## 3 Discussion
Further analyses, such as differential expression analysis and GO enrichment analysis, provided more insights into the specific genes and pathways affected by the TF disruption. Identifying the target genes of the TF is crucial to understanding its precise role in the cellular processes. The reversed gene expression patterns observed could lead to altered cellular functions and potentially contribute to a specific phenotype in the M7_5 mutant. Further phenotypic characterization of M7_5 is warranted to investigate the consequences of the gene expression reversal. The transcriptomics analyses of fruit from the _llll4_ mutant lines M7_5 and M29_2 identified a collection of DEGs exhibiting opposing expression trends. A considerable number of genes were upregulated in line M7_5 (M7_5 UP) while they were being downregulated in line M29_2 (M29_2 DOWN). These DEGs spanned a wide array of functions, including metabolic processes (such as alcohol dehydrogenase and hydroxysteroid dehydrogenase), stress responses (including dehydrin and late embryogenesis abundant proteins), protein processing (like vacuolar-processing enzyme and cysteine proteinase), and transport mechanisms (such as ABC transporter and sodium/hydrogen exchanger). Several genes encoded seed storage proteins (for example, 11S globulin, 2S albumin, and vicilin-like proteins), indicating possible changes in the nutritional makeup of the fruit. The identification of transcription factors like AP2-like ethylene-responsive TF suggests disruptions in the hormonal signaling pathways. At the same time, alterations in the genes related to DNA repair and cell wall remodeling emphasize the complex physiological modifications occurring in these mutant fruits. The differing gene expression profiles between the _llll4_ mutant lines highlight the multifaceted role of the L1L4 complex in regulating fruit development. These gene expression differences likely contribute to the phenotypic variations observed during the development and ripening of the fruits from these two _llll4_ mutant lines. Tomato fruit ripening involves significant epigenetic reprogramming [12; 13; 14], which is largely driven by the posttranslational histone modifications that influence the chromatin structure and gene expression [15; 16]. The histone modification H3K27 me3 has emerged as a key regulator of fruit ripening [17]. Despite this, direct genetic evidence linking histone methylases/demethylases to the regulation of flavonoid biosynthesis remains limited. However, a recent study observed increases in H3K27 me3 levels at the _CHST_ locus in the peels of YB-CD-R fruit [5]. We discovered that differential expression of histone modification genes in the _l114_ disruption lines provides evidence that the L1L4 complex influences epigenetic regulation in tomato fruit development. The downregulation of _HKMT_s and _histone deacetylases_ (_HDACs_) suggests that _L1L4_ disruption may lead to a more open chromatin state, potentially increasing gene expression. Histone deacetylation is generally associated with gene repression. The strong downregulation of _Solyc03g112410.2_ in both mutant lines, especially in M7_5, points to a potential disruption of gene-s Silencing mechanisms. However, the specific impact of these changes on gene expression and fruit development will depend on the target genes of these histone-modifying enzymes. In addition, the differential expression of the histone proteins (H1, H2A, H2B, H3, and H4) themselves is also significant. Changes in the histone protein levels can alter the stoichiometry of nucleosomes and impact the chromatin structure. The combination of altered histone modification and histone protein levels could lead to widespread changes in gene expression patterns. Our analysis revealed a significant downregulation of various TF families, including WRKY, GRAS, NF-YB, Dof, bHLH, ARF, TCP, MYB, ERF, and C2H2, across both mutant lines.