RNA oxidation in chromatin modification and DNA-damage response following exposure to formaldehyde

Abstract Formaldehyde is an environmental and occupational chemical carcinogen implicated in the damage of proteins and nucleic acids. However, whether formaldehyde provokes modifications of RNAs such as 8-oxo-7,8-dihydroguanine (8-oxoG) and the role that these modifications play on conferring long-term adverse health effects remains unexplored. Here, we profile 8-oxoG modifications using RNA-immunoprecipitation and RNA sequencing (8-oxoG RIP-seq) to identify 343 RNA transcripts heavily enriched in oxidations in human bronchial epithelial BEAS-2B cell cultures exposed to 1 ppm formaldehyde for 2 h. RNA oxidation altered expression of many transcripts involved in chromatin modification and p53-mediated DNA-damage responses, two pathways that play key roles in sustaining genome integrity and typically deregulated in tumorigenesis. Given that these observations were identified in normal cells exhibiting minimal cell stress and death phenotypes (for example, lack of nuclear shrinkage, F-actin alterations or increased LDH activity); we hypothesize that oxidative modification of specific RNA transcripts following formaldehyde exposure denotes an early process occurring in carcinogenesis analogous to the oxidative events surfacing at early stages of neurodegenerative diseases. As such, we provide initial investigations of RNA oxidation as a potentially novel mechanism underlying formaldehyde-induced tumorigenesis.

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Neuroanatomy and behavior in mice with a haploinsufficiency of AT-rich interactive domain 1B (ARID1B) throughout development

Molecular Autism ◽

10.1186/s13229-021-00432-y ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

J. Ellegood ◽

S. P. Petkova ◽

A. Kinman ◽

L. R. Qiu ◽

A. Adhikari ◽

...

Keyword(s):

Corpus Callosum ◽

Ex Vivo ◽

Chromatin Modification ◽

Autism Spectrum ◽

Repetitive Behaviors ◽

Social Deficits ◽

Altered Expression ◽

Developmental Growth ◽

And Behavior

Abstract Background One of the causal mechanisms underlying neurodevelopmental disorders (NDDs) is chromatin modification and the genes that regulate chromatin. AT-rich interactive domain 1B (ARID1B), a chromatin modifier, has been linked to autism spectrum disorder and to affect rare and inherited genetic variation in a broad set of NDDs. Methods A novel preclinical mouse model of Arid1b deficiency was created and validated to characterize and define neuroanatomical, behavioral and transcriptional phenotypes. Neuroanatomy was assessed ex vivo in adult animals and in vivo longitudinally from birth to adulthood. Behavioral testing was also performed throughout development and tested all aspects of motor, learning, sociability, repetitive behaviors, seizure susceptibility, and general milestones delays. Results We validated decreased Arid1b mRNA and protein in Arid1b+/− mice, with signatures of increased axonal and synaptic gene expression, decreased transcriptional regulator and RNA processing expression in adult Arid1b+/− cerebellum. During neonatal development, Arid1b+/− mice exhibited robust impairments in ultrasonic vocalizations (USVs) and metrics of developmental growth. In addition, a striking sex effect was observed neuroanatomically throughout development. Behaviorally, as adults, Arid1b+/− mice showed low motor skills in open field exploration and normal three-chambered approach. Arid1b+/− mice had learning and memory deficits in novel object recognition but not in visual discrimination and reversal touchscreen tasks. Social interactions in the male–female social dyad with USVs revealed social deficits on some but not all parameters. No repetitive behaviors were observed. Brains of adult Arid1b+/− mice had a smaller cerebellum and a larger hippocampus and corpus callosum. The corpus callosum increase seen here contrasts previous reports which highlight losses in corpus callosum volume in mice and humans. Limitations The behavior and neuroimaging analyses were done on separate cohorts of mice, which did not allow a direct correlation between the imaging and behavioral findings, and the transcriptomic analysis was exploratory, with no validation of altered expression beyond Arid1b. Conclusions This study represents a full validation and investigation of a novel model of Arid1b+/− haploinsufficiency throughout development and highlights the importance of examining both sexes throughout development in NDDs.

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PDTB-10. INHIBITION OF RADIATION-INDUCED DNA DAMAGE REPAIR MEDIATED CHROMATIN MODIFICATION BY HISTONE H3 DEMETHYLASE INHIBITOR IN PEDIATRIC BRAINSTEM GLIOMA

Neuro-Oncology ◽

10.1093/neuonc/now212.630 ◽

2016 ◽

Vol 18 (suppl_6) ◽

pp. vi151-vi152

Author(s):

Quanhong Ma ◽

Andrea Plunti ◽

Amanda Saratsis ◽

Rishi Lulla ◽

Jason R Fangusaro ◽

...

Keyword(s):

Dna Damage ◽

Dna Damage Repair ◽

Chromatin Modification ◽

Histone H3 ◽

Brainstem Glioma ◽

Damage Repair ◽

Radiation Induced

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Apurinic endonuclease-1 preserves neural genome integrity to maintain homeostasis and thermoregulation and prevent brain tumors

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1809682115 ◽

2018 ◽

Vol 115 (52) ◽

pp. E12285-E12294 ◽

Cited By ~ 6

Author(s):

Lavinia C. Dumitrache ◽

Mikio Shimada ◽

Susanna M. Downing ◽

Young Don Kwak ◽

Yang Li ◽

...

Keyword(s):

Dna Damage ◽

Nervous System ◽

Brain Tumors ◽

Oxidative Dna Damage ◽

Early Death ◽

Etiologic Agent ◽

Dna Lesions ◽

Oxidative Modification ◽

Early Gene ◽

Content Type

Frequent oxidative modification of the neural genome is a by-product of the high oxygen consumption of the nervous system. Rapid correction of oxidative DNA lesions is essential, as genome stability is a paramount determinant of neural homeostasis. Apurinic/apyrimidinic endonuclease 1 (APE1; also known as “APEX1” or “REF1”) is a key enzyme for the repair of oxidative DNA damage, although the specific role(s) for this enzyme in the development and maintenance of the nervous system is largely unknown. Here, using conditional inactivation of murine Ape1, we identify critical roles for this protein in the brain selectively after birth, coinciding with tissue oxygenation shifting from a placental supply to respiration. While mice lacking APE1 throughout neurogenesis were viable with little discernible phenotype at birth, rapid and pronounced brain-wide degenerative changes associated with DNA damage were observed immediately after birth leading to early death. Unexpectedly, Ape1Nes-cre mice appeared hypothermic with persistent shivering associated with the loss of thermoregulatory serotonergic neurons. We found that APE1 is critical for the selective regulation of Fos1-induced hippocampal immediate early gene expression. Finally, loss of APE1 in combination with p53 inactivation resulted in a profound susceptibility to brain tumors, including medulloblastoma and glioblastoma, implicating oxidative DNA lesions as an etiologic agent in these diseases. Our study reveals APE1 as a major suppressor of deleterious oxidative DNA damage and uncovers specific and broad pathogenic consequences of respiratory oxygenation in the postnatal nervous system.

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DNA Polymerase and dRP-lyase activities of polymorphic variants of human Pol ι

Biochemical Journal ◽

10.1042/bcj20200491 ◽

2021 ◽

Vol 478 (7) ◽

pp. 1399-1412

Author(s):

Evgeniy S. Shilkin ◽

Anastasia S. Gromova ◽

Margarita P. Smal ◽

Alena V. Makarova

Keyword(s):

Dna Damage ◽

Dna Polymerase ◽

Polymerase Activity ◽

Altered Expression ◽

Dna Polymerase Iota ◽

Nucleotide Incorporation ◽

Lyase Activity ◽

Polymorphic Variants ◽

Y Family

Y-family DNA polymerase iota (Pol ι) is involved in DNA damage response and tolerance. Mutations and altered expression level of POLI gene are linked to a higher incidence of cancer. We biochemically characterized five active site polymorphic variants of human Pol ι: R71G (rs3218778), P118L (rs554252419), I236M (rs3218784), E251K (rs3218783) and P365R (rs200852409). We analyzed fidelity of nucleotide incorporation on undamaged DNA, efficiency and accuracy of DNA damage bypass, as well as 5′-deoxyribophosphate lyase (dRP-lyase) activity. The I236M and P118L variants were indistinguishable from the wild-type Pol ι in activity. The E251K and P365R substitutions altered the spectrum of nucleotide incorporation opposite several undamaged DNA bases. The P365R variant also reduced the dRP-lyase activity and possessed the decreased TLS activity opposite 8-oxo-G. The R71G mutation dramatically affected the catalytic activities of Pol ι. The reduced DNA polymerase activity of the R71G variant correlated with an enhanced fidelity of nucleotide incorporation on undamaged DNA, altered lesion-bypass activity and reduced dRP-lyase activity. Therefore, this amino acid substitution likely alters Pol ι functions in vivo.

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Arabidopsis Mediator subunit 17 connects transcription with DNA repair after UV-B exposure

10.1101/2021.08.02.454780 ◽

2021 ◽

Author(s):

Marisol Giustozzi ◽

Santiago Freytes ◽

Aime Jaskolowski ◽

Micaela Lichy ◽

Julieta L. Mateos ◽

...

Keyword(s):

Dna Damage ◽

Dna Repair ◽

Transcription Initiation ◽

Plant Responses ◽

Repair System ◽

Root Tips ◽

Direct Role ◽

Altered Expression ◽

Eukaryotic Organisms

Mediator 17 (MED17) is a subunit of the Mediator complex that regulates transcription initiation in eukaryotic organisms. In yeast and humans, MED17 also participates in DNA repair, physically interacting with proteins of the Nucleotide Excision DNA Repair system. We here analyzed the role of MED17 in Arabidopsis plants exposed to UV-B radiation, which role has not been previously described. Comparison of med17 mutant transcriptome to that of WT plants showed that almost one third of transcripts with altered expression in med17 plants are also changed by UV-B exposure in WT plants. To validate the role of MED17 in UV-B irradiated plants, plant responses to UV-B were analyzed, including flowering time, DNA damage accumulation and programmed cell death in the meristematic cells of the root tips. Our results show that med17 and OE MED17 plants have altered responses to UV-B; and that MED17 participates in various aspects of the DNA damage response (DDR). Increased sensitivity to DDR after UV-B in med17 plants can be due to altered regulation of UV-B responsive transcripts; but additionally MED17 physically interacts with DNA repair proteins, suggesting a direct role of this Mediator subunit during repair. Finally, we here also show that MED17 is necessary to regulate the DDR activated by ATR, and that PDCD5 overexpression reverts the deficiencies in DDR shown in med17 mutants. Together, the data presented demonstrates that MED17 is an important regulator of the DDR after UV-B radiation in Arabidopsis plants.

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Prolonged use of finasteride-induced gonadal sex steroids alterations, DNA damage and menstrual bleeding in women

Bioscience Reports ◽

10.1042/bsr20191434 ◽

2020 ◽

Vol 40 (2) ◽

Author(s):

Gadah Albasher ◽

May Bin-Jumah ◽

Saleh Alfarraj ◽

Fatimah Al-Otibi ◽

Nouf K. Al-Sultan ◽

...

Keyword(s):

Gene Expression ◽

Dna Damage ◽

Sex Steroids ◽

Serum Levels ◽

Treated Group ◽

Heavy Menstrual Bleeding ◽

Menstrual Bleeding ◽

Control Group ◽

Dna Integrity ◽

Adverse Health Effects

Abstract The aim of the present study was to examine the effect of prolonged use of finasteride on serum levels of dihydrotestosterone (DHT), estradiol (E2), progesterone, testosterone and androstenedione in women during the menstrual period. Further, to screen and compare the 5α-reductase activities through the expression of SRD5A1, SRD5A2 and AR gene and to determine the level of VEGF, VKOR and SAA gene expression and DNA damage. A total of 30 Saudi women aged between 25 and 35 years were enrolled in the study. The selected women were divided into two groups. The first group (n = 15) received 5 mg finasteride/day for prolonged period of one year and second group (n = 15) was taken as a healthy control. ELISA technique was used for measuring the serum levels of the targeted hormones, and Comet assay was used for checking the DNA integrity. Our findings revealed significant decrement of DHT, E2, progesterone and androstenedione levels and elevated levels of testosterone in group treated with daily oral doses of 5 mg finasteride/day compared with the control subjects. mRNA expression suggested that finasteride has concrete effects on the gene expression of the selected genes from the treated group in comparison with the control group. In addition, finasteride induced DNA damage, and heavy menstrual bleeding was noted in women treated with finasteride. In conclusion, the present findings revealed that finasteride has adverse health effects in women associated with gonadal sex steroids alterations, DNA damage and heavy menstrual bleeding with no consensus in the treatment of androgenetic alopecia in women.

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Bromodomain proteins: repairing DNA damage within chromatin

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2016.0286 ◽

2017 ◽

Vol 372 (1731) ◽

pp. 20160286 ◽

Cited By ~ 19

Author(s):

Li-Ya Chiu ◽

Fade Gong ◽

Kyle M. Miller

Keyword(s):

Dna Damage ◽

Chromatin Modification ◽

Chromatin Remodelling ◽

Dna Double Strand Breaks ◽

Dna Breaks ◽

Cellular Functions ◽

Strand Breaks ◽

Bromodomain Proteins ◽

Molecular Signals ◽

Key Participants

Genome surveillance and repair, termed the DNA damage response (DDR), functions within chromatin. Chromatin-based DDR mechanisms sustain genome and epigenome integrity, defects that can disrupt cellular homeostasis and contribute to human diseases. An important chromatin DDR pathway is acetylation signalling which is controlled by histone acetyltransferase (HAT) and histone deacetylase (HDAC) enzymes, which regulate acetylated lysines within proteins. Acetylated proteins, including histones, can modulate chromatin structure and provide molecular signals that are bound by acetyl-lysine binders, including bromodomain (BRD) proteins. Acetylation signalling regulates several DDR pathways, as exemplified by the preponderance of HATs, HDACs and BRD proteins that localize at DNA breaks to modify chromatin for lesion repair. Here, we explore the involvement of acetylation signalling in the DDR, focusing on the involvement of BRD proteins in promoting chromatin remodelling to repair DNA double-strand breaks. BRD proteins have widespread DDR functions including chromatin remodelling, chromatin modification and transcriptional regulation. We discuss mechanistically how BRD proteins read acetylation signals within chromatin to trigger DDR and chromatin activities to facilitate genome–epigenome maintenance. Thus, DDR pathways involving BRD proteins represent key participants in pathways that preserve genome–epigenome integrity to safeguard normal genome and cellular functions. This article is part of the themed issue ‘Chromatin modifiers and remodellers in DNA repair and signalling’.

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Rbms3 functions in craniofacial development by posttranscriptionally modulating TGF-β signaling

The Journal of Cell Biology ◽

10.1083/jcb.201204138 ◽

2012 ◽

Vol 199 (3) ◽

pp. 453-466 ◽

Cited By ~ 22

Author(s):

Chathurani S. Jayasena ◽

Marianne E. Bronner

Keyword(s):

Neural Crest ◽

Rna Binding ◽

Transforming Growth Factor ◽

Neural Crest Cells ◽

Transforming Growth Factor Β ◽

Facial Skeleton ◽

Altered Expression ◽

Rna Immunoprecipitation ◽

Β Receptor ◽

Cranial Neural Crest Cells

Cranial neural crest cells form much of the facial skeleton, and abnormalities in their development lead to severe birth defects. In a novel zebrafish protein trap screen, we identified an RNA-binding protein, Rbms3, that is transiently expressed in the cytoplasm of condensing neural crest cells within the pharyngeal arches. Morphants for rbms3 displayed reduced proliferation of prechondrogenic crest and significantly altered expression for chondrogenic/osteogenic lineage markers. This phenotype strongly resembles cartilage/crest defects observed in Tgf-βr2:Wnt1-Cre mutants, which suggests a possible link with TGF-β signaling. Consistent with this are the findings that: (a) Rbms3 stabilized a reporter transcript with smad2 3′ untranslated region, (b) RNA immunoprecipitation with full-length Rbms3 showed enrichment for smad2/3, and (c) pSmad2 levels were reduced in rbms3 morphants. Overall, these results suggest that Rbms3 posttranscriptionally regulates one of the major pathways that promotes chondrogenesis, the transforming growth factor β receptor (TGF-βr) pathway.

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Topoisomerase II and histone deacetylase inhibitors delay the G2/M transition by triggering the p38 MAPK checkpoint pathway

The Journal of Cell Biology ◽

10.1083/jcb.200405167 ◽

2004 ◽

Vol 166 (4) ◽

pp. 517-526 ◽

Cited By ~ 98

Author(s):

Alexei Mikhailov ◽

Mio Shinohara ◽

Conly L. Rieder

Keyword(s):

Dna Damage ◽

Histone Deacetylase ◽

P38 Mapk ◽

Topoisomerase Ii ◽

Histone Deacetylase Inhibitors ◽

Chromatin Modification ◽

Early Prophase ◽

Global Changes ◽

Atm Kinase ◽

Topo Ii

When early prophase PtK1 or Indian muntjac cells are exposed to topoisomerase II (topo II) inhibitors that induce little if any DNA damage, they are delayed from entering mitosis. We show that this delay is overridden by inhibiting the p38, but not the ATM, kinase. Treating early prophase cells with hyperosmotic medium or a histone deacetylase inhibitor similarly delays entry into mitosis, and this delay can also be prevented by inhibiting p38. Together, these results reveal that agents or stresses that induce global changes in chromatin topology during G2 delay entry into mitosis, independent of the ATM-mediated DNA damage checkpoint, by activating the p38 MAPK checkpoint. The presence of this pathway obviates the necessity of postulating the existence of multiple “chromatin modification” checkpoints during G2. Lastly, cells that enter mitosis in the presence of topo II inhibitors form metaphase spindles that are delayed in entering anaphase via the spindle assembly, and not the p38, checkpoint.

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Generation of inducible SMARCAL1 knock-down iPSC to model severe Schimke immune-osseous dysplasia reveals a link between replication stress and altered expression of master differentiation genes

10.1101/546093 ◽

2019 ◽

Cited By ~ 1

Author(s):

Giusj Monia Pugliese ◽

Federico Salaris ◽

Valentina Palermo ◽

Veronica Marabitti ◽

Nicolò Morina ◽

...

Keyword(s):

Dna Damage ◽

Dna Damage Response ◽

Severe Form ◽

Model Systems ◽

Altered Expression ◽

Osseous Dysplasia ◽

Human Ipscs ◽

Damage Response ◽

Transcription Interference

ABSTRACTThe Schimke immuno-osseous dysplasia is an autosomal recessive genetic osteochondrodysplasia characterized by dysmorphism, spondyloepiphyseal dysplasia, nephrotic syndrome and frequently T cell immunodeficiency. Several hypotheses have been proposed to explain pathophysiology of the disease, however, the mechanism by which SMARCAL1 mutations cause the syndrome is elusive. Indeed, animal models of the disease are absent or useless to provide insight into the disease mechanism, since they do not recapitulate the phenotype. We generated a conditional knockdown model of SMARCAL1 in iPSCs to mimic conditions of cells with severe form the disease. Here, we characterize this model for the presence of phenotype linked to the replication caretaker role of SMARCAL1 using multiple cellular endpoints. Our data show that conditional knockdown of SMARCAL1 in human iPSCs induces replication-dependent and chronic accumulation of DNA damage triggering the DNA damage response. Furthermore, they indicate that accumulation of DNA damage and activation of the DNA damage response correlates with increased levels of R-loops and replication-transcription interference. Finally, we provide data showing that, in SMARCAL1-deficient iPSCs, DNA damage response can be maintained active also after differentiation, possibly contributing to the observed altered expression of a subset of germ layer-specific master genes. In conclusion, our conditional SMARCAL1 iPSCs may represent a powerful model where studying pathogenetic mechanisms of severe Schimke immuno-osseous dysplasia, thus overcoming the reported inability of different model systems to recapitulate the disease.

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