A Genome-wide siRNA Screen Reveals Diverse Cellular Processes and Pathways that Mediate Genome Stability

Paulsen, Renee D.; Soni, Deena V.; Wollman, Roy; Hahn, Angela T.; Yee, Muh-Ching; Guan, Anna; Hesley, Jayne; Miller, Shannon C.; Cromwell, Evan F.; Solow-Cordero, David E.; Meyer, Tobias; Cimprich, Karlene A.

doi:10.1016/j.molcel.2009.06.021

Cited by 504 publications

(539 citation statements)

References 58 publications

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“…Several recent studies have proposed that defects in mRNA processing can contribute to genome instability (14,28,38). One proposed mechanism for this effect is through the failure to resolve transcriptional R-loops, transient RNA:DNA hybrid structures that form during transcription that displace the nontemplate DNA strand and generate susceptibility to DNA damage if stabilized.…”

Section: Smnmentioning

confidence: 99%

SMN deficiency in severe models of spinal muscular atrophy causes widespread intron retention and DNA damage

Jangi

Fleet

Cullen

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

108

111

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Spinal muscular atrophy (SMA), an autosomal recessive neuromuscular disease, is the leading monogenic cause of infant mortality. Homozygous loss of the gene survival of motor neuron 1 (SMN1) causes the selective degeneration of lower motor neurons and subsequent atrophy of proximal skeletal muscles. The SMN1 protein product, survival of motor neuron (SMN), is ubiquitously expressed and is a key factor in the assembly of the core splicing machinery. The molecular mechanisms by which disruption of the broad functions of SMN leads to neurodegeneration remain unclear. We used an antisense oligonucleotide (ASO)-based inducible mouse model of SMA to investigate the SMN-specific transcriptome changes associated with neurodegeneration. We found evidence of widespread intron retention, particularly of minor U12 introns, in the spinal cord of mice 30 d after SMA induction, which was then rescued by a therapeutic ASO. Intron retention was concomitant with a strong induction of the p53 pathway and DNA damage response, manifesting as γ-H2A.X positivity in neurons of the spinal cord and brain. Widespread intron retention and markers of the DNA damage response were also observed with SMN depletion in human SH-SY5Y neuroblastoma cells and human induced pluripotent stem cell-derived motor neurons. We also found that retained introns, high in GC content, served as substrates for the formation of transcriptional R-loops. We propose that defects in intron removal in SMA promote DNA damage in part through the formation of RNA:DNA hybrid structures, leading to motor neuron death.

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Section: Smnmentioning

confidence: 99%

SMN deficiency in severe models of spinal muscular atrophy causes widespread intron retention and DNA damage

Jangi

Fleet

Cullen

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

108

111

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“…More specifically, FUS participates in both homologous recombination (HR) and nonhomologous end joining (NHEJ)-directed DSB repair (6,7). The evidence suggesting a role for FUS in DNA repair is particularly intriguing for ALS pathogenesis, given growing evidence that RNA binding proteins are active in the prevention and repair of transcription-associated DNA damage (8)(9)(10)(11)(12). Other ALS-related RNAbinding proteins like SETX, EWSR1, and TAF15 have also been linked to DNA damage and repair, further suggesting the importance of a breakdown in this process in ALS pathogenesis (11,(13)(14)(15)(16).…”

Section: Dna Damage Response | Als | Transcription | R Loopmentioning

confidence: 99%

“…Depletion of various RNA binding/processing proteins triggers γH2AX (gamma H2A histone family, member X) focus formation, a canonical marker of DNA damage (10). This result suggests that these proteins are important in preventing or repairing DNA damage associated with transcription and RNA processing (10).…”

Section: Significancementioning

confidence: 99%

Two familial ALS proteins function in prevention/repair of transcription-associated DNA damage

Hill

Mordes

Cameron

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

108

119

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Amyotrophic lateral sclerosis (ALS) is a progressive motor neuron dysfunction disease that leads to paralysis and death. There is currently no established molecular pathogenesis pathway. Multiple proteins involved in RNA processing are linked to ALS, including FUS and TDP43, and we propose a disease mechanism in which loss of function of at least one of these proteins leads to an accumulation of transcription-associated DNA damage contributing to motor neuron cell death and progressive neurological symptoms. In support of this hypothesis, we find that FUS or TDP43 depletion leads to increased sensitivity to a transcription-arresting agent due to increased DNA damage. Thus, these proteins normally contribute to the prevention or repair of transcription-associated DNA damage. In addition, both FUS and TDP43 colocalize with active RNA polymerase II at sites of DNA damage along with the DNA damage repair protein, BRCA1, and FUS and TDP43 participate in the prevention or repair of R loopassociated DNA damage, a manifestation of aberrant transcription and/or RNA processing. Gaining a better understanding of the role(s) that FUS and TDP43 play in transcription-associated DNA damage could shed light on the mechanisms underlying ALS pathogenesis.A myotrophic lateral sclerosis (ALS) is a disease of both upper and lower motor neuron dysfunction that leads to progressive paralysis and eventually death due to respiratory failure. No single model of ALS disease pathogenesis has been revealed; however, multiple disease-associated genes are known (1). The variation in function of these genes suggests that there may be multiple ALS molecular subtypes. That said, the familial ALS gene product list is also enriched in protein groups with related functions.Mutations in multiple RNA processing genes, including FUS (FUS RNA-binding protein), TDP43 (TAR DNA-binding protein), SETX (senataxin), TAF15 (TATA box-binding protein-associated factor 15), EWSR1 (EWS RNA-binding protein 1), HNRNPA1 (heterogeneous nuclear ribonucleoprotein A1), and HNRNPA2B1 (heterogeneous nuclear ribonucleoprotein A2/B1), among others, give rise to familial ALS (fALS) (1). FUS and TDP43 are currently the best studied, given that mutations in these genes lead to classic histologic findings in ALS neural tissue and that similar histologic findings can be found in neural tissue of sporadic ALS cases (2). At autopsy, cytoplasmic TDP43 inclusions are found in ALS motor neurons from patients with (i) TDP43 mutations and (ii) sporadic ALS (i.e., patients with no FUS, TDP43, or other known pathogenic mutation) (2). They are also present in neurons in various parts of the brains of patients with either sporadic or familial versions of the ALS-related disorder, fronto-temporal lobar dementia (FTLD) (2). At autopsy, FUS inclusions were detected in the cytoplasm of motor neurons of FUS mutation-bearing fALS patients and in the cytoplasm of neurons in various regions of the brain in some FTLD patients (2).FUS and TDP43 exhibit a wide range of functions, most of which involv...

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“…7,29 In the presence of DNA damage, the DNA damage checkpoint is triggered and delays cell cycle progression in G2 to allow time to repair the damage. 5 To test whether the G2 arrest we observed after SNRPB depletion was due to DNA damage, we first quantified gH2AX, a marker of DNA double-strand breaks, by immunostaining ( Fig.…”

Section: Spliceosome Depletion Increases Dna Damage and Elicits A G2 mentioning

confidence: 99%

“…1,5 Several genome-wide small interfering RNA (siRNA) screens designed to identify genes with roles in genome maintenance and cell cycle progression have reported a role for spliceosome components in these processes. [6][7][8][9][10][11][12] Mutations in multiple spliceosome subunits have been found in leukemia, myeloid neoplasms, and some solid tumors, 13,14 suggesting that spliceosome defects might promote tumorigenesis perhaps through its roles in genome maintenance and cell division.…”

Section: Introductionmentioning

confidence: 99%

Graded requirement for the spliceosome in cell cycle progression

Karamysheva¹,

Díaz-Martínez

Warrington

et al. 2015

Cell Cycle

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Genome stability is ensured by multiple surveillance mechanisms that monitor the duplication, segregation, and integrity of the genome throughout the cell cycle. Depletion of components of the spliceosome, a macromolecular machine essential for mRNA maturation and gene expression, has been associated with increased DNA damage and cell cycle defects. However, the specific role for the spliceosome in these processes has remained elusive, as different cell cycle defects have been reported depending on the specific spliceosome subunit depleted. Through a detailed cell cycle analysis after spliceosome depletion, we demonstrate that the spliceosome is required for progression through multiple phases of the cell cycle. Strikingly, the specific cell cycle phenotype observed after spliceosome depletion correlates with the extent of depletion. Partial depletion of a core spliceosome component results in defects at later stages of the cell cycle (G2 and mitosis), whereas a more complete depletion of the same component elicits an early cell cycle arrest in G1. We propose a quantitative model in which different functional dosages of the spliceosome are required for different cell cycle transitions.

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A Genome-wide siRNA Screen Reveals Diverse Cellular Processes and Pathways that Mediate Genome Stability

Cited by 504 publications

References 58 publications

SMN deficiency in severe models of spinal muscular atrophy causes widespread intron retention and DNA damage

SMN deficiency in severe models of spinal muscular atrophy causes widespread intron retention and DNA damage

Two familial ALS proteins function in prevention/repair of transcription-associated DNA damage

Graded requirement for the spliceosome in cell cycle progression

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