PMC

Schematic representation of newly identified TF transcripts. Newly identified transcripts encoding TFs (black)—ZNF266, SATB1, ELF2, SP140L, ARID5B, NCOA2 and IRF1—are schematically compared to known gene annotations: RefSeq (blue), AceView predictions (purple) and Gencode (red).

Computational and experimental workflow. Schematic overview of the in silico procedures used to infer the presence of new transcription factors (TFs) transcripts from the re-analysis of our RNA-Seq datasets. The experimental approach used to validate the presence of the new variants is also depicted.

Multiple alignment of the N-terminal residues of the novel predicted ZNF266 variants. The evolutionary conservation of the new 67 amino acids is shown in (A); Krüppel-associated box (KRAB)-A and -B boxes (dashed lines) alignment with other human genes is shown in (B). Identical residues are indicated by “*”, conservation between groups of strongly and weakly similar properties by “:” and “.” respectively. Black arrow indicates the start of the canonical ZNF266 protein isoform.

In silico characterization of ZNF266 predicted protein. Panel A shows relative surface accessibility (RSA) per residue; 3D structure of both annotated (left) and new (right) ZNF266 isoforms are shown in panel B. The protein backbone is shown in grey. The arrows show the direction of the beta-sheets, which is from the N- to the C-terminus. In both panels, functional domains and motifs are highlighted. In particular, the KRAB domain of the new ZNF266 isoform is shown in green, three predicted additional ZNF motifs in orange and the annotated ZNF motifs in yellow.

Graphical representation of newly identified splicing events in TF genes. General scheme of the new alternative splicing events identified for SATB1 (A); ELF2 (B); SP140L (C); ARID5B (D); NCOA2 (E) and ZNF266 (F). For all the genes, the genomic region encompassing the gene is shown in the upper part. Nucleotide sequences (and electropherograms by Sanger sequencing) of the new splice junctions are shown below the exon/intron structure for each gene. White numbers indicate exons’ numbers. Donor and acceptor splice sites are shown in bold. Red arrows indicate the primers annealing sites.