RESEARCH HIGHLIGHTS
DIGITAL VISION
Nature Reviews Molecular Cell Biology | AOP, published online 29 May 2014; doi:10.1038/nrm3818
TRANSCRIPTION
Transcript elongation: pause at your peril Transcription can contribute to genomic instability by impeding DNA replication, but the mechanisms underlying transcriptionassociated genomic instability are poorly understood. Saponaro et al. now show that RECQL5, a member of a family of DNA helicases that maintain genome integrity, modifies transcript elongation and suppresses chromosomal rearrangements that are associated with transcription and replication stresses. The researchers used genomewide chromatin immunoprecipitation followed by sequencing (ChIP–seq) to show that RECQL5 knockdown in HEK293 cells resulted in a stark increase in RNA polymerase II (Pol II) binding at transcription start sites and a concomitant decrease in Pol II binding downstream at gene bodies. This is indicative of
RECQL5 … modifies transcript elongation and suppresses chromosomal rearrange ments
fast transcript elongation rates. Overexpression of RECQL5 had the opposite effect, with a similar set of genes affected in both conditions. To measure transcript elongation rates, the authors generated ‘RECQL5 shut-off ’ cells, in which the endo genous protein was stably depleted and a short hairpin RNA-resistant RECQL5 was expressed instead in a doxycycline-dependent manner. These cells were treated with a drug that synchronizes transcript elongation, which enabled genome-wide measurement of transcript elongation rates, in the presence and absence of RECQL5. This revealed a 27% increase in the median elongation rate in the absence of RECQL5 and a decrease associated with RECQL5 overexpression, which indicates that RECQL5 globally inhibits transcript elongation. The RECQL5 shut-off cells were then used to investigate the effect of RECQL5 depletion on genome integrity. The authors found that within days after doxycycline removal and RECQL5 depletion, the cells accumulated many genomic rearrangements, approximately one-third of which occurred in the same loci in two independent experiments. Genomic losses (but not gains) coincided with common fragile sites (CFS; loci that are susceptible to replication stress and are prone to chromosomal breaks), and most deletion breakpoints fell within transcribed regions.
NATURE REVIEWS | MOLECULAR CELL BIOLOGY
The ChIP–seq analysis also revealed preferential binding of Pol II at specific sites in genes, which is indicative of transcription stress (arrest or pause of Pol II) at these sites. This preferential binding was markedly increased following RECQL5 knockdown, which suggests that although transcript elongation rates are higher on average in the absence of RECQL5, such cells also suffer from increased transcription stress. Importantly, Pol II preferential binding sites within genes were significantly co-localized with chromosomal breaks, which revealed a connection between transcription stress and chromosomal breaks. In summary, the data suggest that RECQL5 has a role in moderating transcription stress levels and consequently in suppressing chromosomal breaks at CFS and in transcribed regions. Saponaro et al. propose that RECQL5 may buffer transcript elongation by promoting slower but smoother transcription, which in turn diminishes Pol II collisions with the DNA replication machinery and hence genomic instability. It remains to be seen whether RECQL5 deficiency plays a part in the aetiology of chromosomal aberrations in disease. Eytan Zlotorynski ORIGINAL RESEARCH PAPER Saponaro, M. et al. RECQL5 controls transcript elongation and suppresses genome instability associated with transcription stress. Cell http://dx.doi. org/10.1016/j.cell.2014.03.048 (2014)
VOLUME 15 | JULY 2014 © 2014 Macmillan Publishers Limited. All rights reserved
DIGITAL VISION
Nature Reviews Molecular Cell Biology | AOP, published online 29 May 2014; doi:10.1038/nrm3818
TRANSCRIPTION
Transcript elongation: pause at your peril Transcription can contribute to genomic instability by impeding DNA replication, but the mechanisms underlying transcriptionassociated genomic instability are poorly understood. Saponaro et al. now show that RECQL5, a member of a family of DNA helicases that maintain genome integrity, modifies transcript elongation and suppresses chromosomal rearrangements that are associated with transcription and replication stresses. The researchers used genomewide chromatin immunoprecipitation followed by sequencing (ChIP–seq) to show that RECQL5 knockdown in HEK293 cells resulted in a stark increase in RNA polymerase II (Pol II) binding at transcription start sites and a concomitant decrease in Pol II binding downstream at gene bodies. This is indicative of
RECQL5 … modifies transcript elongation and suppresses chromosomal rearrange ments
fast transcript elongation rates. Overexpression of RECQL5 had the opposite effect, with a similar set of genes affected in both conditions. To measure transcript elongation rates, the authors generated ‘RECQL5 shut-off ’ cells, in which the endo genous protein was stably depleted and a short hairpin RNA-resistant RECQL5 was expressed instead in a doxycycline-dependent manner. These cells were treated with a drug that synchronizes transcript elongation, which enabled genome-wide measurement of transcript elongation rates, in the presence and absence of RECQL5. This revealed a 27% increase in the median elongation rate in the absence of RECQL5 and a decrease associated with RECQL5 overexpression, which indicates that RECQL5 globally inhibits transcript elongation. The RECQL5 shut-off cells were then used to investigate the effect of RECQL5 depletion on genome integrity. The authors found that within days after doxycycline removal and RECQL5 depletion, the cells accumulated many genomic rearrangements, approximately one-third of which occurred in the same loci in two independent experiments. Genomic losses (but not gains) coincided with common fragile sites (CFS; loci that are susceptible to replication stress and are prone to chromosomal breaks), and most deletion breakpoints fell within transcribed regions.
NATURE REVIEWS | MOLECULAR CELL BIOLOGY
The ChIP–seq analysis also revealed preferential binding of Pol II at specific sites in genes, which is indicative of transcription stress (arrest or pause of Pol II) at these sites. This preferential binding was markedly increased following RECQL5 knockdown, which suggests that although transcript elongation rates are higher on average in the absence of RECQL5, such cells also suffer from increased transcription stress. Importantly, Pol II preferential binding sites within genes were significantly co-localized with chromosomal breaks, which revealed a connection between transcription stress and chromosomal breaks. In summary, the data suggest that RECQL5 has a role in moderating transcription stress levels and consequently in suppressing chromosomal breaks at CFS and in transcribed regions. Saponaro et al. propose that RECQL5 may buffer transcript elongation by promoting slower but smoother transcription, which in turn diminishes Pol II collisions with the DNA replication machinery and hence genomic instability. It remains to be seen whether RECQL5 deficiency plays a part in the aetiology of chromosomal aberrations in disease. Eytan Zlotorynski ORIGINAL RESEARCH PAPER Saponaro, M. et al. RECQL5 controls transcript elongation and suppresses genome instability associated with transcription stress. Cell http://dx.doi. org/10.1016/j.cell.2014.03.048 (2014)
VOLUME 15 | JULY 2014 © 2014 Macmillan Publishers Limited. All rights reserved
