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| Status |
Public on Jul 05, 2019 |
| Title |
Gene expression and alternative splicing profile of MFAP1- and THOC1-depleted human cells |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
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.
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| 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.
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| Contributor(s) |
Salas-Armenteros I, Pérez M, Andújar E, Luna R, Aguilera A |
| Citation(s) |
31390568 |
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| Submission date |
Sep 04, 2018 |
| Last update date |
Aug 26, 2019 |
| Contact name |
Andrés Aguilera |
| Organization name |
CABIMER, Universidad de Sevilla
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| Department |
Genome BIology
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| Lab |
Genome Instability & Cancer
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| Street address |
Av. Américo Vespucio 24
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| City |
Seville |
| ZIP/Postal code |
41092 |
| Country |
Spain |
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| Platforms (2) |
| GPL17585 |
[HTA-2_0] Affymetrix Human Transcriptome Array 2.0 [probe set (exon) version] |
| GPL17586 |
[HTA-2_0] Affymetrix Human Transcriptome Array 2.0 [transcript (gene) version] |
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| Samples (18)
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| GSM3374431 |
HeLa cells transfected with control siC for 72 h, biological rep1 |
| GSM3374432 |
HeLa cells transfected with control siC for 72 h, biological rep2 |
| GSM3374433 |
HeLa cells transfected with control siC for 72 h, biological rep3 |
| GSM3374434 |
Hela cells transfected with siMFAP1 for 72 h, biological rep1 |
| GSM3374435 |
Hela cells transfected with siMFAP1 for 72 h, biological rep2 |
| GSM3374436 |
Hela cells transfected with siMFAP1 for 72 h, biological rep3 |
| GSM3374437 |
Hela cells transfected with siTHOC1 for 72 h, biological rep1 |
| GSM3374438 |
Hela cells transfected with siTHOC1 for 72 h, biological rep2 |
| GSM3374439 |
Hela cells transfected with siTHOC1 for 72 h, biological rep3 |
| GSM3374440 |
HeLa cells transfected with control siC for 72 h, biological rep1 [alternative splicing] |
| GSM3374441 |
HeLa cells transfected with control siC for 72 h, biological rep2 [alternative splicing] |
| GSM3374442 |
HeLa cells transfected with control siC for 72 h, biological rep3 [alternative splicing] |
| GSM3374443 |
Hela cells transfected with siMFAP1 for 72 h, biological rep1 [alternative splicing] |
| GSM3374444 |
Hela cells transfected with siMFAP1 for 72 h, biological rep2 [alternative splicing] |
| GSM3374445 |
Hela cells transfected with siMFAP1 for 72 h, biological rep3 [alternative splicing] |
| GSM3374446 |
Hela cells transfected with siTHOC1 for 72 h, biological rep1 [alternative splicing] |
| GSM3374447 |
Hela cells transfected with siTHOC1 for 72 h, biological rep2 [alternative splicing] |
| GSM3374448 |
Hela cells transfected with siTHOC1 for 72 h, biological rep3 [alternative splicing] |
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| Relations |
| BioProject |
PRJNA489195 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE119412_RAW.tar |
475.9 Mb |
(http)(custom) |
TAR (of CEL, CHP) |
| Processed data included within Sample table |
| Processed data provided as supplementary file |
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