Noncoding translation mitigation.

Translation is pervasive outside of canonical coding regions, occurring in long noncoding RNAs, canonical untranslated regions and introns1-4, especially in ageing4-6, neurodegeneration5,7 and cancer8-10. Notably, the majority of tumour-specific antigens are results of noncoding translation11-13. Although the resulting polypeptides are often nonfunctional, translation of noncoding regions is nonetheless necessary for the birth of new coding sequences14,15. The mechanisms underlying the surveillance of translation in diverse noncoding regions and how escaped polypeptides evolve new functions remain unclear10,16-19. Functional polypeptides derived from annotated noncoding sequences often localize to membranes20,21. Here we integrate massively parallel analyses of more than 10,000 human genomic sequences and millions of random sequences with genome-wide CRISPR screens, accompanied by in-depth genetic and biochemical characterizations. Our results show that the intrinsic nucleotide bias in the noncoding genome and in the genetic code frequently results in polypeptides with a hydrophobic C-terminal tail, which is captured by the ribosome-associated BAG6 membrane protein triage complex for either proteasomal degradation or membrane targeting. By contrast, canonical proteins have evolved to deplete C-terminal hydrophobic residues. Our results reveal a fail-safe mechanism for the surveillance of unwanted translation from diverse noncoding regions and suggest a possible biochemical route for the preferential membrane localization of newly evolved proteins.

A joint NCBI and EMBL-EBI transcript set for clinical genomics and research.

Comprehensive genome annotation is essential to understand the impact of clinically relevant variants. However, the absence of a standard for clinical reporting and browser display complicates the process of consistent interpretation and reporting. To address these challenges, Ensembl/GENCODE1 and RefSeq2 launched a joint initiative, the Matched Annotation from NCBI and EMBL-EBI (MANE) collaboration, to converge on human gene and transcript annotation and to jointly define a high-value set of transcripts and corresponding proteins. Here, we describe the MANE transcript sets for use as universal standards for variant reporting and browser display. The MANE Select set identifies a representative transcript for each human protein-coding gene, whereas the MANE Plus Clinical set provides additional transcripts at loci where the Select transcripts alone are not sufficient to report all currently known clinical variants. Each MANE transcript represents an exact match between the exonic sequences of an Ensembl/GENCODE transcript and its counterpart in RefSeq such that the identifiers can be used synonymously. We have now released MANE Select transcripts for 97% of human protein-coding genes, including all American College of Medical Genetics and Genomics Secondary Findings list v3.0 (ref. 3) genes. MANE transcripts are accessible from major genome browsers and key resources. Widespread adoption of these transcript sets will increase the consistency of reporting, facilitate the exchange of data regardless of the annotation source and help to streamline clinical interpretation.

Long non-coding RNA generated from CDKN1A gene by alternative polyadenylation regulates p21 expression during DNA damage response.

Alternative Polyadenylation (APA) is an emerging mechanism for dynamic changes in gene expression. Previously, we described widespread APA occurrence in introns during the DNA damage response (DDR). Here, we show that a DDR-activated APA event occurs in the first intron of CDKN1A, inducing an alternate last exon-containing lncRNA. We named this lncRNA SPUD (Selective Polyadenylation Upon DNA Damage). SPUD localizes to polysomes in the cytoplasm and is detectable as multiple isoforms in available high-throughput studies. SPUD has low abundance compared to the CDKN1A full-length isoform under non-stress conditions, and SPUD is induced in cancer and normal cells under a variety of DNA damaging conditions in part through p53. The RNA binding protein HuR binds to and promotes the stability of SPUD precursor RNA. SPUD induction increases p21 protein, but not mRNA levels, affecting p21 functions in cell-cycle, CDK2 expression and cell growth. Like CDKN1A full-length isoform, SPUD can bind two competitive p21 translational regulators, the inhibitor calreticulin and the activator CUGBP1; SPUD alters their association with CDKN1A full-length in a DDR-dependent manner, promoting CDKN1A translation. Together, these results show a new regulatory mechanism by which a lncRNA controls p21 expression post-transcriptionally, highlighting lncRNA relevance in DDR progression and cell-cycle.

Improved reference genome of Aedes aegypti informs arbovirus vector control.

Female Aedes aegypti mosquitoes infect more than 400 million people each year with dangerous viral pathogens including dengue, yellow fever, Zika and chikungunya. Progress in understanding the biology of mosquitoes and developing the tools to fight them has been slowed by the lack of a high-quality genome assembly. Here we combine diverse technologies to produce the markedly improved, fully re-annotated AaegL5 genome assembly, and demonstrate how it accelerates mosquito science. We anchored physical and cytogenetic maps, doubled the number of known chemosensory ionotropic receptors that guide mosquitoes to human hosts and egg-laying sites, provided further insight into the size and composition of the sex-determining M locus, and revealed copy-number variation among glutathione S-transferase genes that are important for insecticide resistance. Using high-resolution quantitative trait locus and population genomic analyses, we mapped new candidates for dengue vector competence and insecticide resistance. AaegL5 will catalyse new biological insights and intervention strategies to fight this deadly disease vector.

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation.

The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). The RefSeq project leverages the data submitted to the International Nucleotide Sequence Database Collaboration (INSDC) against a combination of computation, manual curation, and collaboration to produce a standard set of stable, non-redundant reference sequences. The RefSeq project augments these reference sequences with current knowledge including publications, functional features and informative nomenclature. The database currently represents sequences from more than 55,000 organisms (>4800 viruses, >40,000 prokaryotes and >10,000 eukaryotes; RefSeq release 71), ranging from a single record to complete genomes. This paper summarizes the current status of the viral, prokaryotic, and eukaryotic branches of the RefSeq project, reports on improvements to data access and details efforts to further expand the taxonomic representation of the collection. We also highlight diverse functional curation initiatives that support multiple uses of RefSeq data including taxonomic validation, genome annotation, comparative genomics, and clinical testing. We summarize our approach to utilizing available RNA-Seq and other data types in our manual curation process for vertebrate, plant, and other species, and describe a new direction for prokaryotic genomes and protein name management.

PARN deadenylase is involved in miRNA-dependent degradation of TP53 mRNA in mammalian cells.

mRNA deadenylation is under the control of cis-acting regulatory elements, which include AU-rich elements (AREs) and microRNA (miRNA) targeting sites, within the 3' untranslated region (3' UTRs) of eukaryotic mRNAs. Deadenylases promote miRNA-induced mRNA decay through their interaction with miRNA-induced silencing complex (miRISC). However, the role of poly(A) specific ribonuclease (PARN) deadenylase in miRNA-dependent mRNA degradation has not been elucidated. Here, we present evidence that not only ARE- but also miRNA-mediated pathways are involved in PARN-mediated regulation of the steady state levels of TP53 mRNA, which encodes the tumor suppressor p53. Supporting this, Argonaute-2 (Ago-2), the core component of miRISC, can coexist in complexes with PARN resulting in the activation of its deadenylase activity. PARN regulates TP53 mRNA stability through not only an ARE but also an adjacent miR-504/miR-125b-targeting site in the 3' UTR. More importantly, we found that miR-125b-loaded miRISC contributes to the specific recruitment of PARN to TP53 mRNA, and that can be reverted by the ARE-binding protein HuR. Together, our studies provide new insights into the role of PARN in miRNA-dependent control of mRNA decay and into the mechanisms behind the regulation of p53 expression.

RefSeq: an update on mammalian reference sequences.

The National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database is a collection of annotated genomic, transcript and protein sequence records derived from data in public sequence archives and from computation, curation and collaboration (http://www.ncbi.nlm.nih.gov/refseq/). We report here on growth of the mammalian and human subsets, changes to NCBI's eukaryotic annotation pipeline and modifications affecting transcript and protein records. Recent changes to NCBI's eukaryotic genome annotation pipeline provide higher throughput, and the addition of RNAseq data to the pipeline results in a significant expansion of the number of transcripts and novel exons annotated on mammalian RefSeq genomes. Recent annotation changes include reporting supporting evidence for transcript records, modification of exon feature annotation and the addition of a structured report of gene and sequence attributes of biological interest. We also describe a revised protein annotation policy for alternatively spliced transcripts with more divergent predicted proteins and we summarize the current status of the RefSeqGene project.

Mouse genome annotation by the RefSeq project.

Complete and accurate annotation of the mouse genome is critical to the advancement of research conducted on this important model organism. The National Center for Biotechnology Information (NCBI) develops and maintains many useful resources to assist the mouse research community. In particular, the reference sequence (RefSeq) database provides high-quality annotation of multiple mouse genome assemblies using a combinatorial approach that leverages computation, manual curation, and collaboration. Implementation of this conservative and rigorous approach, which focuses on representation of only full-length and non-redundant data, produces high-quality annotation products. RefSeq records explicitly link sequences to current knowledge in a timely manner, updating public records regularly and rapidly in response to nomenclature updates, addition of new relevant publications, collaborator discussion, and user feedback. Whole genome re-annotation is also conducted at least every 12-18 months, and often more frequently in response to assembly updates or availability of informative data. This article highlights key features and advantages of RefSeq genome annotation products and presents an overview of NCBI processes to generate these data. Further discussion of NCBI's resources highlights useful features and the best methods for accessing our data.

Shared learning in an interconnected world: innovations to advance global health equity.

The notion of "reverse innovation"--that some insights from low-income countries might offer transferable lessons for wealthier contexts--is increasingly common in the global health and business strategy literature. Yet the perspectives of researchers and policymakers in settings where these innovations are developed have been largely absent from the discussion to date. In this Commentary, we present examples of programmatic, technological, and research-based innovations from Rwanda, and offer reflections on how the global health community might leverage innovative partnerships for shared learning and improved health outcomes in all countries.

Long Non-Coding RNA Generated from CDKN1A Gene by Alternative Polyadenylation Regulates p21 Expression during DNA Damage Response.

Alternative Polyadenylation (APA) is an emerging mechanism for dynamic changes in gene expression. Previously, we described widespread APA occurrence in introns during the DNA damage response (DDR). Here, we show that a DNA damage activated APA event occurs in the first intron of CDKN1A , inducing an alternate last exon (ALE)-containing lncRNA. We named this lncRNA SPUD (Selective Polyadenylation Upon Damage). SPUD localizes to polysomes in the cytoplasm and is detectable as multiple isoforms in available high throughput studies. SPUD has low abundance compared to the CDKN1A full-length isoform and is induced in cancer and normal cells under a variety of DNA damaging conditions in part through p53 transcriptional activation. RNA binding protein (RBP) HuR and the transcriptional repressor CTCF regulate SPUD levels. SPUD induction increases p21 protein, but not CDKN1A full-length levels, affecting p21 functions in cell-cycle, CDK2 expression, and cell viability. Like CDKN1A full-length isoform, SPUD can bind two competitive p21 translational regulators, the inhibitor calreticulin and the activator CUGBP1; SPUD can change their association with CDKN1A full-length in a DDR-dependent manner. Together, these results show a new regulatory mechanism by which a lncRNA controls p21 expression post-transcriptionally, highlighting lncRNA relevance in DDR progression and cellcycle.

Collateral activity of the CRISPR/RfxCas13d system in human cells.

CRISPR/Cas13 systems are increasingly used for programmable targeting of RNAs. While Cas13 nucleases are capable of degrading both target RNAs and bystander RNAs in vitro and in bacteria, initial studies fail to detect collateral degradation of non-target RNAs in eukaryotic cells. Here we show that RfxCas13d, also known as CasRx, a widely used Cas13 system, can cause collateral transcriptome destruction when targeting abundant reporter RNA and endogenous RNAs, resulting in proliferation defect in target cells. While these results call for caution of using RfxCas13d for targeted RNA knockdown, we demonstrated that the collateral activity can be harnessed for selective depletion of a specific cell population defined by a marker RNA in an in vitro setting.

The female to male calf sex ratio is associated with the number of services to achieve a calf and parity of lactating dairy cows.

Commercial dairy producers may get frustrated by the lower ratio of female to male calves born because female calves are more valuable than bull calves. Our objective was to determine if parity or stage of lactation at the time of breeding, using conventional semen, influenced the sex of the calf. Data from the University of Illinois and the University of New Hampshire dairy herds were collected and summarized for calf sex, the number of services to achieve a calf and the lactation number when conception of that calf occurred. Logistical regression procedures were used to analyze the dataset via version 9.4 of SAS. The final dataset contained 2,987 calvings, which consisted of 1,406 females and 1,581 males (47.1% and 52.9% for females and males, respectively). The frequency distribution of the number of services to achieve a calf was highest for the first service and progressively declined with increasing services (52.06%, 21.66%, 10.75%, 6.66%, 4.22%, and 4.65% for 1 to 6 services, respectively). The frequency distribution of calvings by lactation number was greatest for first lactation cows becoming pregnant with their second calf and declined with increasing parity (35.49%, 28.22%, 17.01%, 9.61%, 5.02%, 2.51%, 1.14%, 0.70%, and 0.30% for lactation numbers 1 to 9, respectively). Logistic stepwise regression indicated that the number of services to achieve a calf was significant in predicting the ratio of female to male calves. Calculation of odds ratios indicated that as the lactation number increased the likelihood of getting a bull calf decreased. Parity, services, and parity by services interaction were significant for cows having a greater number of parities and cows with a greater number of services yielding more heifer calves. However, an interaction occurred where cows with greater number of services along with greater parities more likely to have a bull calf. These data provide evidence that increasing the number of services to achieve a calf and increasing age of the cow increased the probability of a heifer calf being born. These data indicate that cows with greater parties (lesser cull rate) are more likely to produce heifer calves.

Effects of Autolyzed Yeast Supplementation in a High-Starch Diet on Rumen Health, Apparent Digestibility, and Production Variables of Lactating Holstein Cows.

Fifteen multiparous rumen-cannulated Holstein cows were assigned to one of five treatments in a replicated 5 × 5 Latin square design. The treatments were low-starch (LS) (22.8 ± 1% of dry matter; DM) without autolyzed yeast (AY; LS0, control), high-starch (HS) (31.2 ± 4% of DM) without AY (HS0), and HS with either 15 g (HS15), 30 g (HS30), or 45 g (HS45) of AY supplementation. Cows in HS0 had increased (p < 0.03) dry matter intake (DMI; 24.9 kg/d) and energy-corrected milk (ECM; 34.4 kg/d) compared to cows in LS0 (19.9 and 31.3 kg/d, respectively). There was a tendency for a quadratic treatment effect for feed efficiency (ECM/DMI, p = 0.07) and crude protein (CP) apparent digestibility (AD) (p = 0.09). Cows in HS45 tended (p = 0.09) to have increased DMI (25.6 kg/d) compared to cows in HS0 (24.9 kg/d). Cows in HS0 had greater (p < 0.04) milk protein nitrogen (N; 166 g/d) and microbial N production (161 g/d) than those in LS0 (140 and 138 g/d, respectively). In conclusion, the addition of AY tended to improve DMI, feed efficiency, and CP AD when cows were fed the HS diet.

Total, average and marginal rates of basal heat production during human growth.

Our goal was to examine how total, average (heat production rate per unit mass) and marginal (the increase in the heat production rate per unit increase in mass) rates of basal heat production changed as mass increased in growing humans. Specifically, our hypotheses were that the marginal basal heat production rate did not decrease monotonically as humans grew; and that an energetically optimal mass, one at which the average basal heat production rate of a growing human was minimal, existed. Marginal rates of heat production were estimated and six potential models to describe the effect of mass during human growth on basal heat production rate were evaluated using a large, meticulously curated, dataset from the literature. Marginal rates of heat production were quadratically related to body mass during growth; they declined initially, reached a minimum, and then increased. This suggested that the relationship between basal heat production rate and mass was cubic. Of the six potential models evaluated, a three-parameter cubic polynomial best described the data. Marginal rates of heat production were minimal for 56-kg females and 62-kg males. Basal heat production rates per unit mass of a growing human were minimal (i.e., energetically optimal) for 83-kg females and 93-kg males; the average masses of U.S. adults have been increasing and approaching these optima over the last 60 yr.

Radiofrequency-radiation exposure does not induce detectable leakage of albumin across the blood-brain barrier.

The blood-brain barrier (BBB) consists of tight junctions between the endothelial cells that line the capillaries in the central nervous system. This structure protects the brain, and neurological damage could occur if it is compromised. Several publications by researchers at Lund University have reported alterations in the BBB after exposure to low-power 915 MHz energy. These publications increased the level of concern regarding the safety of wireless communication devices such as mobile phones. We performed a confirmation study designed to determine whether the BBB is altered in rats exposed in a transverse electromagnetic (TEM) transmission line cell to 915 MHz energy at parameters similar to those in the Lund University studies. Unanesthetized rats were exposed for 30 min to either continuous-wave or modulated (16 or 217 Hz) 915 MHz energy at power levels resulting in whole-body specific absorption rates (SARs) of 0.0018-20 W/kg. Albumin immunohistochemistry was performed on perfused brain tissue sections to determine the integrity of the BBB. Chi-square analysis revealed no significant increase in albumin extravasation in any of the exposed animals compared to the sham-exposed or home cage control animals.

Plasma membrane permeabilization by 60- and 600-ns electric pulses is determined by the absorbed dose.

We explored how the effect of plasma membrane permeabilization by nanosecond-duration electric pulses (nsEP) depends on the physical characteristics of exposure. The resting membrane resistance (R(m)) and membrane potential (MP) were measured in cultured GH3 and CHO cells by conventional whole-cell patch-clamp technique. Intact cells were exposed to a single nsEP (60 or 600 ns duration, 0-22 kV/cm), followed by patch-clamp measurements after a 2-3 min delay. Consistent with earlier findings, nsEP caused long-lasting R(m) decrease, accompanied by the loss of MP. The threshold for these effects was about 6 kV/cm for 60 ns pulses, and about 1 kV/cm for 600 ns pulses. Further analysis established that it was neither pulse duration nor the E-field amplitude per se, but the absorbed dose that determined the magnitude of the biological effect. In other words, exposure to nsEP at either pulse duration caused equal effects if the absorbed doses were equal. The threshold absorbed dose to produce plasma membrane effects in either GH3 or CHO cells at either pulse duration was found to be at or below 10 mJ/g. Despite being determined by the dose, the nsEP effect clearly is not thermal, as the maximum heating at the threshold dose is less than 0.01 degrees C. The use of the absorbed dose as a universal exposure metric may help to compare and quantify nsEP sensitivity of different cell types and of cells in different physiological conditions. The absorbed dose may also prove to be a more useful metric than the incident E-field in determining safety limits for high peak, low average power EMF emissions.

Progressive limit feeding to maximize profit in the feedlot1.

Our objective was to examine the potential of limit feeding that keeps a previously growing animal at a constant size (termed progressive limit feeding) to maximize profit using a 3D surface to integrate the effects of animal size, feeding rate, and time in the feedlot. The constant size contours of the surface were determined using a combination of results. We used data from a study of growing beef cattle being fed to maintain specified sizes coupled with modern growth rate data for animals fed ad libitum in a feedlot. These feed rate contours were best-fit declining exponentials. They shared the same exponent and they originated on the ad libitum curve, thus defining the entire possible growth surface. The asymptotes of these exponentials coincided with the interspecies mean for the metabolic body size of mature animals. This surface also demonstrated the phenomenon of compensatory growth. We proved that the most profitable growth path across this surface is of a particular form under realistic assumptions. Specifically, we proved that the profit maximizing growth path in the feedlot began with a period of progressive limit feeding and then allowed ad libitum feeding to the same market time as experienced by the standard continuous ad libitum fed animal. The opportunity cost of holding the progressively limit-fed animal longer in the feedlot than the animal fed ad libitum quickly overpowered any profit gained by limit feeding. Consequently the progressively limit-fed animal on the optimal feeding path at sale time was slightly smaller but potentially more profitable than the animal fed ad libitum, both slaughtered at the same time. It may also have an economically favorable body composition. Thus we have demonstrated a process for maximizing profit in the feedlot. The approach involved developing a growth surface to integrate the effects of progressive limit feeding and subsequent compensatory growth. After refinement this same process could be applied to other livestock.

Influence of the concentration of dietary digestible calcium on growth performance, bone mineralization, plasma calcium, and abundance of genes involved in intestinal absorption of calcium in pigs from 11 to 22 kg fed diets with different concentrations of digestible phosphorus.

BACKGROUND: A 21-day experiment was conducted to test the hypothesis that Ca requirements to maximize growth performance expressed as the standardized total tract digestible (STTD) Ca to STTD P ratio is less than 1.40:1. The second hypothesis was that increasing dietary Ca increases plasma Ca concentration and downregulates abundance of genes related to Ca absorption (TRPV6, S100G, and ATP2B1) in the duodenum, and tight junction proteins (OCLN, CLDN1, and ZO1) in the duodenum and ileum. METHODS: Twenty corn-soybean meal diets were formulated using a 4 × 5 factorial design with diets containing 0.16%, 0.33%, 0.42%, or 0.50% STTD P, and 0.14%, 0.29%, 0.44%, 0.59%, or 0.74% STTD Ca. Six hundred and forty pigs (initial weight: 11.1 ± 1.4 kg) were allotted to 20 diets and 5 blocks in a randomized complete block design. On day 21, weights of pigs and feed left in feeders were recorded and blood, duodenal tissue, ileal mucosa, and the right femur were collected from 1 pig per pen. Abundance of mRNA was determined in duodenal and ileal tissue via quantitative RT-PCR. Data were analyzed using a response surface model. RESULTS: The predicted maximum ADG (614 g), G:F (0.65), and bone ash (11.68 g) was obtained at STTD Ca:STTD P ratios of 1.39:1, 1.25:1, and 1.66:1, respectively, when STTD P was provided at the requirement (0.33%). If dietary STTD P was below the requirement, increasing dietary Ca resulted in reduced (P < 0.05) ADG and G:F. However, if dietary STTD P was above the requirement, negative effects (P < 0.05) on ADG and G:F of increasing STTD Ca were observed only if dietary STTD Ca exceeded 0.6%. Plasma Ca concentration was positively affected by STTD Ca over the range studied (quadratic, P < 0.01) and negatively affected by increasing STTD P (linear, P < 0.01). There was a linear negative effect (P < 0.05) of STTD Ca on the abundance of S100G, TRPV6, OCLN, and ZO1 in duodenum, and CLDN and ZO1 in ileum. CONCLUSIONS: The STTD Ca:STTD P ratio needed to maximize growth performance of 11- to 25-kg pigs is less than 1.40:1, if P is at the estimated requirement. Increasing dietary Ca reduces transcellular absorption of Ca and increases paracellular absorption of Ca.

Nuclear Tau, p53 and Pin1 Regulate PARN-Mediated Deadenylation and Gene Expression.

While nuclear tau plays a role in DNA damage response (DDR) and chromosome relaxation, the mechanisms behind these functions are not fully understood. Here, we show that tau forms complex(es) with factors involved in nuclear mRNA processing such as tumor suppressor p53 and poly(A)-specific ribonuclease (PARN) deadenylase. Tau induces PARN activity in different cellular models during DDR, and this activation is further increased by p53 and inhibited by tau phosphorylation at residues implicated in neurological disorders. Tau's binding factor Pin1, a mitotic regulator overexpressed in cancer and depleted in Alzheimer's disease (AD), also plays a role in the activation of nuclear deadenylation. Tau, Pin1 and PARN target the expression of mRNAs deregulated in AD and/or cancer. Our findings identify novel biological roles of tau and toxic effects of hyperphosphorylated-tau. We propose a model in which factors involved in cancer and AD regulate gene expression by interactions with the mRNA processing machinery, affecting the transcriptome and suggesting insights into alternative mechanisms for the initiation and/or developments of these diseases.

mRNA Processing Factor CstF-50 and Ubiquitin Escort Factor p97 Are BRCA1/BARD1 Cofactors Involved in Chromatin Remodeling during the DNA Damage Response.

The cellular response to DNA damage is an intricate mechanism that involves the interplay among several pathways. In this study, we provide evidence of the roles of the polyadenylation factor cleavage stimulation factor 50 (CstF-50) and the ubiquitin (Ub) escort factor p97 as cofactors of BRCA1/BARD1 E3 Ub ligase, facilitating chromatin remodeling during the DNA damage response (DDR). CstF-50 and p97 formed complexes with BRCA1/BARD1, Ub, and some BRCA1/BARD1 substrates, such as RNA polymerase (RNAP) II and histones. Furthermore, CstF-50 and p97 had an additive effect on the activation of the ubiquitination of these BRCA1/BARD1 substrates during DDR. Importantly, as a result of these functional interactions, BRCA1/BARD1/CstF-50/p97 had a specific effect on the chromatin structure of genes that were differentially expressed. This study provides new insights into the roles of RNA processing, BRCA1/BARD1, the Ub pathway, and chromatin structure during DDR.