrates the affected histone-related genes in core histones (H2A, H2B, H3, and H4), linker histone H1, and histone modifiers (histone-lysine N-methyltransferasease and histone deacetylase). Figure 6: The top 20 families of the TFs and their members. (**A**) The heatmap displays the top DEGs in the M7_5 fruits, with red indicating upregulation and blue indicating downregulation relative to WT. The values represent the fold change in gene expression. (**B**) The heatmap displays the top DEGs in the M7_5 fruits. (**C**) The heatmap displays the top DEGs in the M29_2 fruits. Color scheme (red for upregulation, blue for downregulation) and representing values as a fold change compared to WT. The transcriptomics analysis of the M7_5 fruits revealed extensive DEGs compared to the WT. Focusing on the 30 most upregulated and 30 most downregulated genes (Figure 6B, Supplementary Table S2), we observed significant enrichment in the functional categories related to cell wall modification, stress response, and ethylene biosynthesis. Specifically, the upregulated genes included several involved in cell wall degradation, such as _Pectate Lyase_ (10.21), multiple _Endoglucanalyses_ (10.26, 9.99, 9.41), and _Pectinesterase_ (9.45). The increased expression of these enzymes suggests a potential shift in cell wall dynamics, possibly reflecting a compensatory mechanism or an altered ripening process. Additionally, stress- and defense-related genes like _pathogenesis-related family protein_ (9.71) and Class I _heat shock protein_ 3 (9.48) were also upregulated, potentially indicating a response to developmental cues or environmental challenges. The upregulation of _serine decarboxylase_ (11.22) and _histidine decarboxylase_ (_HD_) (10.02) points towards increased ethylene biosynthesis, a key regulator of ripening. Furthermore, the increased expression of _Chalcone synthase 2_ (_CHS2_) (9.95) and _Dilhydroflavound-4-reductase_ (9.24) suggests modifications to flavonoid metabolism, potentially influencing the fruit color and antioxidant capacity.