Quantifying constraint in the human mitochondrial genome DOI Creative Commons
Nicole J. Lake, Wei Liu, Stephanie L. Battle

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: Dec. 19, 2022

Abstract Mitochondrial DNA (mtDNA) has an important, yet often overlooked, role in health and disease. Constraint models quantify the removal of deleterious variation from population by selection, representing a powerful tool for identifying genetic underlying human phenotypes 1–4 . However, constraint model mtDNA not been developed, due to its unique features. Here we describe development mitochondrial application Genome Aggregation Database (gnomAD), large-scale dataset reporting across 56,434 humans 5 Our results demonstrate strong depletion expected variation, suggesting most variants remain undiscovered. To aid their identification, compute metrics every protein, tRNA, rRNA gene, revealing spectrum intolerance variation. We characterize constrained regions within genes via regional constraint, positions entire local showing enrichment pathogenic functionally critical sites, including topological clustering 3D protein RNA structures. Notably, identify at overlooked such as rRNAs non-coding regions. Lastly, how these can improve discovery rare common phenotypes.

Language: Английский

CellBouncer, A Unified Toolkit for Single-Cell Demultiplexing and Ambient RNA Analysis, Reveals Hominid Mitochondrial Incompatibilities DOI Creative Commons
Nathan K. Schaefer, Bryan J. Pavlovic, Alex A. Pollen

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: March 23, 2025

Pooled processing, in which cells from multiple sources are cultured or captured together, is an increasingly popular strategy for droplet-based single cell sequencing studies. This design allows efficient scaling of experiments, isolation cell-intrinsic differences, and mitigation batch effects. We present CellBouncer, a computational toolkit demultiplexing analyzing single-cell data pooled experiments. demonstrate that CellBouncer can separate quantify multi-species multi-individual mixtures, identify unknown mitochondrial haplotypes cells, assign treatments lipid-conjugated barcodes CRISPR sgRNAs, infer pool composition, outperforming existing methods. also introduce methods to ambient RNA contamination per cell, individual donors' contributions the pool, determine consensus doublet rate harmonized across types. Applying these tools tetraploid composite we competitive advantage human over chimpanzee mitochondria 10 fusion lines provide evidence inter-mitochondrial incompatibility mito-nuclear between species.

Language: Английский

Citations

0
Mitochondrial DNA signals driving immune responses: Why, How, Where? DOI Creative Commons
Luca Giordano, Sarah A. Ware, Claúdia Jacques Lagranha

et al.

Cell Communication and Signaling, Journal Year: 2025, Volume and Issue: 23(1)

Published: April 22, 2025

Abstract There has been a recent expansion in our understanding of DNA-sensing mechanisms. Mitochondrial dysfunction, oxidative and proteostatic stresses, instability impaired disposal nucleoids cause the release mitochondrial DNA (mtDNA) from mitochondria several human diseases, as well cell culture animal models. mislocalized to cytosol and/or extracellular compartments can trigger innate immune inflammation responses by binding receptors (DSRs). Here, we define features that make mtDNA highly immunogenic mechanisms its into compartments. We describe major DSRs bind such cyclic guanosine-monophosphate-adenosine-monophosphate synthase (cGAS), Z-DNA-binding protein 1 (ZBP1), NOD-, LRR-, PYD- domain-containing 3 receptor (NLRP3), absent melanoma 2 (AIM2) toll-like 9 (TLR9), their downstream signaling cascades. summarize key findings, novelties, gaps driving signal vascular, metabolic, kidney, lung, neurodegenerative viral bacterial infections. Finally, common strategies induce or inhibit propose challenges advance field.

Language: Английский

Citations

0
Nucleic acid sequence determinants of transcriptional pausing by human mitochondrial RNA polymerase (POLRMT) DOI Creative Commons
An Hsieh, Tatiana V. Mishanina

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: April 26, 2025

ABSTRACT Transcription by RNA polymerase (RNAP) lies at the heart of gene expression in all organisms. The speed with which RNAPs produce is tuned part signals transcribed nucleic-acid sequences, temporarily arrange into a paused conformation unable to extend RNA. In turn, altered transcription kinetics determines three-dimensional shape ultimately folds, dictates chromatin state, and promotes or inhibits co-transcriptional events. While pause sequence determinants have been characterized for multi-subunit bacteria eukaryotic nuclei, this information lacking single-subunit RNAP human mitochondria, POLRMT. Here, we developed robust scaffold system reconstitute POLRMT vitro identified multiple transcriptional sites on mitochondrial genomic (mtDNA). Using one sequences as representative, performed suite mutational studies pinpoint elements that enhance, weaken, completely abolish pausing. Finally, search mtDNA motif revealed predicted sites, potential roles processes.

Language: Английский

Citations

0
No role for nuclear transcription regulators in mammalian mitochondria? DOI Creative Commons
Diana Rubalcava-Gracia,

Rodolfo García-Villegas,

Nils‐Göran Larsson

et al.

Molecular Cell, Journal Year: 2022, Volume and Issue: 83(6), P. 832 - 842

Published: Sept. 30, 2022

Although the mammalian mtDNA transcription machinery is simple and resembles bacteriophage systems, there are many reports that nuclear regulators, as exemplified by MEF2D, MOF, PGC-1α, hormone receptors, imported into mitochondria directly interact with machinery. However, supporting experimental evidence for this concept open to alternate interpretations, a main issue difficulty in distinguishing indirect regulation of transcription, caused altered gene expression, from direct intramitochondrial effects. We provide critical discussion guidelines stringently assess roles factors implicated transcription.

Language: Английский

Citations

18
The molecular machinery for maturation of primary mtDNA transcripts DOI Creative Commons
Ana Vučković, Christoph Freyer, Anna Wredenberg

et al.

Human Molecular Genetics, Journal Year: 2024, Volume and Issue: 33(R1), P. R19 - R25

Published: May 22, 2024

Human mitochondria harbour a circular, polyploid genome (mtDNA) encoding 11 messenger RNAs (mRNAs), two ribosomal (rRNAs) and 22 transfer (tRNAs). Mitochondrial transcription produces long, polycistronic transcripts that span almost the entire length of genome, hence contain all three types RNAs. The primary then undergo number processing maturation steps, which constitute key regulatory points mitochondrial gene expression. first step RNA consists separation into individual, functional molecules can occur by distinct pathways. Both are carried out dedicated molecular machineries substantially differ from enzymes found elsewhere. As result, underlying mechanisms remain poorly understood. Over last years, genetic, biochemical structural studies have identified players involved in both pathways provided insights mechanisms. Here, we review our current understanding mammalian provide an outlook on open questions field.

Language: Английский

Citations

3
Mitochondrial adenine base editing of mouse somatic tissues via adeno-associated viral delivery DOI Open Access
Christian D. Mutti, Lindsey Van Haute, L. Gutiérrez

et al.

Published: March 4, 2025

The development of adenine base editing in mitochondria, alongside cytidine editing, has significantly expanded the genome engineering capabilities mitochondrial DNA. We tested recent advancements technology using optimised TALEs targeting genes Mt-Cytb, Mt-CoII and Mt-Atp6 mouse cells, observed successful A:T to G:C conversions within target windows each gene. Then, we used best performing pairs gene inject mice adeno-associated viral delivery post-mitotic tissue. limited efficiency edits somatic tissue after 4 weeks, suggesting necessity further optimisation this technology.

Language: Английский

Citations

0
Mitochondrial adenine base editing of mouse somatic tissues via adeno-associated viral delivery DOI Open Access
Christian D. Mutti, Lindsey Van Haute, L. Gutiérrez

et al.

Published: March 4, 2025

The development of adenine base editing in mitochondria, alongside cytidine editing, has significantly expanded the genome engineering capabilities mitochondrial DNA. We tested recent advancements technology using optimised TALEs targeting genes Mt-Cytb, Mt-CoII and Mt-Atp6 mouse cells, observed successful A:T to G:C conversions within target windows each gene. Then, we used best performing pairs gene inject mice adeno-associated viral delivery post-mitotic tissue. limited efficiency edits somatic tissue after 4 weeks, suggesting necessity further optimisation this technology.

Language: Английский

Citations

0
Central dogma rates in human mitochondria DOI
Erik McShane, L. Stirling Churchman

Human Molecular Genetics, Journal Year: 2024, Volume and Issue: 33(R1), P. R34 - R41

Published: May 22, 2024

In human cells, the nuclear and mitochondrial genomes engage in a complex interplay to produce dual-encoded oxidative phosphorylation (OXPHOS) complexes. The coordination of these dynamic gene expression processes is essential for producing matched amounts OXPHOS protein subunits. This review focuses on our current understanding central dogma rates, highlighting striking differences rates between genes. We synthesize coherent model kinetics, emerging principles emphasizing where more precise measurements would be beneficial. Such an pivotal grasping unique aspects function its role cellular energetics, it has profound implications aging, metabolic disorders, neurodegenerative diseases.

Language: Английский

Citations

3
Mechanisms and pathologies of human mitochondrial DNA replication and deletion formation DOI Creative Commons
Tiago Gomes, Amy E. Vincent, Katja E. Menger

et al.

Biochemical Journal, Journal Year: 2024, Volume and Issue: 481(11), P. 683 - 715

Published: May 28, 2024

Human mitochondria possess a multi-copy circular genome, mitochondrial DNA (mtDNA), that is essential for cellular energy metabolism. The number of copies mtDNA per cell, and their integrity, are maintained by nuclear-encoded replication repair machineries. Aberrant breakage believed to cause deletions within mtDNA. genomic location breakpoint sequences these show similar patterns across various inherited acquired diseases, also observed during normal ageing, suggesting common mechanism deletion formation. However, an ongoing debate over the which replicates has made it difficult develop clear testable models how rearrangements arise propagate at molecular level. These may impair metabolism if present in high proportion can be seen primary either sporadic cases or caused autosomal variants maintenance genes. diseases have diverse genetic causes multiple modes inheritance, notoriously broad clinical heterogeneity with complex tissue specificities, further makes establishing genotype-phenotype relationships challenging. In this review, we aim cover our current understanding human genome replicated, mechanisms lead instability form large-scale rearrangements, rearranged mtDNAs subsequently accumulate cells, pathological consequences when occurs.

Language: Английский

Citations

3
Two type I topoisomerases maintain DNA topology in human mitochondria DOI Creative Commons
Katja E. Menger, James Chapman, Héctor Díaz-Maldonado

et al.

Nucleic Acids Research, Journal Year: 2022, Volume and Issue: 50(19), P. 11154 - 11174

Published: Sept. 26, 2022

Abstract Genetic processes require the activity of multiple topoisomerases, essential enzymes that remove topological tension and intermolecular linkages in DNA. We have investigated subcellular localisation six human topoisomerases with a view to understanding maintenance mitochondrial Our results indicate mitochondria contain two TOP1MT TOP3A. Using molecular, genomic biochemical methods we find both proteins contribute mtDNA replication, addition decatenation role TOP3A, is stimulated by mtSSB. Loss TOP3A or also dysregulates gene expression, promote transcription elongation vitro. no evidence for TOP2 mitochondria, TOP2B knockout does not affect expression. suggest division labour between topology control required proper expression mtDNA.

Language: Английский

Citations

11