Gene expression and alternative splicing profile of MFAP1- and THOC1-depleted human cells. Gene expression and alternative splicing profile of MFAP1- and THOC1-depleted human cells

THO/TREX is a conserved complex with a role in messenger ribonucleoprotein biogenesis that links gene expression and genome instability. Here we show that human THO interacts with MFAP1, a spliceosome-associated factor. Interestingly, MFAP1 depletion impairs cell proliferation and genome integrity, increasing γH2AX foci and DNA breaks. This phenotype is not dependent either on transcription or RNA-DNA hybrids. Mutations in the yeast orthologous gene SPP381, also confer a similar transcription-independent genome instability supporting a conserved role. MFAP1 depletion has a wide effect on splicing and gene expression in human cells, determined by transcriptome analyses, that affects a number of DNA damage response (DDR) genes, which supports an indirect role of MFAP1 on genome integrity. Our work defines a novel functional interaction between THO and RNA processing and argues that splicing factors may contribute to genome integrity indirectly by regulating the expression of DDR genes rather than by a direct role. HeLa cells were depleted of MFAP1 or THOC1 by siRNA during 72 h and their global gene expression and alternative splicing profiles were analyzed. Data were used to describe genes that were up- or down-regulated or showed alternative splicing changes after MFAP1 or THOC1 depletion. Overall design: We analyzed RNA from control cells (siC), MFAP1-depleted cells (siMFAP1) and THOC1-depleted cells (siTHOC1). For each condition, microarray analysis was conducted in triplicate from three different biological replicates (Total = 9 samples). We compared siMFAP1 vs siC, siTHOC1 vs siC and siMFAP1 vs siTHOC1.