Base by Base

️ Episode 174: TMEM217–SLC9C1: Wiring the cAMP Switch for Sperm Motility and Male Fertility In this episode of PaperCast Base by Base, we explore a PNAS study revealing how TMEM217 forms a complex with the sperm-specific Na+/H+ exchanger SLC9C1 to organize cAMP signaling, sustain motility, and enable fertilization in mice. Study Highlights:Using phylogenetic profiling and interactomics, the authors identified TMEM217 as a conserved partner of the exchanger SLC9C1 and showed that both proteins localize to the principal piece of the sperm flagellum. Knockout of Tmem217 produced severe motility defects and infertility with hairpin flagellar bending, accompanied by loss of SLC9C1 and full-length soluble adenylyl cyclase, reduced cAMP levels, and dampened PKA and tyrosine phosphorylation. Co-immunoprecipitation and AlphaFold3 modeling demonstrated that TMEM217 binds the voltage-sensing domain of SLC9C1, supporting a mechanism that assembles the SLC9C1–sAC–cAMP axis during spermiogenesis. Pharmacologic boosting of cAMP paired with membrane-conditioning media restored motility and fertilization in vitro, yielding viable offspring after embryo transfer. Conclusion:Dissecting the TMEM217–SLC9C1 interface and local cAMP control suggests diagnostics and mutation-agnostic therapeutic strategies for asthenozoospermia and male infertility. Reference:Iida-Norita R, Miyata H, Ninomiya A, Emori C, Kamoshita M, Pan C, Wang H, Ikawa M. Formation of a complex between TMEM217 and the sodium-proton exchanger SLC9C1 is crucial for mouse sperm motility and male fertility. Proceedings of the National Academy of Sciences. 2025;122(42):e2513924122. https://doi.org/10.1073/pnas.2513924122 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.castos.com/ Chapters (00:00:00) - The mystery of athenosomes(00:02:00) - How SLC9C1 regulates sperm motility(00:06:43) - Knockout SLC9C1(00:11:08) - TMP 217 restores sperm to full function(00:12:35) - Immunity of TMM217 in mammalian sperm(00:16:03) - Base by base science

️ Episode 163: Animal origins: looping back in time In this episode of PaperCast Base by Base, we explore how chromatin folding mechanisms emerged alongside animal evolution, focusing on a Spotlight article that synthesizes high-resolution 3D genome maps across unicellular relatives of animals and early-branching metazoans to probe when enhancer–promoter looping first appeared. Study Highlights:This Spotlight reviews evidence from micro-C datasets spanning ichthyosporeans, filastereans, choanoflagellates, sponges, ctenophores, placozoans, and cnidarians, showing that broad A/B-like chromatin compartments and, crucially, enhancer–promoter chromatin loops are features that arise within animals rather than in their unicellular relatives. It emphasizes that loops are readily detected in early metazoans such as ctenophores, placozoans, and cnidarians, while sponges show weaker or absent looping signals, hinting at lineage-specific trajectories or possible secondary loss. The article highlights unusual promoter hubs in placozoans, where hundreds of transcription start sites cluster, potentially coordinating housekeeping expression programs. Mechanistically, ctenophores appear to use abundant C2H2 zinc-finger proteins that bind unmethylated motifs at loop anchors, suggesting alternative loop-formation strategies distinct from the CTCF-driven loop extrusion and insulated TAD architecture characterized in vertebrates. Together, these observations argue that chromatin loops emerged with complex gene regulation in animals and diversified across lineages instead of following a single universal mechanism. Conclusion:Chromatin looping likely originated at the dawn of animal life and diversified across lineages, underpinning the rise of complex gene regulation before the canonical, CTCF-insulated TAD architecture seen in many bilaterians. Reference:Matar, O., & Marlétaz, F. (2025). Animal origins: looping back in time. Trends in Genetics. https://doi.org/10.1016/j.tig.2025.06.013 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.castos.com/ Episode Slug: animal-origins-looping-back-in-time Keywords: chromatin loops; animal evolution; Micro-C; ctenophores; enhancer–promoter interactions

️ Episode 173: Bottlebrush Block Copolymer Shields Muscles and Prevents DMD Onset In this episode of PaperCast Base by Base, we explore a PNAS study showing how a synthetic bottlebrush block copolymer can act as a powerful membrane stabilizer to protect dystrophin-deficient muscle in Duchenne muscular dystrophy. Study Highlights:Researchers engineered and tested an amphiphilic bottlebrush diblock polymer, B–PEO43_10–PPO15_5, as a membrane stabilizer in the mdx mouse model of Duchenne muscular dystrophy. At nanomolar doses, the polymer rapidly restored twitch contractility in single dystrophin‑deficient fibers and showed ~150,000‑fold greater potency than optimized linear PEO–PPO copolymers. Early systemic dosing from postnatal day 1 to 21 prevented the surge of serum creatine kinase and blocked histologic hallmarks of damage in tibialis anterior and diaphragm while routine liver and kidney panels remained normal. In adult mice, pretreatment prevented IgG entry into myocardium during isoproterenol stress and significantly improved survival during combined handling and β‑adrenergic stress tests. Conclusion:This work positions bottlebrush block copolymers as fast‑acting, mutation‑agnostic membrane stabilizers with potential to preserve skeletal, respiratory, and cardiac muscle when deployed early and to complement gene‑based therapies. Reference:Cohen H, Bez Batti Angulski A, Quick JD, Kuebler TS, Thompson BR, Bauer J, Hahn D, Townsend D, Hassler JF, Hackel BJ, Lodge TP, Sham YY, Bates FS, Metzger JM. Synthetic bottlebrush block copolymer prevents disease onset in Duchenne muscular dystrophy. Proceedings of the National Academy of Sciences. 2025;122(42):e2513599122. https://doi.org/10.1073/pnas.2513599122 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.castos.com/ Chapters (00:00:00) - Duchenne Muscular Dystrophy: Chemical repair(00:02:37) - Synthetic Polymers to stabilize muscle membranes in DC motor dys(00:07:40) - Heart failure in MDX mice(00:08:48) - Bottle Brush Polymer(00:12:58) - Bottle Brush polymer(00:18:14) - Deep Dive: Synthetic polymer fixes dystrophic muscle disease(00:19:31) - Thinking beyond biological replacement to physical synthetic replacement

️ Episode 172: When Random DNA Fights Back: De Novo Gene Birth as Antiphage Defense In this episode of PaperCast Base by Base, we explore a PNAS study showing that short, previously nongenic DNA sequences can quickly evolve into genes that help bacteria survive phage attack, illuminating early steps of gene birth and the host–virus arms race. fileciteturn2file0 Study Highlights:The authors screened two massive libraries totaling ~100 million (semi-)random open reading frames in Escherichia coli and recovered thousands of sequences that improved survival during T4 phage challenge. A set of short proteins, dubbed Random Inhibitors of Phage infection (Rips), broadly protected cells by activating the Rcs envelope-stress pathway and triggering colanic-acid capsule production that physically blocks adsorption. A second class of hits, Random T4 Inhibitor Products (rtp1–4), acted with specificity by reducing expression of the OmpC outer-membrane receptor, thereby limiting T4 and other OmpC-dependent phage entry; for some rtp genes the protective molecule was RNA rather than protein. Transcriptomics, reporter assays, and adsorption measurements supported these mechanisms while showing minimal growth penalties, and evolved T4 variants rapidly gained baseplate mutations that restored adsorption and infectivity. Conclusion:Random sequence space harbors many routes to immediate fitness gains, with de novo protein- and RNA-based functions rewiring bacterial envelopes and receptors in ways that both reveal mechanisms of gene birth and suggest new antiphage strategies. Reference:Frumkin I, Vassallo CN, Chen YH, Laub MT. Emergence of antiphage functions from random sequence libraries reveals mechanisms of gene birth. Proceedings of the National Academy of Sciences. 2025;122(42):e2513255122. https://doi.org/10.1073/pnas.2513255122 fileciteturn2file0 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.castos.com/ Chapters (00:00:14) - Deep Dive: The mystery of gene birth and evolution(00:03:08) - De novo gene birth(00:06:31) - Random but effective phage protection(00:11:03) - Random sequences stop the T4 phage(00:16:27) - The evolutionary process of the phage(00:18:20) - Inventing new microbes: The origins of novelty

️ Episode 171: Virulence Hierarchies in the Tuberculosis Complex—What Makes Some Lineages Deadlier? In this episode of PaperCast Base by Base, we explore a new PNAS study that directly compares the virulence of Mycobacterium tuberculosis, M. bovis, and M. orygis across natural and laboratory hosts to uncover why animal-adapted lineages can be so devastating. Study Highlights:The authors performed side-by-side infections in Holstein calves and C57BL/6 mice, showing that M. bovis and M. orygis consistently caused more severe disease, faster mortality, and higher bacterial burdens than M. tuberculosis. Comparative proteomics identified ESAT‑6/CFP‑10 and the SigK‑regulated antigen MPT70 as prominent secreted factors in animal-adapted lineages, and gene deletions reversed the lethal phenotype for M. bovis but not for M. orygis. Disease outcomes depended on infection route and immune history, with oral priming, BCG vaccination, and a multisubunit vaccine (H107e) markedly prolonging survival after aerosol challenge. Together, the data establish a clear virulence hierarchy within the MTBC and point to lineage‑informed antigen choices for future vaccines and control strategies. Conclusion:Animal-adapted MTBC members can be hypervirulent compared with M. tuberculosis, and their distinct antigenic profiles and route‑dependent biology offer actionable clues for next‑generation zoonotic and human TB vaccines. Reference:Danchuk SN, Duffy SC, Sullivan J, Rufai SB, McIntosh FA, Lupien A, Harrison LB, et al. Virulence hierarchies within the Mycobacterium tuberculosis complex. Proceedings of the National Academy of Sciences. 2025;122(42):e2507104122. https://doi.org/10.1073/pnas.2507104122 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.castos.com/ Chapters (00:00:00) - Virulence hierarchies within the Mycobacterium Tu(00:03:17) - Fighting mbovin in the calf(00:06:05) - M. Bovis vs Amorgis TB pathogenesis(00:09:58) - MTBC virulence and the big mystery(00:11:52) - Immunity studies of human TB(00:13:48) - Animal-adapted TB

️ Episode 170: Maternal Age, Meiotic Recombination Failure, and Triploidy in Humans In this episode of PaperCast Base by Base, we explore how maternal age and failures of meiotic recombination shape the origins of triploid conceptions in humans, drawing on large-scale preimplantation genetic testing datasets from ICSI-derived embryos. Study Highlights:Drawing on 96,660 embryo biopsies with an independent validation cohort of 44,324, the authors quantify the burden of ploidy-level abnormalities in ICSI-derived blastocysts and show that triploidy is about five times more frequent than haploidy at the blastocyst stage. Genotyping and sex-chromosome modeling reveal that nearly all triploid embryos arise from maternal errors, with about one third originating in meiosis I and two thirds in meiosis II, while most haploid embryos reflect loss of the paternal genome. Analysis of parental trios uncovers an unexpected subset of triploid embryos with genome-wide absence of crossovers, indicating a failure to initiate meiotic recombination during oogenesis and implying that such oocytes can still reach ovulation. Maternal age shows a positive, significant association with triploidy/haploidy risk, and the study also identifies rare recombinant maternal isodiploidy among otherwise 46,XX embryos. Evidence of recurrence in a small fraction of couples suggests that beyond age, individual predisposition can elevate the risk of polyploid conceptions. Conclusion:These findings refine the mechanistic picture of human triploidy by linking maternal age and recombination failure to diploid oocyte formation, with practical implications for risk counseling and embryo assessment in reproductive genetics. Reference:Picchetta L, Ottolini CS, Tao X, Zhan Y, Jobanputra V, Marin Vallejo C, Mulas F, Paraboschi EM, Escribá Pérez MJ, Molinaro T, Whitehead C, Gill P, Mounts E, Babariya D, Rienzi LF, Ubaldi FM, Garcia-Velasco JA, Pellicer A, Carmi S, Hoffmann ER, Capalbo A. Maternal age and genome-wide failure of meiotic recombination are associated with triploid conceptions in humans. The American Journal of Human Genetics. 2025;112:1–14. https://doi.org/10.1016/j.ajhg.2025.09.014 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.castos.com/

️ Episode 169: Deep mutational scanning of the insulin receptor guides precision therapy for insulin resistance In this episode of PaperCast Base by Base, we explore how a comprehensive deep mutational scan of the human insulin receptor ectodomain maps the effects of ~14,000 missense variants on surface expression, insulin binding, and downstream signalling, creating a sequence–function atlas to improve diagnosis and treatment of severe insulin resistance. Study Highlights:The authors constructed a saturation mutagenesis library across residues 28–955 of INSR and used barcoded, pooled cell-based assays to quantify variant effects on receptor expression, insulin or antibody binding, and maximal AKT phosphorylation in response to insulin. Results pinpointed site 1 residues, including the αCT helix and L1 domain, as highly sensitive to mutation for insulin binding, and revealed regions where signalling is disproportionately impaired relative to binding, consistent with spare receptor behavior. The atlas showed strong concordance with known pathogenic variants and reclassified many variants of uncertain significance by linking function scores to clinical phenotypes across Donohue syndrome, Rabson–Mendenhall syndrome, and Type A insulin resistance. Importantly, the screen identified hundreds of loss‑of‑insulin‑response variants that remain selectively activatable by anti‑INSR monoclonal antibodies, nominating patients who may benefit from non‑canonical receptor agonists and highlighting distinct structural hotspots of antibody sensitivity. Conclusion:This multidimensional INSR variant map refines genetic interpretation, illuminates receptor structure–function relationships, and enables precision stratification for future antibody‑based therapies in extreme insulin resistance. Reference:Aslanzadeh V, Brierley GV, Kumar R, Çubuk H, Vigouroux C, Matreyek KA, Kudla G, Semple RK. Deep mutational scanning of the human insulin receptor ectodomain to inform precision therapy for insulin resistance. Nature Communications. 2025;16:9143. https://doi.org/10.1038/s41467-025-64178-4 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.castos.com/   On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

️ Episode 168: Low circulating miR-190a-5p predicts progression of chronic kidney disease In this episode of PaperCast Base by Base, we explore how unbiased small RNA sequencing and multi-cohort validation identify circulating miR-190a-5p as a prognostic marker of chronic kidney disease that reflects tubular health and points to a potential therapeutic strategy. Study Highlights:Using small RNA-sequencing of plasma from people with and without CKD in the context of type 2 diabetes, the authors found miR-190a-5p to be significantly reduced in those with impaired kidney function.In an independent prospective CKD cohort, lower serum miR-190a-5p predicted progression among patients with none to moderate albuminuria and improved risk prediction when added to standard clinical variables.Kidney biopsy analyses showed that tissue miR-190a-5p correlates with circulating levels, estimated GFR, and tubular epithelial mass, and inversely with interstitial fibrosis, with expression enriched in proximal tubules.In mouse models, restoring miR-190a-5p reduced tubular injury and fibrosis and repressed ADAM10 expression, supporting a mechanistic role for miR-190a-5p in maintaining tubular cell health. Conclusion:miR-190a-5p emerges as a tubular-derived biomarker that enhances prognostication in CKD with low–moderate proteinuria and represents a promising candidate for miRNA-mimic therapy development. Reference:Baird DP, Zang J, Connor KL, Teenan O, Reck M, Cairns C, Sutherland C, Bell RMB, Traynor JP, Wong R, Ferenbach DA, Hughes J, Mark PB, Maxwell AP, McKay GJ, Simpson DA, Conway BR, Denby L. Low circulating miR-190a-5p predicts progression of chronic kidney disease. Nature Communications. 2025;16:9154. https://doi.org/10.1038/s41467-025-64168-6 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.castos.com/

️ Episode 167: DeepScence: Detecting Senescent Cells at Single-Cell and Spatial Resolution In this episode of PaperCast Base by Base, we explore a Cell Genomics study introducing DeepScence, a deep-learning autoencoder that leverages a compact “CoreScence” gene set to identify senescent cells across single-cell and spatial transcriptomics data, outperforming marker- and gene set–based approaches. Study Highlights:The authors systematically compared nine published senescence gene sets and distilled a consensus 39‑gene CoreScence panel that is consistently associated with senescence across tissues and conditions. DeepScence models expression counts with a zero‑inflated negative binomial autoencoder whose bottleneck separates senescence‑related signal from unrelated variation and outputs a continuous senescence score that can be optionally binarized. Benchmarking on multiple in vitro and in vivo single‑cell datasets shows that DeepScence achieves higher AUROCs than competing methods, and its scores track experimentally validated enrichment of senescent cells in disease or injury contexts. The method generalizes to spatial platforms including Visium and simulated Xenium panels, retaining strong performance with small targeted panels and across species and tissue types. Conclusion:By centering analysis on a robust core signature and a modality‑aware autoencoder, DeepScence provides a scalable, cross‑platform way to map senescent cells and accelerate aging and disease research. Reference:Qu Y, Ji B, Dong R, Gu L, Chan C, Xie J, Glass C, Wang X‑F, Nixon AB, Ji Z. Single‑cell and spatial detection of senescent cells using DeepScence. Cell Genomics. 2025;5:101035. https://doi.org/10.1016/j.xgen.2025.101035 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.castos.com/ On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

️ Episode 166: Molecular Squeezing: How Coronin, Cofilin, and AIP1 Rapidly Disassemble Actin Filaments In this episode of PaperCast Base by Base, we explore a Cell study that uses single-particle cryo-EM to reveal the stepwise, synergistic mechanism by which coronin, cofilin, and AIP1 drive rapid actin filament disassembly in eukaryotic cells. Study Highlights:The authors solve a series of cryo-EM structures showing that coronin binds cooperatively to F-actin, opens a molecular backdoor to accelerate inorganic phosphate release, and undertwists the filament to prime it for cofilin binding. Cofilin then binds in a strand-restricted cooperative manner that converts subunits to a C-actin state and sterically displaces coronin without immediately severing the filament. AIP1 recognizes the cofilactin platform and triggers severing via a clamp-like molecular squeezing mechanism while remaining at the barbed end to cap it. This structural choreography explains how rapid filament turnover can occur at high cellular cofilin concentrations and clarifies the distinct roles of each factor in actin dynamics. Conclusion:By redefining AIP1 as the severing effector acting on cofilactin while capping the barbed end, the work provides a unifying structural model for fast actin network disassembly and points to testable predictions for reconstituted and cellular systems. Reference:Oosterheert W, Boiero Sanders M, Hofnagel O, Bieling P, Raunser S. Choreography of rapid actin filament disassembly by coronin, cofilin, and AIP1. Cell. 2025;188:1–16. https://doi.org/10.1016/j.cell.2025.09.016 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.castos.com/ On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics. 

️ Episode 165: Protist Genomics: Key to Understanding Eukaryotic Evolution In this episode of PaperCast Base by Base, we explore how accelerating protist genomics—spanning single-cell approaches, metagenomics, and long-read assemblies—unlocks deep insights into eukaryotic evolution, symbiosis, organelle origins, ecosystem dynamics, and the methodological shifts needed to go beyond plant/animal-centric standards. Study Highlights:This review argues that protists encompass most eukaryotic diversity yet remain severely underrepresented in genome databases, creating blind spots in phylogenomics and models of eukaryotic evolution. It synthesizes emerging wet-lab and computational strategies—such as FACS-enabled single-cell sequencing, nuclei extraction for high-molecular-weight DNA, and long-read plus Hi-C scaffolding—to recover genomes from uncultured and symbiotic taxa. The authors emphasize tailored decontamination and annotation pipelines, taxon-specific BUSCO core sets, and the value of releasing intermediate-quality assemblies to bootstrap reference databases. The article connects genomic advances to big-picture questions including endosymbiosis, repeated origins of multicellularity, terrestrialization, and the roles of protists in biogeochemical cycles and community networks. Conclusion:Centering protist diversity in genome initiatives, and embracing fit-for-purpose standards and pipelines, will rapidly expand high-quality resources and transform our understanding of eukaryotic cell evolution and ecosystem function. Reference:Schoenle A, Francis O, Archibald JM, Burki F, de Vries J, Dumack K, Eme L, Florent I, Hehenberger E, Hoffmeyer TT, Irisarri I, Lara E, Leger MM, Lukeš J, Massana R, Mathur V, Nitsche F, Strassert JFH, Worden AZ, Yurchenko V, del Campo J, Waldvogel A-M. Protist genomics: key to understanding eukaryotic evolution. Trends in Genetics. 2025. https://doi.org/10.1016/j.tig.2025.05.004 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.castos.com/

️ Episode 164: m6A in the coding sequence: linking deposition, translation, and decay In this episode of PaperCast Base by Base, we explore how N6-methyladenosine (m6A) marks within coding sequences orchestrate a fast, translation-coupled route to mRNA decay, and how splicing- and chromatin-linked mechanisms shape where those marks are placed across transcripts. Study Highlights:The authors synthesize recent mapping and mechanistic studies to show that exon-junction complexes restrict METTL3 activity in coding regions, helping define the mature m6A landscape. They describe CDS–m6A decay (CMD), a translation-dependent pathway in which m6A within A-site codons slows decoding, triggers ribosome pausing and collisions, and accelerates selective mRNA degradation. They integrate evidence that CMD targets are enriched in P-bodies and may interface with decapping machinery, while also noting that reader proteins such as YTHDFs and tRNA modifications like mcm5s2U modulate the strength of pausing and decay. They further discuss how deposition timing spans co- and post-transcriptional windows, with transcription dynamics, histone marks, and nuclear retention fine-tuning site selection and stoichiometry. Finally, they highlight physiological links, including regulation of developmentally important transcripts and potential relevance to cancer biology and METTL3-targeted therapeutics. Conclusion:CDS-localized m6A acts as a precise switch that couples translation dynamics to rapid mRNA turnover, offering new levers to tune gene expression and potential therapeutic entry points in disease. Reference:Ćorović M, Hoch-Kraft P, Zhou Y, Hallstein S, König J, Zarnack K (2025). m6A in the coding sequence: linking deposition, translation, and decay. Trends in Genetics. https://doi.org/10.1016/j.tig.2025.06.002 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.castos.com/

️ Episode 162: Spatially Resolved microRNA Expression in Tissues: Technologies, Challenges, and Opportunities In this episode of PaperCast Base by Base, we explore how emerging “spatial miRNomics” methods map microRNA expression directly within intact tissues, revealing cell- and region-specific regulatory patterns that bulk and even single-cell assays can miss. Study Highlights:This review charts the field from established singleplex imaging with LNA probes and miRNAscope to early multiplex strategies and sequencing-based workflows that add poly(A) tails in situ to capture small RNAs. It explains how spatial total RNA sequencing (STRS) and Patho-DBiT adapt commercial spatial transcriptomics to detect miRNAs, reporting tissue- and disease-specific signatures in FFPE and fresh-frozen samples. The authors detail fixation chemistry, probe design, and sensitivity constraints unique to short RNAs, and they outline bioinformatic needs including isomiR-aware alignment, rRNA depletion strategies, and target-based activity inference such as miTEA‑HiRes. They close with a roadmap to scale from low-plex detection toward omics-level profiling and clinical translation across oncology, neurology, cardiology, and immune pathology. Conclusion:Spatial miRNomics is poised to unlock the location-specific layer of post-transcriptional regulation, but robust chemistry, higher multiplexing, single-cell resolution, and standardized pipelines are essential for clinical impact. Reference:Robles‑Remacho, A., Zou, Y., Grillo, M., & Nilsson, M. (2025). Spatially resolved microRNA expression in tissues: technologies, challenges, and opportunities. Trends in Genetics. https://doi.org/10.1016/j.tig.2025.06.005 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.castos.com/

️ Episode 161: Decoding Genomic Landscapes of Introgression In this episode of PaperCast Base by Base, we explore how modern population genetics dissects the genomic footprints of introgression across species, reviewing summary statistic approaches, probabilistic modeling, and supervised learning, and showing how these methods reveal adaptive and ghost introgression and the functional roles of introgressed loci. Study Highlights:The authors organize the field into three complementary pillars: summary statistics for fast exploratory scans, probabilistic models for principled inference of local ancestry and selection, and supervised deep learning for scalable, high‑resolution predictions. They explain why windowed statistics such as fd, df, and fdM improve on D for localizing introgressed loci and how methods like S*, S′, and topology weighting tackle ghost introgression and gene‑tree discordance. They show that probabilistic tools including IBDmix, VolcanoFinder, HMM‑based local ancestry, and ARG‑based frameworks can quantify fragment properties and selection while handling complex scenarios such as multi‑source and low‑coverage data. They highlight emerging CNN‑ and segmentation‑based models (e.g., IntroUNET) that operate on genotype matrices to mark introgressed alleles with fine resolution, alongside real‑world applications beyond humans that implicate loci tied to immunity, reproduction, and environmental adaptation. Conclusion:Together, these approaches map introgression at increasing resolution and generality, and the field is moving toward transparent, benchmarked, and accessible tools that integrate statistics, probabilistic modeling, and machine learning to decode how gene flow shapes genomes across the tree of life. Reference:Huang X, Hackl J, Kuhlwilm M (2025) Decoding genomic landscapes of introgression. Trends in Genetics. https://doi.org/10.1016/j.tig.2025.07.001 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.castos.com/

️ Episode 159: The Untapped Potential of Short‑Read Sequencing in Biodiversity Research In this episode of PaperCast Base by Base, we explore how modern short‑read sequencing and genome skimming are reshaping biodiversity science—from rapid species identification and biomass estimation to scalable phylogenomics and holobiont studies—while keeping costs and sample requirements low. Study Highlights:This review synthesizes how low‑coverage short‑read data can recover organellar genomes and high‑copy nuclear markers, enabling robust taxonomic identification and phylogenetic inference across diverse taxa. It explains assembly‑free and mapping approaches that extract universal single‑copy orthologs or k‑mer signatures directly from raw reads, expanding analyses even when DNA is degraded or coverage is sparse. The authors show that genome size and repeat content (mobilome) can be estimated accurately from skims, supporting comparative genomics without reference‑quality assemblies. They highlight museum and type specimens as genomic treasure troves for building curated reference databases at scale, crucial for monitoring programs tied to the Global Biodiversity Framework. Finally, the paper surveys emerging short‑read platforms that further reduce per‑gigabase costs, pointing to rapid growth in throughput and accessibility for biodiversity applications. Conclusion:Short‑read sequencing remains a powerful, scalable backbone for biodiversity genomics, offering cost‑effective, reference‑complementary insights that accelerate conservation, monitoring, and evolutionary discovery. Reference:Bleidorn C, Sandberg F, Martin S, Vogler AP, Podsiadlowski L. The untapped potential of short‑read sequencing in biodiversity research. Trends in Genetics. 2025. https://doi.org/10.1016/j.tig.2025.09.001 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.castos.com/

️ Episode 158: Interruptions in Repeat Expansion Diseases: How Are They Gained and Lost? In this episode of PaperCast Base by Base, we explore how small sequence changes—“interruptions”—within expanded tandem repeats shape the onset and severity of repeat expansion disorders, and a new mechanistic model that may explain how these interruptions are gained and lost across generations. Study Highlights:Interruptions within repeat tracts can dampen somatic expansion and shift clinical trajectories, helping to explain variability in age at onset and phenotype across disorders such as Huntington’s disease, myotonic dystrophy type 1, spinocerebellar ataxias, and fragile X. Advances in long-read sequencing now reveal interrupted alleles with greater fidelity, expanding diagnostic and research possibilities. The authors propose synthesis-dependent microhomology-mediated end joining (SD-MMEJ) as a unifying mechanism that can generate locus-specific interruptions, create the apparent bias toward repeat–flanking boundaries, and produce complex alleles within a single generation. The model yields clear predictions—about the role of double-strand breaks, polymerase θ activity, and the influence of flanking sequence structures—that can be tested as new cellular systems emerge. Conclusion:Understanding and ultimately controlling interruption dynamics could open therapeutic avenues to stabilize pathogenic repeats and modify disease course. Reference:Aston AN, Dion V. Interruptions impact clinical features of repeat expansion diseases, but how are they gained and lost? Trends in Genetics. 2025. https://doi.org/10.1016/j.tig.2025.07.005 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.castos.com/ On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

️ Episode 157: Synthetic gametes and the non-identity problem: the babies of tomorrow In this episode of PaperCast Base by Base, we explore how synthetic DNA technologies may enable the creation of synthetic gametes and why this possibility forces a rethinking of identity, harm, and responsibility in human reproduction. Study Highlights:The authors argue that while building a full human genome remains infeasible today, engineering haploid genomes for gametes is a nearer-term and more tractable objective, drawing on advances such as synthetic chromosomes in yeast. They analyze how synthetic gametes differ ethically from embryo editing and PGD: instead of altering an existing embryo, they may bring into existence a different individual altogether, shifting the moral lens from person‑affecting harms to impersonal benefits and reproductive autonomy. The paper situates the debate within the “non‑identity problem,” explaining that reducing heritable disease risk via designed gametes can be justified as improving overall outcomes even if no particular future person is directly benefited. The authors further distinguish this approach from coercive eugenics, emphasizing voluntary use to minimize preventable suffering rather than to pursue perfection. Conclusion:Synthetic gametes reframe reproductive genetics from selection and modification to creation, raising urgent but navigable ethical questions about wellbeing, autonomy, and how societies should evaluate bringing a better‑off child into existence. Reference:Villalba A, Räsänen J. 2025. Synthetic gametes and the non-identity problem: the babies of tomorrow. Trends in Genetics. https://doi.org/10.1016/j.tig.2025.08.004 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.castos.com/ On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

️ Episode 156: RAEFISH: Sequencing-free whole-genome spatial transcriptomics at single-molecule resolution In this episode of PaperCast Base by Base, we explore RAEFISH, a reverse-padlock amplicon-encoding FISH method that delivers whole-transcriptome imaging at single-molecule resolution without sequencing. The study demonstrates genome-scale coverage across cells and intact tissues and extends to direct readout of CRISPR guide RNAs, enabling high-content functional screens with spatial context. Study Highlights:RAEFISH introduces a “reversed” padlock design with splint-assisted ligation, rolling-circle amplification, and MERFISH-style sequential readouts to barcode >20,000 transcripts while remaining compatible with cost-efficient oligo pool amplification. In A549 cells, the authors report an average of 3,749 decoded RNA molecules per cell from about 1,287 genes, with expression levels correlating with bulk RNA-seq and strong replicate reproducibility. The method generalizes to mouse tissues, mapping cell-type architectures and zonation programs in liver, placenta, and lymph node at single-molecule resolution. Finally, the Perturb-RAEFISH extension directly decodes gRNA spacer sequences in pooled CRISPR screens, detecting dozens of gRNA copies per cell and linking perturbations to spatial phenotypes without separate barcodes. Conclusion:RAEFISH expands spatial transcriptomics to genome-wide, single-molecule imaging and unlocks direct, image-based CRISPR perturbation readouts, setting the stage for unbiased discovery of spatial gene programs in development, physiology, and disease. Reference:Cheng Y, Dang S, Zhang Y, Chen Y, Yu R, Liu M, Jin S, Han A, Katz S, Wang S (2025). Sequencing-free whole-genome spatial transcriptomics at single-molecule resolution. Cell 188:1–18. https://doi.org/10.1016/j.cell.2025.09.006 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.castos.com/ Episode Slug: raefish-sequencing-free-whole-genome-spatial-transcriptomics Keywords: RAEFISH; spatial transcriptomics; single-molecule imaging; image-based CRISPR screen; liver zonation

️ Episode 155: EIF3A/EIF3B Loss-of-Function: A Cardiocraniofacial Neurodevelopmental Syndrome In this episode of PaperCast Base by Base, we explore how loss-of-function variants in EIF3A and EIF3B—core components of the eIF3 translation initiation complex—cause a multisystem disorder marked by congenital heart defects, craniofacial differences, and mild neurodevelopmental features. The study brings clinical genetics together with functional zebrafish models to establish gene–disease validity and illuminate developmental mechanisms. Study Highlights:An international cohort of eighteen individuals was assembled with de novo or loss-of-function variants in EIF3A (n=4) or EIF3B (n=14), revealing a consistent phenotype spectrum that prominently includes congenital heart defects—most notably tetralogy of Fallot—alongside craniofacial dysmorphisms and variable neurodevelopmental findings. Genomic analyses showed that both genes are highly constrained against loss of function, and a subset of cases involved a 7p22.3 microdeletion implicating EIF3B within the minimal critical region for cardiac anomalies. To test causality, the authors generated CRISPR-Cas9 zebrafish mutants in the orthologs eif3s10 (EIF3A) and eif3ba (EIF3B), which developed thin, poorly looped heart tubes, absent craniofacial cartilage, microphthalmia/coloboma, growth delay, and early lethality. Cardiac videomicroscopy demonstrated bradycardia, arrhythmia, and impaired chamber function, reinforcing a primary developmental defect rather than secondary edema. Integrated human and animal data support an autosomal-dominant eIF3-related syndrome driven largely by haploinsufficiency. Conclusion:EIF3A and EIF3B should be considered in genetic testing panels for syndromic congenital heart disease and neurocristopathies, with functional data indicating that dosage-sensitive disruption of the eIF3 complex perturbs early cardiocraniofacial development. Reference:Erkut E, Somerville C, Schwartz MLB, McDonald L, Ding Q, Moran OM, Chen X, Manshaei R, Riedijk A-S, Schnürer M-T, Koboldt DC, Antonarakis SE, Bedoukian EC, Blanc X, Conlin LK, Cox H, Diderich KEM, Dingmann B, Dubourg C, Elmslie F, Escobar LF, Gosselin R, Guillen Sacoto MJ, Haag CD, Herzig L, Jeeneea R, Kenia P, Kolokotronis K, Kopps AM, Kupper C, Lees H, Leonard J, Levy J, Littlejohn R, Mayer D, McLean SD, Pattani N, Perrin L, Pingault V, Quelin C, Ranza E, Rauch A, Reichert SL, Rosmaninho-Salgado J, Skraban C, Sousa S, Stuebben M, Zanoni P, Kim RH, Scott IC, Jobling RK. A cardiovascular, craniofacial, and neurodevelopmental disorder caused by loss-of-function variants in the eIF3 complex component genes EIF3A and EIF3B. The American Journal of Human Genetics. 2025;112:1–18. https://doi.org/10.1016/j.ajhg.2025.09.008 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.castos.com/

️ Episode 154: Multiple-testing corrections in selection scans using identity-by-descent segments In this episode of PaperCast Base by Base, we explore how Temple and Browning develop principled genome-wide significance thresholds for IBD-based scans of recent positive selection by explicitly modeling correlation along the genome. Study Highlights:The authors model standardized IBD-rate scan statistics as an Ornstein–Uhlenbeck process and derive both an analytical threshold and a fast simulation-based alternative that control the family-wise error rate while adapting to genetic-map spacing and autocorrelation. In extensive coalescent simulations, the approach achieves approximate FWER control and shows that Bonferroni can be overly conservative or dependent on arbitrary test spacing, whereas OU-based thresholds better reflect the effective number of tests. Power analyses indicate more than 50% power for hard sweeps with selection coefficients around or above 0.01 when the sweeping allele is at intermediate present-day frequency, and negligible power for weaker or nearly fixed sweeps. Applying the framework to TOPMed and UK Biobank cohorts, they identify a limited set of genome-wide significant loci across ancestry groups and show that some large cross-ancestry signals concentrate near structural-variant–rich regions rather than reflecting recent adaptation. Conclusion:OU-based multiple-testing corrections make IBD selection scans more reliable by calibrating significance to genomic correlation, improving reproducibility and reducing false positives in large biobank-scale analyses. Reference:Temple SD, Browning SR (2025). Multiple-testing corrections in selection scans using identity-by-descent segments. The American Journal of Human Genetics 112:1–21. https://doi.org/10.1016/j.ajhg.2025.09.004 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.castos.com/