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This repository holds the mass spectrometry raw data and sequence conservation data for Drosophila and human transcription-related proteins. Mass spectrometry raw data files for two runs containing different samples: IP-MS1_raw.xlsm and IP-MS1_raw.xlsm Conservation analyses files: Drosophila_human_motif_instances_FIMO.tar Instances of each peptide motif in all Drosophila and human proteins mapped by FIMO DrosophilaMelanogaster_orthogroups.tar *aacon.UniProtID.aacon files contain the sequence conservation scoresfor the Dorsophilatranscription-related proteins twist_library_CDs_pep.fa.mapped_peps.fa Protein sequences of the insect transcription factor database mapped to UniProt twist_library_CDs_pep.fa.mapping.tsv Annotation and orthogroups of theDosophila transcription factor database HomoSapiens_orthogroups.tar *aacon.UniProtID.aacon files contain the sequence conservation scoresfor the human transcription-related proteins human_TFs_and_tx-related_proteins.tsv.mapped_peps.fa Protein sequences of the human transcription factor database mapped to UniProt human_TFs_and_tx-related_proteins.tsv.mapping.tsv Annotation and orthogroups of thehuman transcription factor database

This repository holds the mass spectrometry raw data,MobiDB-lite search data, FIMO motif instances for all tiles, sequences used to make the AA sequence logosand sequence conservation data for Drosophila and human transcription-related proteins. Mass spectrometry raw data files for two runs containing different samples:IP-MS1_raw.xlsm and IP-MS1_raw.xlsm MobiDB-lite search(from interpro scanning) for entire Drosophila melanogaster proteome (used to compare % of IDRs):MobiDBLite_twist007_CDs_pep.tsv Motif scanning with FIMO for all tilesused to distinguish motif versus non-motif tiles: Motifs_FIMO_all_tiles.tar.gz Sequences used to make the AA sequence logos in Suppl Fig 6B:Sequences_for_AA_logos.tar.gz Conservation analyses files: Drosophila_human_motif_instances_FIMO.tar.gz Instances of each peptide motif in all Drosophila and human proteins mapped by FIMO DrosophilaMelanogaster_orthogroups.tar.gz *aacon.UniProtID.aacon files contain the sequence conservation scoresfor theDosophilatranscription-related proteins twist_library_CDs_pep.fa.mapped_peps.fa Protein sequences of the insect transcription factor database mapped to UniProt twist_library_CDs_pep.fa.mapping.tsv Annotation and orthogroups of theDosophilatranscription factor database Dmel_motif_cons_table_AA.txt Conservation per position (core and flanks) for each motif instance in Drosophila proteins (Data for Suppl Fig 5) HomoSapiens_orthogroups.tar.gz *aacon.UniProtID.aacon files contain the sequence conservation scoresfor the human transcription-related proteins human_TFs_and_tx-related_proteins.tsv.mapped_peps.fa Protein sequences of the human transcription factor database mapped to UniProt human_TFs_and_tx-related_proteins.tsv.mapping.tsv Annotation and orthogroups of thehuman transcription factor database &nbsp

Saccharomyces cerevisiae is an intron-poor organism with introns present in only 5% of its genes. The most prominent group of intron-containing genes are ribosomal protein (RP) genes. They are highly expressed and most of them are present as two paralogs. Parenteau et al. described the existence of intron- dependent intergenic regulatory circuits controlling expression ratios of RP paralogs. In this project, we did not confirm the regulation in 6 out of 7 tested regulatory circuits. We validated the regulation between RPL22 paralogs. We further showed that Rpl22 protein blocks the pre-mRNA splicing of both paralogs, with RPL22B paralog being more sensitive. Rpl22 protein binds to the stem-loop of RPL22B intron - disruption of the binding domain of Rpl22 proteins leads to loss of interaction. Moreover, the regulation seems to be working the same way in yeast Kluyveromyces lactis, which has only a single RPL22 copy. Overall, these results lead to better understanding of intergenic regulation, which adjusts the expression ratio between functionally different RPL22 paralogs. Key words introns, ribosomal protein genes, Rpl22, RPL22 paralogs, pre-mRNA splicing, Saccharomyces cerevisiae

Saccharomyces cerevisiae cells produce 2000 ribosomes per minute under normal conditions. The expression of ribosomal proteins is massive - it takes 50% of RNA polymerase II transcription and 90% of pre-mRNA splicing in rapidly growing cells. Since cells need an equimolar amount of individual ribosomal proteins, the tight coregulation of gene expression is required. The transcription is a main target of regulation, however, it is inherently unable to set a stoichiometric balance of ribosomal proteins. Various types of post-transcriptional regulation deal with fluctuations of individual ribosomal proteins and fine-tune their expression. Intron-dependent regulation appears to by predominant among ribosomal protein genes. Besides balancing their expression, presence of introns provides a rapid global regulation (repression) of ribosomal protein genes in response to environmental stress. KEY WORDS ribosomal protein genes, RPG, ribosomal protein, gene expression regulation, coregulation, Saccharomyces cerevisiae