Figure 4
Expression pattern of REST-003 and its downregulating effect on MDA-MB-231 cells.
(A) Schematic picture of ncRNAs and coding RNAs transcribed from the E1-3 region. Many new ncRNAs that are enriched at the 5’ boundary of the REST gene (E1-3) are predicted as S (yellow) and AS (purple) sequences. (B) (C) Differential expression of REST-003 in MCF-7 and MDA-MB-231 cells using northern blot analysis. RNA samples were prepared from each cell line transfected with controls and different siRNAs, as indicated. Hybridizations were performed using32 P-labeled DNA oligonucleotide probes complementary to the S and AS transcripts probes: AS (B*) sequence of E1-3 for S (B) and S (3*) sequence for AS (C) detection. Human U6 RNA (~105 nt) was probed as an internal control. (D) Genes downregulated by REST-003 downregulation using RNA-seq analysis. Downregulated gene expression in si-REST-003-treated cells is shown using DESeq from our pipeline (adjusted P-value < 0.05; yellow). The downregulated genes were compared with published RNA-seq data35 from MCF-7 and MDA-MB-231 cell lines (BCCLs, purple), 42 triple negative (TNBC) tissues and 58 non-malignant control tissues (blue). (E) Schematic of the regulatory interactions among REST, REST-003 and SRRM3 that may coordinate gene regulation required for development of the invasive phenotype.
