bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of H4K16 and Gene Mutation on Sensitivity to DNA Damaging Agents and Silencing
Authors: Enya Blessing , Young Tiffany , Kirchmaier Ann 
Published: November 2023

The “Central Dogma” involves replication of DNA, transcription of mRNA, and translation of mRNA into protein. When a gene maintains its sequence, but portrays heritable differences in expression, these differences are often as a result of a process known as epigenetics. Epigenetic regulation of gene expression involves histone modification, chromatin structure, and other factors in all eukaryotes. Using budding yeast (Saccharomyces cerevisiae) as a model to study epigenetics, has provided a strong understanding of how histone modifications and chromatin structures are inherited and maintained throughout the cell cycle. S. cerevisiae has also served as a good model for analyzing genetic interactions. Identifying genetic interaction can be performed by observing differences in growth rate in the presence and absence of DNA damaging agents, of single and double mutants compared to Wild‐type. Mutations that occur in many genes responsible for replication, chromatin assembly, or histone modifications cause growth sensitivity in the presence of DNA damage. However, it is not known what role H4 K16 acetylation plays in responses to DNA damage and if this modification genetically interacts with chromatin assembly factor and histone acetyltransferase mutants. We hypothesized that H4K16 acetylation mutants would synthetically interact with defects in chromatin assembly factors and histone modifying‐enzymes in the presence of DNA damage.Several genes such as ASF1, CAC1, RTT106, HIF1, etc., were mutated and combined with wild‐type histones or H4K16 acetylation mutants. These combinations were assessed in synthetic interaction analyses in yeast, in order to evaluate how this modification influences responses to DNA damage and silencing. Yeast were grown in Yeast Peptone Dextrose media in the absence or presence of different drugs or environmental conditions such as hydroxyurea, methyl methane sulfonate, zeocin, and ultraviolet exposure. Images were taken and compared to see how each drug and mutant combination affect yeast growth. Results show presence of growth defects in single and double mutants in the presence relative to the absence of different DNA damaging agents, highlighting synthetic interaction between the gene mutation and histone mutants in yeast. Silencing was determined based on colony color to indicate expression of HMR:ADE2 in the mutated strains. Red colonies indicate the silencing of ADE2 and loss of gene expression. White colonies indicate fully expressed ADE2 and enhanced gene expression. The results suggest that loss of HMR:ADE2 silencing means defects of silent chromatin formation, and combination of H3K56 and H4K16 acetylation mutants affect yeast growth under different DNA damaging conditions. Combining mutated genes with other altered histone modification, to compare growth defects and DNA damage sensitivity will be conducted to understand genetic pathways regulating DNA damage responses and epigenetic processes.
Determination of E. coli cellular factors that contribute to survival upon exposure to the alkylating agent benzyl bromide
Authors: Aiken Ariel , Bellou Sirine , Wong Kelly , Nash Emma , Kramer Caitlin , Leifer Becky , Muenter Mark , Beuning Penny 
Published: November 2023

Alkylating agents have the ability to add alkyl groups onto DNA at various positions. There are many of these agents present in our environment that can ultimately lead to damaged DNA and mutations. While some mutations are beneficial many of the ones caused by these chemicals can have detrimental effects. Benzyl bromide is a known alkylating agent and can be a byproduct of industrial processes and then released into the environment. The goal of my work is to identify genes responsible for cellular responses to DNA damage caused by benzyl bromide using a library of E. coli knockout strains. E. coli knockout strains are being created using bacteriophage‐mediated transduction and the identities confirmed by colony PCR and DNA sequencing. The genes deleted in the knockout strains are those that encode various proteins that play a role in some aspect of DNA repair. While carrying out these experiments the knockouts in comparison to the wild type E. coli are expected to have a lower survival rate. After optimizing the assay conditions, we are determining the survival of strains in our library of now more than 30 knockout strains. Insight to how these E. coli strains react when exposed to this alkylating agent will give us more information on how these genes affect DNA repair and allow further studies to be done. We will be able to determine which genes have a more significant role in comparison to others and focus on other causes and possibly ways to reduce its effects.Support or Funding InformationSupported by American Cancer Society (RSG‐12‐161‐01‐DMC) and NIEHS ROUTES program.
GPS2 regulates mitochondrial biogenesis via mitochondria retrograde signaling and modulation of nuclear‐encoded mitochondrial genes core promoter accessibility
Authors: Cardamone Maria Dafne , Tanasa Bogdan , Cederquist Carly T , Huang Jiawen , Mahdaviani Kiana , Orofino Joseph L , Lentucci Claudia , Li Wenbo , Rosenfeld Michael Geoff , Liesa Marc , Perissi Valentina 
Published: November 2023

A key step in the evolution of eukaryotic cells has been the acquisition of oxidative metabolism through the symbiotic incorporation of an aerobic prokaryote. As this primordial organism evolved into an intracellular organelle, now known as mitochondrion, most of its genetic information was transferred to the nuclear genome. While this implies that mitochondrial biogenesis, health and functionality, ultimately depend on the nucleus being informed of the metabolic needs of the cell and the status of existing mitochondria, much is still unknown about direct mitochondria‐to‐nucleus communication strategies, particularly in mammalian cells. Here, we have identified a key mediator of the mitochondria retrograde signaling pathway in the transcriptional cofactor G‐Protein Suppressor 2 (GPS2). Our data reveals that GPS2 translocates from the outer mitochondrial membrane to the nucleus in a regulated manner to promote the activation of the nuclear‐encoded mitochondrial gene program through the establishment of a chromatin environment permissive for RNA polymerase II (POL2)‐mediated transcriptional activation. We will present in vitro data characterizing GPS2 role in regulating mitochondrial biogenesis during adipocyte differentiation and dissecting the molecular mechanism of GPS2‐mediated transcriptional regulation of nuclear encoded mitochondrial genes in both human and murine cell lines, as well as discuss the in vivo physiological relevance of this newly described pathway in brown adipose tissue. Together, our findings shed new light on the strategies evolved in eukaryotic cells to maintain efficient mitochondria:nuclear inter‐organellar communication, with important implications for our understanding of the molecular mechanisms underlying the regulation of mitochondria biogenesis and metabolic flexibility in both homeostasis and disease.Support or Funding InformationPilot and Feasibility Award from Boston Nutrition and Obesity Research Center (BNORC) to M.D.C Joslin/Boston University (Pilot and Feasibility Award) and NIH/NIDDK (R01DK100422) to V.P.
Metabolic Regulation of Gene Expression by Histone Lysine β‐hydroxybutyrylation
Authors: Zhang Di , Xie Zhongyu , Chung Dongjun , Tang Zhanyun , Huang He , Dai Lunzhi , Qi Shankang , Li Jingya , Colak Gozde , Chen Yue , Peng Chao , Ruan Haibin , Wang Danli , Jensen Lindy M. , Kwon Oh Kwang , Lee SangKyu , Pletcher Scott D. , Tan Minjia , Lombard David B. , White Kevin P. , Zhao Hongyu , Li Jia , Roeder Robert G. , Yang Xiaoyong , Zhao Yingming 
Published: November 2023

®‐hydroxybutyrate has been used to treat epilepsy and plays a neuro‐protective role in models of neurodegenerative diseases. Ketogenic diets are under evaluation as adjunctive treatment for patients with brain tumors and other malignancies. These lines of evidence suggest a regulatory role for ketone bodies beyond serving as an energy source. However, the mechanisms underlying these physiological and pharmacological effects of ketone bodies remain largely unknown.We had previously identified lysine ®‐hydroxybutyrylation (Kbhb) as a new type of histone modification. We showed that histone Kbhb is dramatically induced in livers from mice subjected to prolonged fasting or streptozotocin‐induced diabetic ketoacidosis. By ChIP‐seq and RNA‐seq analysis, we demonstrated that histone Kbhb is a mark enriched in active gene promoters, and that the increased H3K9bhb levels during starvation are associated with genes up‐regulated in starvation‐responsive metabolic pathways. We now have new data to show that p300 can catalyze histone Kbhb both in vitro and in cultured cell lines. Using in vitro transcription assay with recombinant chromatin, we demonstrate that p300‐catalyzed histone Kbhb can activate transcription directly.All together, our study suggest histone Kbhb as a new epigenetic regulatory mark that couples metabolism to gene expression, offering a new avenue to study chromatin regulation and the diverse functions of ®‐hydroxybutyrate in the context of important human pathophysiological states, including diabetes, epilepsy, and neoplasia.Support or Funding InformationThe work was supported by: NIH DK089098, P01 DK057751, CT DPH 2014‐0139 and Ellison Medical Foundation to X.Y.; NIH DK71900 and the Starr Foundation Tri‐Institutional Stem Cell Initiative (2014‐021) to R.G.R.; NIH R01GM101171 and R21CA177925 to D.L.; NIH GM59507 to H. Z.; NIH R01AG030593 and R01AG023166 to S.D.P.; National Natural Science Foundation of China (81125023) and Shanghai Commission of Science and Technology (14431902800) to J.L and J.L.; National Basic Research Program of China (973 Program) (No. 2014CBA02004) and the Shanghai Municipal Science and Technology Commission (No. 15410723100) to M.T.
Biological Function and Histone Recognition of Family IV Bromodomain‐Containing Proteins
Authors: Lloyd Jonathan T. , Poplawaski Amanda , Lubula Mulu Y. , Carlson Samuel , Gay Jamie , Glass Karen C. 
Published: November 2023

Bromodomain proteins function as epigenetic readers that recognize acetylated histone tails to facilitate transcription of target genes. There are approximately 60 known human bromodomains, and these are split into 8 sub‐families based on structural conservation. The bromodomain‐containing proteins in family IV consist of 7 members (BRPF1, BRPF2, BRPF3, BRD7, BRD9, ATAD2a, and ATAD2b). The bromodomains of each of these proteins recognize and bind acetyllysine residues on histone tails protruding from the nucleosome. However, the histone marks recognized by each bromodomain protein, can be very different. Our research revealed that the BRPF1 subunit of the MOZ histone acetyltransferase (HAT) recognizes histone acetylated at H2AK5ac, H4K12ac, H3K14ac, H4K8ac and H4K5ac1. While the bromodomain of BRD7, a member of the SWI/SNF complex, was shown to preferentially recognize histones H3K9ac, H3K14ac, H4K8ac, H4K12ac and H4K16ac2. The bromodomains of BRPF2 and BRPF3 are very similar in amino acid sequence, and function as part of the HBO1 HAT complex, but there is limited data on which histone ligands they bind3. Similarly, there is little known about the histone targets of the BRD9 and ATAD2b bromodomain proteins. Interestingly, the ATAD2a bromodomain was recently shown to preferentially bind to H4K5acK12ac in newly synthesized histones following DNA replication4. ATAD2 is a co‐activator of the estrogen and androgen receptors, and has also been shown to stimulate MYC and E2F‐dependent cell proliferation. Additionally, ATAD2a is overexpressed in a range of cancers including lung, breast, and prostate cancer, as well as ovarian and hepatocellular carcinoma. However, despite the physiological importance of the family IV bromodomains, little is known about how they function at the molecular or atomic level. Here, we summarize our understanding of how family IV bromodomains recognize and select for acetyllysine marks by providing the molecular details of ligand binding, which will be critical for the development of new therapeutic interventions targeting these bromodomains.Support or Funding InformationSupported by a National Institutes of Health grant, NIGMS 1R15GM104865, and an ACPHS scholarship of discovery grant.
Class I‐Specific HDAC Inhibitor Stimulates the Expression of Npr1 in Haplotype Mice by Enhanced Histone Acetylation at Different Lysine Residues
Authors: Kumar Prerna , Gogulamudi Venkateshwara R. , Nguyen Christian , Pandey Kailash N. 
Published: November 2023

Guanylyl cyclase/natriuretic peptide receptor‐A (GC‐A/NPRA) signaling activates natriuresis/diuresis, vasodilatation, and inhibits the cell proliferation and fibrosis. The objective of the present study was to gain insight into the mechanisms of Npr1 (coding for GC‐A/NPRA) expression and receptor function involving epigenetic regulatory mechanisms activated by class I histone deacetylase (HDAC) inhibitor, mocetinostat (MGCD0103). We utilized 20‐ to 22‐weeks old male Npr1 gene‐knockout haplotype (1‐copy; Npr1+/−), wild‐type (2‐copy; Npr1+/+) and gene‐duplicated heterozygous (3‐copy; Npr1++/+) mice. The mice were injected intraperitonealy with MGCD0103 (5 mg/kg) at the alternate days for 2‐weeks. The Western blot analysis showed that MGCD0103 significantly increased the renal NPRA mRNA and protein levels in all mice groups compared with vehicle‐treated controls. There was marked increase in renal cGMP levels in MGCD0103‐treated mice groups. The Npr1 haplotype mice exhibited increased HDAC activity and decreased acetylated histone levels; however, 3‐copy mice showed lower HDAC activity compared with 2‐copy mice. Treatment with MGCD0103 significantly attenuated HDAC activity by almost 50% in Npr1 haplotype mice. A substantial global increase in acetylation levels of histone 3 at different lysine positions (H3‐K9/14ac, H3‐K18ac, and H3‐K27ac) and histone 4 lysine 8 (H4‐K8ac) was observed in the kidneys of MGCD0103‐treated mice. The present results suggest that MGCD0103 epigenetically regulates NPRA expression in vivo via HDAC inhibition and histone modifications, which might have important implications in the renal function in disease states.Support or Funding InformationThis work was supported by NIH grants (HL057531 and HL062147) and by an Institutional Development Award (IDeA) from the NIGMS.
Regulation of Histone Methylation via Methionine Metabolism
Authors: Haws Spencer A. , Denu John M. 
Published: November 2023

S‐adenosylmethionine (SAM) is the sole methyl‐donor for methyltransferase reactions in the cell. However, given SAM's inherent instability and high energetic cost of synthesis, the mechanism by which methyltransferases acquire this metabolite poses an interesting problem as uptake via diffusion appears inefficient. Recent data suggest that SAM may be directly channeled from its synthetase to histone methyltransferases (HMTs) in response to glucose‐derived serine metabolism as well as oxidative stress. We have investigated the influence of one‐carbon metabolism on nuclear SAM utilization, using methionine restriction to mimic methyl‐donor metabolite depletion in HCT116 cells. When HCT116 cells are subjected to methionine restriction, we identify significant alterations in one‐carbon metabolism, including a complete loss of free intracellular methionine after 5 minutes and a 5‐fold reduction in SAM concentrations after 1 hour. To determine how these fluctuations in one‐carbon metabolism influence histone post‐translational modifications (PTMs), we used mass spectrometry to identify the global histone PTM profiles of HCT116 cells subjected to a methionine restriction time course. While we observed an overall decrease in histone methylation throughout the time course, we also detected a preservation of mono‐methyl PTMs on H3K9 and H3K27. Knowing that the mammalian SAM synthetase MAT2A is responsive to methionine availability, we next analyzed the histone PTM profiles of MAT2A knockdown cells via mass spectrometry. In agreement with the methionine restriction results, we observed maintenance of mono‐methyl PTMs on H3K9 and H3K27 while global histone methylation levels decreased. These results suggest that MAT2A may be preferentially providing SAM to H3K9 and H3K27 mono‐methyl HMTs during one‐carbon metabolite depletion in an attempt to preserve crucial epigenetic memory until environmental conditions improve.Support or Funding InformationThis project was supported by NIH GM059789‐15/P250V A.
O‐GlcNAc Regulates Erythroid Genes Controlled by GATA‐1
Authors: ZHANG ZHEN , Graw Stefan , Tan Ee Phie , Koestler Devin C. , Peterson Kenneth R. , Slawson Chad 
Published: November 2023

Transcription factor GATA‐1 is essential for erythropoiesis and many GATA‐1 controlled genes are up‐regulated or down‐regulated as differentiation occurs. The mechanisms underlying how GATA‐1 target genes are regulated is unclear. One possible mechanism is through the post‐translational modification O‐GlcNAc. O‐linked N‐Acetylglucosamine (O‐GlcNAc) is added and removed from serine and threonine residues by the O‐GlcNAc processing enzymes, O‐GlcNAc‐transferase (OGT) and O‐GlcNAcase (OGA), respectively. In this study, we utilized a well‐established cell model of erythropoiesis, G1E‐ER4 cells, a murine GATA‐1 null erythroblast line that undergoes erythroid differentiation when GATA‐1 activity is restored by the addition of β‐estradiol. Interestingly, overall O‐GlcNAc levels dramatically decreased after GATA‐1 activation in G1E‐ER4 cells, with a slight increase of OGA and a decrease of OGT protein levels. We performed transcriptome analysis of G1E‐ER4 cells treated with β‐estradiol and/or Thiamet‐G (TMG, an OGA inhibitor). Approximately 6,800 transcripts expression patterns were changed following GATA‐1 activation. When the cells were treated with β‐estradiol and TMG, 1,100 genes changed expression patterns compared to cells treated with β‐estradiol only. The transcriptome profile changes induced by TMG likely alter GATA‐1 regulated pathways during erythropoiesis. Our data suggests that O‐GlcNAcylation plays a role in regulating erythroid gene expression controlled by GATA‐1.Support or Funding InformationThis work was supported by NIDDK Grant R01DK100595 (to C. S. and K. R. P.) and Biomedical Research Training Program from The University of Kansas Medical Center.
Regulation of Cellular Proliferation in B‐cell Acute Lymphoblastic Leukemia by Ikaros
Authors: Dovat Elanora , Payne Jonathon L , Song Chunhua , Desai Dhimant 
Published: November 2023

B‐cell acute lymphoblastic leukemia (B‐ALL) is the most common malignancy of childhood. IKZF1 encodes the Ikaros protein that acts as a tumor suppressor in B‐ALL. In high‐risk B‐ALL that is characterized by poor prognosis, the activity of Ikaros as a tumor suppressor is impaired. The goal of our research is to define the mechanisms through which Ikaros regulates cellular proliferation in high‐risk B‐ALL. In gain‐of‐function experiments, we overexpressed Ikaros in B‐ALL cells via retroviral transduction. Ikaros overexpression results in transcriptional repression of a large set of genes that promote cell cycle progression and several genes that promote the Phosphoinositide 3‐kinase (PI3K) pathway. This was associated with increased Ikaros binding at promoters of these genes. Ikaros loss‐of‐function experiments in which Ikaros in B‐ALL was downregulated by transfection with a specific Ikaros shRNA, resulted in increased transcription of Ikaros target genes. These results suggest that Ikaros can regulate the cell cycle and PI3K pathway in B‐ALL by functioning as a transcriptional repressor of the genes that promote cell cycle progression and the PI3K pathway. Since both cell cycle control and the PI3K pathway are dysregulated in high‐risk B‐ALL, these data provide a mechanism for how impaired Ikaros function results in the development of high‐risk B‐ALL. To determine the mechanism trough which Ikaros represses transcription of genes that regulate cellular proliferation in B‐ALL, we performed fine mapping of Ikaros binding and identified the epigenetic signature of the promoters of Ikaros target genes in B‐ALL cells using serial quantitative chromatin immunoprecipitation (qChIP). Results showed that Ikaros binding to the promoters of its target genes is associated with the formation of repressive chromatin that is characterized by the presence of specific histone modifications – H3K27me3 or H3K9me3. These data suggest that Ikaros represses the transcription of genes that regulate cellular proliferation via chromatin remodeling. In summary, the presented data demonstrate that Ikaros controls cellular proliferation in B‐ALL by direct transcriptional repression of genes that promote cell cycle progression and the PI3K pathway via epigenetic mechanisms. The loss of Ikaros function results in the deregulation of cell cycle control and the PI3K pathway and the development of high‐risk B‐ALL. Results provide the groundwork for further studies of the epigenetic regulation of gene expression in B‐ALL.Support or Funding InformationSupported by St. Baldrick's Foundation Summer Fellowship (E.D.)
MSK‐1 mediated Histone H3 phosphorylation is critical for ethanol‐induced inhibition of IL‐2 gene transcription in CD4+ T lymphocytes
Authors: Ghare Smita , Joshi‐Barve Swati , McClain Craig , Barve Shirish 
Published: November 2023

Immune suppression due to decreased CD4+ T cell function is a significant pathogenic component of multiple diseases including alcoholism, HIV infection and aging; however, the underlying mechanisms are not yet fully understood. We have previously shown that immunosuppressive effects of alcohol involve a decrease in the expression of interleukin‐2 (IL‐2), which critically regulates T cell proliferation, clonal expansion and homeostasis. In the present study we investigated the role of ethanol‐induced promoter histone modifications in the context of dysregulated IL‐2 gene expression. Chromatin immunoprecipitation (ChIP) analysis revealed that ethanol significantly prevented TCR inducible transcriptionally permissive histone H3 modifications at IL‐2 promoter in CD4+ T lymphocytes. Specifically, ethanol treatment inhibited phosphorylation of H3 serine 10 (H3S10ph) which then coordinately down regulated histone H3 lysine 4 tri‐methylation (H3K4Me3) and H3 lysine 9 acetylation (H3K9Ac). Notably, data showed that ethanol mediated transcriptional repression at IL‐2 promoter involves inhibition of Mitogen and Stress activated protein kinase (MSK‐1). Treatment of CD4+ T cells with MSK‐1 inhibitor further confirm the role of MSK‐1 mediated phosphorylation in regulating IL‐2 gene expression. Importantly, ethanol inhibited MSK‐1 activation via PP1 activation and could be reversed by okadaic acid‐phosphatase inhibitor treatment of CD4+ T lymphocytes. Overall, these observations suggest that, ethanol‐induced MSK‐1 inhibition and resultant decrease in promoter histone phosphorylation constitute a significant pathogenic mechanism underpinning the loss of IL‐2 expression and subsequent CD4+ T cell function associated with alcohol‐induced immune suppression.Support or Funding InformationThis work was supported by NIH grants.