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Article ; Online: The circular logic of mRNA homeostasis.

Bryll, Alysia R / Peterson, Craig L

2023 Volume 14, Issue 1-2, Page(s) 18–26

Abstract: Eukaryotic cells rely upon dynamic, multifaceted regulation at each step of RNA biogenesis to maintain mRNA pools and ensure normal protein synthesis. Studies in budding yeast indicate a buffering phenomenon that preserves global mRNA levels through the ... ...

Abstract	Eukaryotic cells rely upon dynamic, multifaceted regulation at each step of RNA biogenesis to maintain mRNA pools and ensure normal protein synthesis. Studies in budding yeast indicate a buffering phenomenon that preserves global mRNA levels through the reciprocal balancing of RNA synthesis rates and mRNA decay. In short, changes in transcription impact the efficiency of mRNA degradation and defects in either nuclear or cytoplasmic mRNA degradation are somehow sensed and relayed to control a compensatory change in mRNA transcription rates. Here, we review current views on molecular mechanisms that might explain this apparent bidirectional sensing process that ensures homeostasis of the stable mRNA pool.
MeSH term(s)	RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Transcription, Genetic ; Cytoplasm/genetics ; Cytoplasm/metabolism ; Homeostasis ; RNA Stability/genetics
Chemical Substances	RNA, Messenger
Language	English
Publishing date	2023-02-26
Publishing country	United States
Document type	Review ; Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2646974-1
ISSN	2154-1272 ; 2154-1264
ISSN (online)	2154-1272
ISSN	2154-1264
DOI	10.1080/21541264.2023.2183684
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Article ; Online: Total times to treatment completion and clinical outcomes in odontogenic sinusitis.

Yassin-Kassab, Abdulkader / Peterson, Edward L / Craig, John R

American journal of otolaryngology

2023 Volume 44, Issue 4, Page(s) 103921

Abstract: Background: Multidisciplinary collaboration is essential for effective odontogenic sinusitis (ODS) management. One point of debate has been the optimal timing of primary dental treatment and endoscopic sinus surgery (ESS), but differences in time to ... ...

Abstract	Background: Multidisciplinary collaboration is essential for effective odontogenic sinusitis (ODS) management. One point of debate has been the optimal timing of primary dental treatment and endoscopic sinus surgery (ESS), but differences in time to completion of these treatment pathways have not been studied. Methods: A retrospective cohort study was conducted on ODS patients from 2015 to 2022. Demographic and clinical variables were recorded, and various durations of time were analyzed from rhinologic consultation through treatment completion. Resolution of sinusitis symptoms and purulence on endoscopy was also recorded. Results: Eighty-nine ODS patients were analyzed (47.2 % male, median 59 years-old). Of the 89 ODS patients, 56 had treatable dental pathology, and 33 had no treatable dental pathology. Median time to treatment completion for all patients was 103 days. Of 56 ODS patients with treatable dental pathology, 33 had primary dental treatment, and 27 (81 %) required secondary ESS. In patients who underwent primary dental treatment followed by ESS, median time from initial evaluation to treatment completion was 236.0 days. If ESS was pursued primarily followed by dental treatment, median time from initial evaluation to treatment completion was 112.0 days, which was significantly shorter than if dental treatment was pursued primarily (p = 0.002). Overall symptomatic and endoscopic resolution was 97.8 %. Conclusions: After dental and sinus surgical treatment, ODS patients experienced 97.8 % resolution of symptoms and purulence on endoscopy. In patients with ODS due to treatable dental pathology, primary ESS followed by dental treatment resulted in a shorter overall treatment duration than primary dental treatment followed by ESS.
MeSH term(s)	Humans ; Male ; Middle Aged ; Female ; Maxillary Sinusitis/etiology ; Maxillary Sinusitis/surgery ; Retrospective Studies ; Sinusitis/complications ; Sinusitis/therapy ; Endoscopy/methods ; Time Factors ; Chronic Disease ; Rhinitis
Language	English
Publishing date	2023-05-04
Publishing country	United States
Document type	Journal Article
ZDB-ID	604541-8
ISSN	1532-818X ; 0196-0709
ISSN (online)	1532-818X
ISSN	0196-0709
DOI	10.1016/j.amjoto.2023.103921
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Article ; Online: Fluorescence approaches for biochemical analysis of ATP-dependent chromatin remodeling enzymes.

Baier, Alexander S / Peterson, Craig L

Methods in enzymology

2022 Volume 673, Page(s) 1–17

Abstract: The dynamic nature of chromatin is an essential mechanism by which gene expression is regulated. Chromatin is comprised of nucleosomes, an octamer of histone proteins wrapped by DNA, and manipulation of these structures is carried out by a family of ... ...

Abstract	The dynamic nature of chromatin is an essential mechanism by which gene expression is regulated. Chromatin is comprised of nucleosomes, an octamer of histone proteins wrapped by DNA, and manipulation of these structures is carried out by a family of proteins known as ATP-dependent chromatin remodeling enzymes. These enzymes carry out a diverse range of activities, from appropriately positioning and adjusting the density of nucleosomes on genes, to installation and removal of histones for sequence variants, to ejection from DNA. These activities have a critical role in the proper maintenance of chromatin architecture, and dysregulation of chromatin remodeling is directly linked to the pathophysiology of various diseases. Mechanistic understanding of chromatin remodeling enzymes is therefore desirable, both as the drivers of this essential cellular activity and as potentially novel therapeutic targets in disease. In this chapter we cover our current methods for characterization of remodeler substrate binding affinity and catalytic activity, leveraging fluorescence polarization and Förster resonance energy transfer assays.
MeSH term(s)	Adenosine Triphosphate/metabolism ; Chromatin ; Chromatin Assembly and Disassembly ; DNA/chemistry ; Fluorescence ; Histones/metabolism ; Nucleosomes ; Transcription Factors/genetics
Chemical Substances	Chromatin ; Histones ; Nucleosomes ; Transcription Factors ; Adenosine Triphosphate (8L70Q75FXE) ; DNA (9007-49-2)
Language	English
Publishing date	2022-03-29
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	1557-7988
ISSN (online)	1557-7988
DOI	10.1016/bs.mie.2022.02.024
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Article ; Online: Functional interaction between the RNA exosome and the sirtuin deacetylase Hst3 maintains transcriptional homeostasis.

Bryll, Alysia R / Peterson, Craig L

Genes & development

2021 Volume 36, Issue 1-2, Page(s) 17–22

Abstract: Eukaryotic cells maintain an optimal level of mRNAs through unknown mechanisms that balance RNA synthesis and degradation. We found that inactivation of the RNA exosome leads to global reduction of nascent mRNA transcripts, and that this defect is ... ...

Abstract	Eukaryotic cells maintain an optimal level of mRNAs through unknown mechanisms that balance RNA synthesis and degradation. We found that inactivation of the RNA exosome leads to global reduction of nascent mRNA transcripts, and that this defect is accentuated by loss of deposition of histone variant H2A.Z. We identify the mRNA for the sirtuin deacetylase Hst3 as a key target for the RNA exosome that mediates communication between RNA degradation and transcription machineries. These findings reveal how the RNA exosome and H2A.Z function together to control a deacetylase, ensuring proper levels of transcription in response to changes in RNA degradation.
MeSH term(s)	Exosome Multienzyme Ribonuclease Complex/genetics ; Exosome Multienzyme Ribonuclease Complex/metabolism ; Histones/genetics ; Histones/metabolism ; Homeostasis/genetics ; RNA, Messenger/genetics ; Sirtuins/genetics ; Sirtuins/metabolism
Chemical Substances	Histones ; RNA, Messenger ; Exosome Multienzyme Ribonuclease Complex (EC 3.1.-) ; Sirtuins (EC 3.5.1.-)
Language	English
Publishing date	2021-12-16
Publishing country	United States
Document type	Journal Article
ZDB-ID	806684-x
ISSN	1549-5477 ; 0890-9369
ISSN (online)	1549-5477
ISSN	0890-9369
DOI	10.1101/gad.348923.121
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Zs.A 2292: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MG 54: Show issues

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Article ; Online: Cadaveric analysis of autonomic nerve fiber density in posterior nasal, posterolateral nasal, and anterior ethmoid nerves.

Craig, John R / Dunn, Raven T / Ray, Amrita / Keller, Christian E / Peterson, Edward L / Eide, Jacob G

International forum of allergy & rhinology

2023 Volume 13, Issue 11, Page(s) 2109–2112

Abstract: Key points: Autonomic nerve densities were equivalent in posterior nasal (PNN), posterolateral nasal (PLNN), and anterior ethmoid nerves (AEN). Rhinitis studies should explore the utility of PLNN and/or AEN transection over PNN alone. ...

Abstract	Key points: Autonomic nerve densities were equivalent in posterior nasal (PNN), posterolateral nasal (PLNN), and anterior ethmoid nerves (AEN). Rhinitis studies should explore the utility of PLNN and/or AEN transection over PNN alone.
Language	English
Publishing date	2023-06-04
Publishing country	United States
Document type	Journal Article
ZDB-ID	2625826-2
ISSN	2042-6984 ; 2042-6976
ISSN (online)	2042-6984
ISSN	2042-6976
DOI	10.1002/alr.23199
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Zs.A 6927: Show issues

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Article: Dual engagement of the nucleosomal acidic patches is essential for deposition of histone H2A.Z by SWR1C.

Baier, Alexander S / Gioacchini, Nathan / Eek, Priit / Tan, Song / Peterson, Craig L

Research square

2023

Abstract: The SWR1C chromatin remodeling enzyme catalyzes the ATP-dependent exchange of nucleosomal histone H2A for the histone variant H2A.Z, a key variant involved in a multitude of nuclear functions. How the 14-subunit SWR1C engages the nucleosomal substrate ... ...

Abstract	The SWR1C chromatin remodeling enzyme catalyzes the ATP-dependent exchange of nucleosomal histone H2A for the histone variant H2A.Z, a key variant involved in a multitude of nuclear functions. How the 14-subunit SWR1C engages the nucleosomal substrate remains largely unknown. Numerous studies on the ISWI, CHD1, and SWI/SNF families of chromatin remodeling enzymes have demonstrated key roles for the nucleosomal acidic patch for remodeling activity, however a role for this nucleosomal epitope in nucleosome editing by SWR1C has not been tested. Here, we employ a variety of biochemical assays to demonstrate an essential role for the acidic patch in the H2A.Z exchange reaction. Utilizing asymmetrically assembled nucleosomes, we demonstrate that the acidic patches on each face of the nucleosome are required for SWR1C-mediated dimer exchange, suggesting SWR1C engages the nucleosome in a "pincer-like" conformation, engaging both patches simultaneously. Loss of a single acidic patch results in loss of high affinity nucleosome binding and nucleosomal stimulation of ATPase activity. We identify a conserved arginine-rich motif within the Swc5 subunit that binds the acidic patch and is key for dimer exchange activity. In addition, our cryoEM structure of a Swc5-nucleosome complex suggests that promoter proximal, histone H2B ubiquitinylation may regulate H2A.Z deposition. Together these findings provide new insights into how SWR1C engages its nucleosomal substrate to promote efficient H2A.Z deposition.
Language	English
Publishing date	2023-07-28
Publishing country	United States
Document type	Preprint
DOI	10.21203/rs.3.rs-3050911/v1
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Article ; Online: Yeast Sirtuin Family Members Maintain Transcription Homeostasis to Ensure Genome Stability.

Feldman, Jessica L / Peterson, Craig L

Cell reports

2019 Volume 27, Issue 10, Page(s) 2978–2989.e5

Abstract: The mammalian sirtuin, SIRT6, is a key tumor suppressor that maintains genome stability and regulates transcription, though how SIRT6 family members control genome stability is unclear. Here, we use multiple genome-wide approaches to demonstrate that the ...

Abstract	The mammalian sirtuin, SIRT6, is a key tumor suppressor that maintains genome stability and regulates transcription, though how SIRT6 family members control genome stability is unclear. Here, we use multiple genome-wide approaches to demonstrate that the yeast SIRT6 homologs, Hst3 and Hst4, prevent genome instability by tuning levels of both coding and noncoding transcription. While nascent RNAs are elevated in the absence of Hst3 and Hst4, a global impact on steady-state mRNAs is masked by the nuclear exosome, indicating that sirtuins and the exosome provide two levels of regulation to maintain transcription homeostasis. We find that, in the absence of Hst3 and Hst4, increased transcription is associated with excessive DNA-RNA hybrids (R-loops) that appear to lead to new DNA double-strand breaks. Importantly, dissolution of R-loops suppresses the genome instability phenotypes of hst3 hst4 mutants, suggesting that the sirtuins maintain genome stability by acting as a rheostat to prevent promiscuous transcription.
MeSH term(s)	Cell Nucleus/metabolism ; DNA Breaks, Double-Stranded ; DNA, Fungal/chemistry ; DNA, Fungal/metabolism ; Exosomes/genetics ; Exosomes/metabolism ; Genomic Instability ; Histone Deacetylases/genetics ; Histone Deacetylases/metabolism ; RNA, Fungal/chemistry ; RNA, Fungal/metabolism ; RNA, Untranslated/metabolism ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Sirtuins/metabolism ; Transcription, Genetic
Chemical Substances	DNA, Fungal ; RNA, Fungal ; RNA, Untranslated ; Saccharomyces cerevisiae Proteins ; Hst3 protein, S cerevisiae (EC 3.5.1.-) ; Hst4 protein, S cerevisiae (EC 3.5.1.-) ; Sirtuins (EC 3.5.1.-) ; Histone Deacetylases (EC 3.5.1.98)
Language	English
Publishing date	2019-06-05
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2019.05.009
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Article ; Online: Using Ipratropium Bromide Nasal Spray Response as a Screening Tool in the Diagnostic Workup of Cerebrospinal Fluid Rhinorrhea.

Nulty, Phillip / Mason, William / Mackie, Hussein / Peterson, Edward L / Cook, Bernard / Rock, Jack / Eide, Jacob / Craig, John R

The Laryngoscope

2023 Volume 134, Issue 1, Page(s) 56–61

Abstract: Objectives: Unilateral clear thin rhinorrhea (UCTR) can be concerning for a nasal cerebrospinal fluid (CSF) leak. Beta-2 transferrin electrophoresis has been the gold standard for initial non-invasive confirmatory testing for CSF rhinorrhea, but there ... ...

Abstract	Objectives: Unilateral clear thin rhinorrhea (UCTR) can be concerning for a nasal cerebrospinal fluid (CSF) leak. Beta-2 transferrin electrophoresis has been the gold standard for initial non-invasive confirmatory testing for CSF rhinorrhea, but there can be issues with fluid collection and testing errors. Ipratropium bromide nasal spray (IBNS) is highly effective at reducing rhinitis-related rhinorrhea, and should presumably not resolve CSF rhinorrhea. This study assessed whether different clinical features and IBNS response helped predict presence or absence of CSF rhinorrhea. Methods: A prospective cohort study was conducted where all patients with UCTR had nasal fluid tested for beta-2 transferrin, and were prescribed 0.06% IBNS. Patients were diagnosed with CSF rhinorrhea or other rhinologic conditions. Clinical variables like IBNS response (rhinorrhea reduction), positional worsening, salty taste, postoperative state, female gender, and body-mass index were assessed for their ability to predict CSF rhinorrhea. Sensitivity, specificity, and predictive values and odds ratios were calculated for all clinical variables. Results: Twenty patients had CSF rhinorrhea, and 53 had non-CSF etiologies. Amongst clinical variables assessed for predicting CSF absence or presence, significant associations were shown for IBNS response (OR = 844.66, p = 0.001), positional rhinorrhea worsening (OR = 8.22, p = 0.049), and body-mass index ≥30 (OR = 2.92, p = 0.048). IBNS response demonstrated 96% sensitivity and 100% specificity, and 100% positive and 91% negative predictive values for predicting CSF rhinorrhea. Conclusions: In patients with UCTR, 0.06% IBNS response is an excellent screening tool for excluding CSF rhinorrhea, and should be considered in the diagnostic workup of CSF rhinorrhea. Level of evidence: 2 Laryngoscope, 134:56-61, 2024.
MeSH term(s)	Humans ; Female ; Ipratropium ; Cerebrospinal Fluid Rhinorrhea/diagnosis ; Nasal Sprays ; Prospective Studies ; Nasal Mucosa ; Cerebrospinal Fluid Leak ; Transferrin/analysis
Chemical Substances	Ipratropium (GR88G0I6UL) ; Nasal Sprays ; Transferrin
Language	English
Publishing date	2023-06-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	80180-x
ISSN	1531-4995 ; 0023-852X
ISSN (online)	1531-4995
ISSN	0023-852X
DOI	10.1002/lary.30801
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Article ; Online: Fact vs. fiction: naloxone in the treatment of opioid-induced respiratory depression in the current era of synthetic opioids.

Dahan, Albert / Franko, Thomas S / Carroll, James W / Craig, David S / Crow, Callie / Galinkin, Jeffrey L / Garrity, Justin C / Peterson, Joanne / Rausch, David B

Frontiers in public health

2024 Volume 12, Page(s) 1346109

Abstract: Opioid-induced respiratory depression (OIRD) deaths are ~80,000 a year in the US and are a major public health issue. Approximately 90% of fatal opioid-related deaths are due to synthetic opioids such as fentanyl, most of which is illicitly manufactured ... ...

Abstract	Opioid-induced respiratory depression (OIRD) deaths are ~80,000 a year in the US and are a major public health issue. Approximately 90% of fatal opioid-related deaths are due to synthetic opioids such as fentanyl, most of which is illicitly manufactured and distributed either on its own or as an adulterant to other drugs of abuse such as cocaine or methamphetamine. Other potent opioids such as nitazenes are also increasingly present in the illicit drug supply, and xylazine, a veterinary tranquilizer, is a prevalent additive to opioids and other drugs of abuse. Naloxone is the main treatment used to reverse OIRD and is available as nasal sprays, prefilled naloxone injection devices, and generic naloxone for injection. An overdose needs to be treated as soon as possible to avoid death, and synthetic opioids such as fentanyl are up to 50 times more potent than heroin, so the availability of new, higher-dose, 5-mg prefilled injection or 8-mg intranasal spray naloxone preparations are important additions for emergency treatment of OIRDs, especially by lay people in the community. Higher naloxone doses are expected to reverse a synthetic overdose more rapidly and the current formulations are ideal for use by untrained lay people in the community. There are potential concerns about severe withdrawal symptoms, or pulmonary edema from treatment with high-dose naloxone. However, from the perspective of first responders, the balance of risks would point to administration of naloxone at the dose required to combat the overdose where the risk of death is very high. The presence of xylazines as an adulterant complicates the treatment of OIRDs, as naloxone is probably ineffective, although it will reverse the respiratory depression due to the opioid. For these patients, hospitalization is particularly vital. Education about the benefits of naloxone remains important not only in informing people about how to treat emergency OIRDs but also how to obtain naloxone. A call to emergency services is also essential after administering naloxone because, although the patient may revive, they may overdose again later because of the short half-life of naloxone and the long-lasting potency of fentanyl and its analogs.
MeSH term(s)	Humans ; Naloxone/therapeutic use ; Analgesics, Opioid/adverse effects ; Narcotic Antagonists/therapeutic use ; Fentanyl/therapeutic use ; Heroin ; Drug Overdose/drug therapy
Chemical Substances	Naloxone (36B82AMQ7N) ; Analgesics, Opioid ; Narcotic Antagonists ; Fentanyl (UF599785JZ) ; Heroin (70D95007SX)
Language	English
Publishing date	2024-02-28
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2711781-9
ISSN	2296-2565 ; 2296-2565
ISSN (online)	2296-2565
ISSN	2296-2565
DOI	10.3389/fpubh.2024.1346109
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Article ; Online: Chromatin remodeling: a complex affair.

Gioacchini, Nathan / Peterson, Craig L

EMBO reports

2017 Volume 18, Issue 10, Page(s) 1673–1674

MeSH term(s)	Adenosine Triphosphate ; Chromatin ; Chromatin Assembly and Disassembly ; Nucleosomes
Chemical Substances	Chromatin ; Nucleosomes ; Adenosine Triphosphate (8L70Q75FXE)
Language	English
Publishing date	2017-08-23
Publishing country	England
Document type	Journal Article ; Comment
ZDB-ID	2020896-0
ISSN	1469-3178 ; 1469-221X
ISSN (online)	1469-3178
ISSN	1469-221X
DOI	10.15252/embr.201744852
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Zs.MG 41: Show issues

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