Transcription System Research Articles

Oxidative Stress in Genetic Cataract Formation

Background: Cataracts are the leading cause of blindness worldwide, and age-related cataracts are the result of environmental insults that largely lead to oxidative stress imposed on a genetic background that determines susceptibility to these stresses. Methods: A comprehensive literature review was performed to identify GWAS, targeted association studies, and TWAS that identified genes associated with age-related cataract. Additional genes associated with age-related cataracts were identified through the CAT-MAP online database. Pathway analysis was performed using Qiagen Ingenuity Pathway Analysis and pathways related to oxidative stress were analyzed using the same program. Results: A large number of genes have been identified as causes of both Mendelian and complex cataracts. Of these, 10 genes related to oxidative stress were identified, and all were associated with age-related cataracts. These genes fall into seven canonical pathways primarily related to glutathione metabolism and other pathways related to detoxifying reactive oxygen species. Conclusions: While a relatively small number of antioxidant related genes were identified as being associated with cataracts, they allow the identification of redox pathways important for lens metabolism and homeostasis. These are largely related to glutathione and its metabolism, other pathways for detoxification of reactive oxygen species, and the transcriptional systems that control their expression.

Electrochemiluminescence Biosensor for Ascorbic Acid Based on Target Transformation of Cell-Free RNA Transcription System and Duplex-Specific Nuclease-Assisted Recycling Amplification.

A cell-free RNA transcription system had been coupled with electrochemiluminescence (ECL) detection technology for the first time to develop an ascorbic acid (AA, acting as a model target) biosensor. The biosensor is composed of single-stranded DNA (ssDNA) sequences modified with alkynyl and azido groups, respectively, alongside an incomplete gene circuit framework. The addition of target AA and copper ions will cause the linkage of the two ssDNA sequences through a click chemistry reaction. This results in the subsequent reconstruction of a complete gene circuit. The reconstituted gene circuit, in conjunction with the T7 RNA polymerase, drives the transcription of substantial quantities of RNA. ssDNA labeled with ferrocene (Fc) (Fc-DNA) had been immobilized on a tris(2,2'-bipyridyl) ruthenium(II) chloride hexahydrate-doped SiO2 nanoparticle (Ru@SiO2 NPs) modified electrode first. The quenching effect of Fc on Ru@SiO2 causes the low ECL detected. The transcribed RNA sequence assisted double-stranded specific nuclease (DSN) to cut the ssDNA-Fc and the ECL of the system was enhanced. Optimal experimental conditions reveal that the ECL signal exhibits a linear correlation with the logarithmic concentration of AA, spanning a detection range from 100 nM to 1 mM, with a detection limit of 45 nM. This innovative methodology expands the utility of a cell-free RNA transcription system within the realm of biosensing applications.

Light-Activated Gene Expression System Using a Caging-Group-Free Photoactivatable Dye.

Optical regulation of transcription using chemical compounds is an effective strategy to manipulate gene expression spatiotemporally. Conventional caging approaches with photoremovable protecting groups may require intense UV-light exposure and release potentially toxic byproducts. To address these problems, here we developed a light-mediated transcriptional regulation system by combining a caging-group-free photoactivatable dye PaX560 and a multidrug-binding transcriptional regulator QacR. The cationic dye generated from PaX560 through traceless photoconversion bound QacR and reduced its repressor function, resulting in transcriptional activation. Importantly, this system allowed transcriptional activation with a large dynamic range under mild visible light exposure and simultaneous detection of the state of the photoactivated effector. This module was integrated into the T7 RNA polymerase expression system to demonstrate light-activated transcription in vitro and in living cells.

Mechanism of polyadenylation-independent RNA polymerase II termination.

The mechanisms underlying the initiation and elongation of RNA polymerase II (Pol II) transcription are well-studied, whereas termination remains poorly understood. Here we analyze the mechanism of polyadenylation-independent Pol II termination mediated by the yeast Sen1 helicase. Cryo-electron microscopy structures of two pretermination intermediates show that Sen1 binds to Pol II and uses its adenosine triphosphatase activity to pull on exiting RNA in the 5' direction. This is predicted to push Pol II forward, induce an unstable hypertranslocated state and destabilize the transcription bubble, thereby facilitating termination. This mechanism of transcription termination may be widely used because it is conceptually conserved in the bacterial transcription system.

Implementation of Real-Time Audio-to-Text Conversion and Processing for Seamless Transformation in Classroom Environment

In modern educational settings, ensuring that all students effectively comprehend lecture content is a significant challenge, particularly when language barriers and varying levels of cognitive processing ability come into play. Traditional classroom instruction often fails to accommodate the diverse needs of all learners, leading to gaps in understanding and academic performance. This research explores the implementation of a real-time audio transcription system as a solution to enhance classroom inclusivity and comprehension. By leveraging mobile technology, students can access live speech-to-text transcriptions of lectures directly on their devices. This system is designed to assist students who struggle with listening due to language differences, hearing impairments, or other cognitive challenges. The study delves into the technological framework of the transcription service, evaluating its accuracy, latency, and usability. It also considers the practical implications of integrating such technology into various classroom settings, from elementary schools to higher education institutions. Through surveys and interviews with students and teachers, the research assesses the impact of live transcription on student engagement, participation, and academic performance. Preliminary findings suggest that live audio transcription can significantly bridge the comprehension gap, offering a practical tool to foster a more inclusive and effective learning environment. Additionally, the study explores potential challenges and solutions for widespread implementation, aiming to provide a comprehensive analysis of the benefits and limitations of this innovative educational tool.

7587 The Estrogen Receptors and ARE/Nrf2 are Involved in Protecting Human Dermal Fibroblasts from Damage Caused by Mitochondrial Disfunction

Abstract Disclosure: A. Darawshe: None. A. Trachtenberg: None. Y. Sharoni: None. Skin ageing is influenced by several factors including environmental exposure and hormonal changes. Reactive oxygen species (ROS), which mediate many of the effects of these factors, can be formed by extrinsic factors, such as sun exposure, or can result from mitochondrial dysfunction as occurs during ageing. Several studies have shown the protective role of estrogens on skin health. The aim of the current study was to examine the damage to dermal fibroblasts by mitochondrially generated ROS, and to study the mechanism of the protective effects of estradiol. Rotenone, a complex I inhibitor, was used to cause mitochondrial dysfunction in human dermal fibroblasts and its effects on mitochondrial and cytosolic ROS levels, mitochondrial respiration, cell death, apoptosis, matrix metalloproteinase-1 (MMP1) and pro-collagen secretion were determined as markers of skin damage. Rotenone caused substantial reduction of respiration, followed by increased mitochondrial and cytosolic ROS which resulted in apoptotic cell death, increased MMP1 secretion and decreased collagen secretion. Pretreatment with estradiol recovered more than 50% of the respiratory activity, reduced mitochondrial and cytosolic ROS levels and MMP1 secretion and increased cell number and collagen secretion. These effects can be partially explained by a cooperative effect of estradiol and rotenone on Antioxidant Response Element (ARE/Nrf2) transcriptional activity, which leads to upregulation of antioxidant proteins such as NQO1 and Trxr1. To determine if estrogen receptors (ER) are involved in the protective effects, we used the ER inhibitor, Fulvestrant. This inhibitor, which completely inhibited ER Response Element reporter activity, partially prevented the protective effects of estradiol. The protective effects of estradiol were Similarly reduced by ML385 and Ochratoxin A, that are inhibitors of the ARE/Nrf2 transcription system. Incubating the cells with Fulvestrant and Ochratoxin A, which inhibit both pathways, completely blocked the protective effect of estradiol. These results suggest that the estrogen receptors and the ARE/Nrf2 signaling pathways are involved in the protective effects of estradiol against the damage caused by rotenone-induced mitochondria generated oxidative stress. Presentation: 6/3/2024

Targeting Hypoxia-Inducible Factor-1α in Pancreatic Cancer: siRNA Delivery Using Hyaluronic Acid-Displaying Nanoparticles

Background/Objectives: Conventional anticancer therapies often lack specificity, targeting both cancerous and normal cells, which reduces efficacy and leads to undesired off-target effects. An additional challenge is the presence of hypoxic regions in tumors, where the Hypoxia Inducible Factor (HIF) transcriptional system drives the expression of pro-survival and drug resistance genes, leading to radio- and chemo-resistance. This study aims to explore the efficacy of targeted nanoparticle (NP)-based small interfering RNA (siRNA) therapies in downregulating these genes to enhance treatment outcomes in pancreatic cancer, a tumor type characterized by high CD44 expression and hypoxia. Methods: We utilized hyaluronic acid (HA)-displaying nanoparticles composed of positively charged chitosan (CS) complexed with siRNA to target and knock down HIF-1α in pancreatic cancer cells. Two NP formulations were prepared using either low molecular weight (LMW) or high molecular weight (HMW) CS. These formulations were evaluated for their internalization by cells and their effectiveness in gene silencing, both in vitro and in vivo. Results: The study found that the molecular weight (MW) of CS influenced the interaction between HA and CD44, as well as the release of siRNA upon internalization. The LMW CS formulation shows faster uptake kinetics, while HMW CS is more effective in gene knockdown across different cell lines in vitro. In vivo, both were able to significantly knockdown HIF-1α and some of its downstream genes. Conclusions: The results suggest that HMW and LMW CS-based NPs exhibit distinct characteristics, showing that both MWs have potential for targeted pancreatic cancer therapy by influencing different aspects of delivery and gene silencing, particularly in the hypoxic tumor microenvironment.

Abstract 39: Tryptophan contributes to the sex-dependent loss of diurnal sodium excretion in BMAL1 knockout rats.

Kidney function is time-of-day-(TOD) dependent irrespective of light, sleep, activity, and meal timing. Recent discoveries reveal that diurnal (day/night) kidney function is maintained by an intrinsic molecular clock. We recently observed that loss of this transcriptional regulatory system impairs functional rhythms in electrolyte excretion in a novel rat model. When the core clock gene, brain and muscle ARNT-like protein 1 (BMAL1) is knocked out of Sprague-Dawley rats we now find that male, but not female, BMAL1 knockout (KO) rats no longer have diurnal changes in both glomerular filtration rate (GFR; Day:1.3±0.1 vs Night:1.2±0.1mL/min/100gBW;t-test p=0.919) along with sodium excretion (UNaV) (Day:819±58 vs Night:756±113 μmol/12h; t-test p=0.439) compared to littermate wildtype controls (CON; GFR Day:1.1±0.1 vs Night:1.6±0.1mL/min/100g; t-test p=0.044; UNaV Day: 849±138 vs Night:1423±102 μmol/12h; t-test p=0.003). LC/MS analysis of plasma from KO rats found that levels of tryptophan (trp) were significantly (2-way ANOVA p Interaction =0.847, p<span style="font-size:10.8333px">Genotype</span>=0.041, p TimeofDay =0.952) lower in KO males during the day (KO:77±6, CON:99±7μM; Sidak post-hoc p=0.049) but not night (KO:78±5, CON:99±12μM; Sidak post-hoc p=0.084) with no differences in plasma trp seen in KO females (Day:110±26,107±14μM vs Night:96±8,96±12μM KO and CON respectively). Trp had recently been shown to both regulate and be regulated by the circadian clock as well as increase GFR similar to other aromatic amino acids. This led us to hypothesize that TOD trp availability may underlie the changes seen in both UNaV and GFR in male KO rats. Therefore, we gave a single dose of trp (100 mg/kg,PO) at either 7pm (lights off, ZT12) or 7am (lights on, ZT0). After a 1 wk washout period, rats were dosed again in a crossover design. Male KO rats receiving trp at ZT0 had no significant change from baseline in UNaV (818±58 vs 784±61 μmol/12h) over the following 12hrs; however, a significant increase in UNaV (756±114 vs 1152±146 μmol/12h) following ZT12 dosing was observed (2-Way ANOVA p Interaction =0.038, p TrpTime =0.087, p TimeofDay =0.210; Sidak Post-Hoc: baseline vs ZT12 trp p=0.003) with no significant change seen in female KO or either male or female CON rats. Taken together these results suggest that BMAL1 is necessary for maintaining kidney physiologic rhythms in sodium excretion potentially through changes in trp availability.

ARE/Nrf2 Transcription System Involved in Carotenoid, Polyphenol, and Estradiol Protection from Rotenone-Induced Mitochondrial Oxidative Stress in Dermal Fibroblasts.

Skin aging is associated with the increased production of mitochondrial reactive oxygen species (mtROS) due to mitochondrial dysfunction, and various phytonutrients and estrogens have been shown to improve skin health. Thus, the aim of the current study was to examine damage to dermal fibroblasts by chemically induced mitochondrial dysfunction and to study the mechanism of the protective effects of carotenoids, polyphenols, and estradiol. Rotenone, a Complex I inhibitor, caused mitochondrial dysfunction in human dermal fibroblasts, substantially reducing respiration and ATP levels, followed by increased mitochondrial and cytosolic ROS, which resulted in apoptotic cell death, an increased number of senescent cells, increased matrix metalloproteinase-1 (MMP1) secretion, and decreased collagen secretion. Pre-treatment with carotenoid-rich tomato extracts, rosemary extract, and estradiol reversed these effects. These protective effects can be partially explained by a cooperative activation of antioxidant response element (ARE/Nrf2) transcriptional activity by the protective compounds and rotenone, which led to the upregulation of antioxidant proteins such as NQO1. To determine if ARE/Nrf2 activity is crucial for cell protection, we inhibited it using the Nrf2 inhibitors ML385 and ochratoxin A. This inhibition markedly reduced the protective effects of the test compounds by diminishing their effect to reduce cytosolic ROS. Our study results indicate that phytonutrients and estradiol protect skin cells from damage caused by mtROS, and thus may delay skin cell senescence and improve skin health.

Adenosine modifications impede SARS-CoV-2 RNA-dependent RNA transcription.

SARS-CoV-2, the causative virus of the COVID-19 pandemic, follows SARS and MERS as recent zoonotic coronaviruses causing severe respiratory illness and death in humans. The recurrent impact of zoonotic coronaviruses demands a better understanding of their fundamental molecular biochemistry. Nucleoside modifications, which modulate many steps of the RNA life cycle, have been found in SARS-CoV-2 RNA, although whether they confer a pro- or antiviral effect is unknown. Regardless, the viral RNA-dependent RNA polymerase will encounter these modifications as it transcribes through the viral genomic RNA. We investigated the functional consequences of nucleoside modification on the pre-steady state kinetics of SARS-CoV-2 RNA-dependent RNA transcription using an in vitro reconstituted transcription system with modified RNA templates. Our findings show that N 6-methyladenosine and 2'-O-methyladenosine modifications slow the rate of viral transcription at magnitudes specific to each modification, which has the potential to impact SARS-CoV-2 genome maintenance.

Design and construction of light-regulated gene transcription and protein translation systems in yeast P. Pastoris

IntroductionP. pastoris is a common host for effective biosynthesis of heterologous proteins as well as small molecules. Accurate regulation of gene transcription and protein synthesis is necessary to coordinate synthetic gene circuits and optimize cellular energy distribution. Traditional methanol or other inducible promoters, natural or engineered, have defects in either fermentation safety or expression capacity. The utilization of chemical inducers typically adds complexity to the product purification process, but there is no other well-controlled protein synthesis system than promoters yet. ObjectiveThe study aimed to address the aforementioned challenges by constructing light-regulated gene transcription and protein translation systems with excellent expression capacity and light sensitivity. MethodsTrans-acting factors were designed by linking the N. crassa blue-light sensor WC-1 with the activation domain of endogenous transcription factors. Light inducible or repressive promoters were then constructed through chimeric design of cis-elements (light-responsive elements, LREs) and endogenous promoters. Various configurations of trans-acting factor/LRE pairs, along with different LRE positions and copy numbers were tested for optimal promoter performance. In addition to transcription, a light-repressive translation system was constructed through the “rare codon brake” design. Rare codons were deliberately utilized to serve as brakes during protein synthesis, which were switched on and off through the light-regulated changes in the expression of the corresponding pLRE-tRNA. ResultsAs demonstrated with GFP, the light-inducible promoter 4pLRE-cPAOX1 was 70 % stronger than the constitutive promoter PGAP, with L/D ratio = 77. The light-repressive promoter PGAP-pLRE was strictly suppressed by light, with expression capacity comparable with PGAP in darkness. As for the light-repressive translation system, the “triple brake” design successfully eliminated leakage and achieved light repression on protein synthesis without any impact on mRNA expression. ConclusionThe newly designed light-regulated transcription and translation systems offer innovative tools that optimize the application of P. pastoris in biotechnology and synthetic biology.

Guide RNA structure design enables combinatorial CRISPRa programs for biosynthetic profiling

Engineering metabolism to efficiently produce chemicals from multi-step pathways requires optimizing multi-gene expression programs to achieve enzyme balance. CRISPR-Cas transcriptional control systems are emerging as important tools for programming multi-gene expression, but poor predictability of guide RNA folding can disrupt expression control. Here, we correlate efficacy of modified guide RNAs (scRNAs) for CRISPR activation (CRISPRa) in E. coli with a computational kinetic parameter describing scRNA folding rate into the active structure (rS = 0.8). This parameter also enables forward design of scRNAs, allowing us to design a system of three synthetic CRISPRa promoters that can orthogonally activate (>35-fold) expression of chosen outputs. Through combinatorial activation tuning, we profile a three-dimensional design space expressing two different biosynthetic pathways, demonstrating variable production of pteridine and human milk oligosaccharide products. This RNA design approach aids combinatorial optimization of metabolic pathways and may accelerate routine design of effective multi-gene regulation programs in bacterial hosts.

Automatic transcription system for parliamentary debates in the context of assembly of the republic of Portugal

The transcription of parliamentary proceedings is essential for democratic governance. Traditional methods are manual and time-consuming. This work introduces an Automatic Transcription System for the Assembly of the Republic of Portugal (STAAR) that uses an automatic speech recognition model and speaker diarization technologies. STAAR was developed after analyzing existing technologies and the Assembly’s specific needs, leading to an effective solution that integrates with current processes. STAAR stands out for its efficiency in transcribing debates and adapting to parliamentary language nuances. It significantly exceeded expectations by presenting a low transcription error rate, ranging from 1.7 to 11.3%, depending on the context and speech style, reducing the time required to produce the official parliamentary debates journal, and improving overall transcription efficiency. Additionally, STAAR enabled the transcription of previously undocumented parliamentary committee meetings, enhancing the documentation of parliamentary activities. This achievement marks a significant step in modernizing parliamentary processes, increasing transparency and accessibility of political information, and positions the Portuguese Parliament at the forefront of technological innovation in parliamentary debates transcription.

Cell-Free Translation Quantification via a Fluorescent Minihelix.

Cell-free gene expression systems are used in numerous applications, including medicine making, diagnostics, and educational kits. Accurate quantification of nonfluorescent proteins in these systems remains a challenge. To address this challenge, we report the adaptation and use of an optimized tetra-cysteine minihelix both as a fusion protein and as a standalone reporter with the FlAsH dye. The fluorescent reporter helix is short enough to be encoded on a primer pair to tag any protein of interest via PCR. Both the tagged protein and the standalone reporter can be detected quantitatively in real time or at the end of cell-free expression reactions with standard 96/384-well plate readers, an RT-qPCR system, or gel electrophoresis without the need for staining. The fluorescent signal is stable and correlates linearly with the protein concentration, enabling product quantification. We modified the reporter to study cell-free expression dynamics and engineered ribosome activity. We anticipate that the fluorescent minihelix reporter will facilitate efforts in engineering in vitro transcription and translation systems.

A Comparative Approach for Pronunciation Instruction in English

A tool is proposed to reinforce the pronunciation of vowels and consonants for the instruction of adult learners in Costa Rica. A critical review of literature on approaches to teaching vowels and consonants is followed by a comparative discussion of two transcription systems: that of the International Phonetic Association, and those found in textbooks, dictionaries and pronunciation websites. This is complemented by a brief comparison of English and Spanish vowels and consonants, and descriptions of common pronunciation challenges for Spanish speakers. Open problems are explored, as are ethical reflections on the teaching of English pronunciation.

Aptamer and Thiol Co-Regulated Color-Shifting Fluorophores via Dynamic Through-Bond/Space Conjugation for Constructing Ratiometric RNA Sensor.

Fluorophores with color-shifting characteristics have attracted enormous research interest in the quantitative application of RNA sensors. It reports here a simple synthesis, luminescent properties, and co-transcription ability of de-conjugated triphenylmethane leucomalachite green (LMG). This novel clusteroluminescence fluorophore is rapidly synthesized from malachite green (MG) in reductive transcription system containing dithiothreitol, emitting fluorescence in the UV region through space conjugation. The co-transcribed MG RNA aptamer (MGA) bound to the ligand, resulting in red fluorescence from the through-bond conjugation. Given the equilibrated color-shifting fluorophores, they are rationally employed in a 3WJ-based rolling circle transcription switch, with the target-aptamer acting as an activator to achieve steric allosterism. This one-pot system allows the target to compete continuously for allosteric sites, and the activated transcription switches continue to amplify MGA forward, achieving accurate Aflatoxin 1 quantification at the picomolar level in 1h. Due to the programmability of this RNA sensor, the design method of target-competitive aptamers is standardized, making it universally applicable.

Strategies to Reduce Promoter-Independent Transcription of DNA Nanostructures and Strand Displacement Complexes.

Bacteriophage RNA polymerases, in particular T7 RNA polymerase (RNAP), are well-characterized and popular enzymes for many RNA applications in biotechnology both in vitro and in cellular settings. These monomeric polymerases are relatively inexpensive and have high transcription rates and processivity to quickly produce large quantities of RNA. T7 RNAP also has high promoter-specificity on double-stranded DNA (dsDNA) such that it only initiates transcription downstream of its 17-base promoter site on dsDNA templates. However, there are many promoter-independent T7 RNAP transcription reactions involving transcription initiation in regions of single-stranded DNA (ssDNA) that have been reported and characterized. These promoter-independent transcription reactions are important to consider when using T7 RNAP transcriptional systems for DNA nanotechnology and DNA computing applications, in which ssDNA domains often stabilize, organize, and functionalize DNA nanostructures and facilitate strand displacement reactions. Here we review the existing literature on promoter-independent transcription by bacteriophage RNA polymerases with a specific focus on T7 RNAP, and provide examples of how promoter-independent reactions can disrupt the functionality of DNA strand displacement circuit components and alter the stability and functionality of DNA-based materials. We then highlight design strategies for DNA nanotechnology applications that can mitigate the effects of promoter-independent T7 RNAP transcription. The design strategies we present should have an immediate impact by increasing the rate of success of using T7 RNAP for applications in DNA nanotechnology and DNA computing.

Novel transcription and replication-competent virus-like particles system modelling the Nipah virus life cycle

ABSTRACT Nipah virus (NiV), a highly pathogenic Henipavirus in humans, has been responsible for annual outbreaks in recent years. Experiments involving live NiV are highly restricted to biosafety level 4 (BSL-4) laboratories, which impedes NiV research. In this study, we developed transcription and replication-competent NiV-like particles (trVLP-NiV) lacking N, P, and L genes. This trVLP-NiV exhibited the ability to infect and continuously passage in cells ectopically expressing N, P, and L proteins while maintaining stable genetic characteristics. Moreover, the trVLP-NiV displayed a favourable safety profile in hamsters. Using the system, we found the NiV nucleoprotein residues interacting with viral RNA backbone affected viral replication in opposite patterns. This engineered system was sensitive to well-established antiviral drugs, innate host antiviral factors, and neutralizing antibodies. We then established a high-throughput screening platform utilizing the trVLP-NiV, leading to the identification of tunicamycin as a potential anti-NiV compound. Evidence showed that tunicamycin inhibited NiV replication by decreasing the infectivity of progeny virions. In conclusion, this trVLP-NiV system provided a convenient and versatile molecular tool for investigating NiV molecular biology and conducting antiviral drug screening under BSL-2 conditions. Its application will contribute to the development of medical countermeasures against NiV infections.

Advanced methods for gene network identification and noise decomposition from single-cell data

Central to analyzing noisy gene expression systems is solving the Chemical Master Equation (CME), which characterizes the probability evolution of the reacting species’ copy numbers. Solving CMEs for high-dimensional systems suffers from the curse of dimensionality. Here, we propose a computational method for improved scalability through a divide-and-conquer strategy that optimally decomposes the whole system into a leader system and several conditionally independent follower subsystems. The CME is solved by combining Monte Carlo estimation for the leader system with stochastic filtering procedures for the follower subsystems. We demonstrate this method with high-dimensional numerical examples and apply it to identify a yeast transcription system at the single-cell resolution, leveraging mRNA time-course experimental data. The identification results enable an accurate examination of the heterogeneity in rate parameters among isogenic cells. To validate this result, we develop a noise decomposition technique exploiting time-course data but requiring no supplementary components, e.g., dual-reporters.

An updated compendium and reevaluation of the evidence for nuclear transcription factor occupancy over the mitochondrial genome.

In most eukaryotes, mitochondrial organelles contain their own genome, usually circular, which is the remnant of the genome of the ancestral bacterial endosymbiont that gave rise to modern mitochondria. Mitochondrial genomes are dramatically reduced in their gene content due to the process of endosymbiotic gene transfer to the nucleus; as a result most mitochondrial proteins are encoded in the nucleus and imported into mitochondria. This includes the components of the dedicated mitochondrial transcription and replication systems and regulatory factors, which are entirely distinct from the information processing systems in the nucleus. However, since the 1990s several nuclear transcription factors have been reported to act in mitochondria, and previously we identified 8 human and 3 mouse transcription factors (TFs) with strong localized enrichment over the mitochondrial genome using ChIP-seq (Chromatin Immunoprecipitation) datasets from the second phase of the ENCODE (Encyclopedia of DNA Elements) Project Consortium. Here, we analyze the greatly expanded in the intervening decade ENCODE compendium of TF ChIP-seq datasets (a total of 6,153 ChIP experiments for 942 proteins, of which 763 are sequence-specific TFs) combined with interpretative deep learning models of TF occupancy to create a comprehensive compendium of nuclear TFs that show evidence of association with the mitochondrial genome. We find some evidence for chrM occupancy for 50 nuclear TFs and two other proteins, with bZIP TFs emerging as most likely to be playing a role in mitochondria. However, we also observe that in cases where the same TF has been assayed with multiple antibodies and ChIP protocols, evidence for its chrM occupancy is not always reproducible. In the light of these findings, we discuss the evidential criteria for establishing chrM occupancy and reevaluate the overall compendium of putative mitochondrial-acting nuclear TFs.