Base by Base

️ Episode 198: Mechanical Confinement and the Shape-Shifting Life of Melanoma Cells In this episode of PaperCast Base by Base, we explore how physical forces in the tumor microenvironment can push melanoma cells to switch from a pigment-producing, proliferative state into an invasive, drug-tolerant one, focusing on new work that links mechanical confinement, chromatin remodeling, and neuronal-like programs in cancer. Study Highlights:Using a zebrafish model of BRAFV600E-driven melanoma together with human tumor samples and single-cell transcriptomics, the authors identify a subpopulation of tumor cells at the tumor–microenvironment interface that displays elongated nuclei and a gene expression program resembling undifferentiated, neuron-like cells. In vitro confinement of human melanoma cells under a polydimethylsiloxane piston recapitulates this interface state, triggering assembly of a perinuclear cage of acetylated microtubules that protects the nucleus from mechanical stress. Mechanical confinement selectively upregulates the chromatin-bending protein HMGB2, whose increased residence time on chromatin opens neuronal and invasive gene loci and engages pathways such as Notch and BRN2 that drive a switch toward an invasive phenotype. Genetic disruption of HMGB2 in zebrafish melanomas and human melanoma cells shifts the balance back toward proliferation with larger but less invasive tumors, whereas HMGB2 overexpression enhances invasion and tolerance to BRAF and MEK inhibition in mouse xenografts. Conclusion:Mechanical confinement within the tumor microenvironment can rewire melanoma cells through HMGB2-dependent chromatin remodeling to favor an invasive, neuronal-like and drug-tolerant state over purely proliferative growth. Music:Enjoy the music based on this article at the end of the episode. Reference:Hunter MV, Joshi E, Bowker S, Montal E, Ma Y, Kim YH, Yang Z, Tuffery L, Li Z, Rosiek E, Browning A, Moncada R, Yanai I, Byrne H, Monetti M, de Stanchina E, Hamard P-J, Koche RP, White RM. Mechanical confinement governs phenotypic plasticity in melanoma. Nature. 2025;647:517–527. https://doi.org/10.1038/s41586-025-09445-6 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:Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official websiteBase by Base – https://basebybase.com/ On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

️ 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

Gori K et al., PNAS - In canine transmissible venereal tumor (CTVT), deep sequencing and cytogenetics identify a 15‑Mb horizontally transferred nuclear element (N-HT1) acquired ~2,000 years ago that is transcriptionally active. Study Highlights:The authors screened 174 transmissible tumor genomes, focusing on CTVT, DFT1, and DFT2, using deep short-read sequencing, long-read PacBio sequencing, structural variant analysis, and metaphase FISH. In CTVT-A they discovered a 15-Mb dicentric element (N-HT1) assembled from 11 fragments of six chromosomes that forms the short arm of a small submetacentric chromosome after centromeric fusion. Mutation density and CpG-based dating place N-HT1 acquisition about 2,000 years ago, and transcriptome allele deconvolution shows N-HT1 is transcriptionally active and adopts the CTVT expression profile. Functional interrogation found no clear oncogenic drivers on N-HT1, with at least one rescued gene (ARFGEF3) later inactivated, consistent with the element behaving as a likely neutral passenger. Conclusion:A single host-to-tumor nuclear horizontal transfer event was detected in sampled transmissible cancers: CTVT-A acquired a 15-Mb N-HT1 element that is transcriptionally active but shows no clear evidence of positive selection. Music:Enjoy the music based on this article at the end of the episode. Reference:Gori K., Baez-Ortega A., Strakova A., Stammnitz M.R., Wang J., Chan J., Hughes K., et al. Horizontal transfer of nuclear DNA in transmissible cancer. Proc. Natl. Acad. Sci. U.S.A. 2025;122:e2424634122. https://doi.org/10.1073/pnas.2424634122 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:Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website https://basebybase.com On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics. Episode link: https://basebybase.castos.com/episodes/ctvt-n-ht1-horizontal-transfer

Ju X-C et al., PNAS - Human-specific ADSL A429V substitution and a common regulatory haplotype reduce ADSL activity and raise purine substrates in the brain, altering mouse behavior. Study Highlights:Model: mice humanized for ADSL carrying the modern-human A429V (with R428Q) were compared to wild-type littermates using ultraperformance LC–Orbitrap metabolomics and automated IntelliCage behavioral assays. Mechanistic/quantitative result: SAICAr and S-Ado concentrations increased up to ~2-fold in liver and 1.8–5.4-fold across cerebrum regions, and these increases correlated negatively with Adsl mRNA expression across tissues. Human genetics: a 7.8-kb haplotype (including rs8135371) at >97% carrier frequency is associated with lower ADSL expression, higher S-Ado in cerebrospinal fluid, and signals of positive selection. Functional implication: female humanized mice accessed water more efficiently under restricted conditions, linking reduced ADSL activity to altered behavior. Conclusion:Two genetic changes on the modern human lineage—a nearly fixed A429V amino acid substitution and a common regulatory haplotype—have reduced ADSL activity and expression, increasing purine substrates particularly in the brain and producing measurable behavioral effects in mice. Music:Enjoy the music based on this article at the end of the episode. Reference:Ju X-C, Huttner W, Ågren R, Machado LC, Xing J, Lee S-Y, Siepel A, Azama C, Roy MC, Pääbo S, Endo T, Fukunaga I, Zeberg H. The activity and expression of adenylosuccinate lyase were reduced during modern human evolution, affecting brain and behavior. Proc. Natl. Acad. Sci. U.S.A. 2025.122:e2508540122. https://doi.org/10.1073/pnas.2508540122 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:Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website https://basebybase.com On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics. Episode link: https://basebybase.castos.com/episodes/adsl-a429v-purine-brain

Morris TT et al., PNAS - EA and cognition polygenic indexes (PGIs) in three British birth cohorts show EA PGI associations with years of education increased from 1946–1970 and were strongest in advantaged socioeconomic backgrounds. Study Highlights:Using three nationally representative British birth cohorts born 1946, 1958, and 1970, the authors analyzed polygenic indexes for educational attainment (EA) and cognition. They generated PGIs with clumping-and-thresholding (PRSice2) and LDpred2, used multiple imputation and inverse probability weighting, and estimated linear models including cohort-by-PGI interactions. EA PGI associations increased from approximately 0.44 to 0.67 years of education per 1-SD and incremental R2 rose from 3.5% to 5.1% across cohorts, while cognition PGI associations were broadly stable. There was strong evidence of gene–environment interaction: returns to EA genetic liability were disproportionately larger among those born into more advantaged socioeconomic backgrounds. Conclusion:Across three British birth cohorts born 1946–1970, genetic liability indexed by an EA PGI became more predictive of years of completed education while cognition PGI prediction remained stable, and EA PGI effects were amplified in advantaged socioeconomic contexts. Music:Enjoy the music based on this article at the end of the episode. Reference:Morris TT, Wright L, Shireby G, Bann D. Genetic associations with education have increased and are patterned by socioeconomic context: Evidence from 3 studies born 1946–1970. Proc. Natl. Acad. Sci. U.S.A. 2026;123:e2516460123. https://doi.org/10.1073/pnas.2516460123 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:Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website https://basebybase.com On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics. Episode link: https://basebybase.castos.com/episodes/ea-pgi-cohort-socioeconomic-interaction Chapters (00:00:00) - Genetics and the socioeconomic gap(00:04:36) - The genetic link between school and success(00:07:42) - Genetics and educational success(00:11:42) - The Wealthy Kids and the Poor(00:12:56) - The genetics of intelligence and personality(00:15:38) - Open Access: Science Podcast(00:16:31) - Inheritance

Spakmana D et al., H., Hickson I. D., Peterman E. J. G., Wuite G. J. L., King G. A. Mechanistic basis for relaxation of DNA supercoils by human topoisomerase IIIα–RMI1–RMI2. Proc. Natl. Acad. Sci. U.S.A - Optical tweezers and fluorescence imaging show human Topoisomerase IIIα–RMI1–RMI2 (TRR) processively relaxes highly negatively supercoiled DNA faster than PICH loops. Study Highlights:Using torsionally constrained end-closed λ-DNA in a multichannel flow cell, the authors combined Optical DNA Supercoiling (ODS), dual-trap optical tweezers, and fluorescence imaging to measure supercoiling density and visualize TRR binding in real time. They find TRR relaxes hyper-negatively supercoiled DNA in a highly processive manner, with single TRR complexes performing thousands (>3,000) of strand-passage reactions and exhibiting a force-dependent rate described by an Arrhenius relation (δ ≈ 1.1–1.4 nm in ensemble and single-molecule fits). Ensemble TRR activity was ~10-fold lower than E. coli TopoI under the same conditions, while single- complex rates indicate a single TRR can relax PICH-generated negative loops within the reported loop lifetime. These results support a mechanistic role for TRR in relaxing PICH-generated negative supercoils that could facilitate ultrafine anaphase bridge resolution. Conclusion:Human topoisomerase IIIα–RMI1–RMI2 (TRR) relaxes highly negatively supercoiled DNA in a force-dependent, highly processive manner and can act within the lifetime of PICH-generated negative loops, supporting a role in ultrafine anaphase bridge resolution. Music:Enjoy the music based on this article at the end of the episode. Reference:Spakmana D., Biebricher A. S., Bizard A. H., Hickson I. D., Peterman E. J. G., Wuite G. J. L., King G. A. Mechanistic basis for relaxation of DNA supercoils by human topoisomerase IIIα–RMI1–RMI2. Proc. Natl. Acad. Sci. U.S.A. 2026;123:e2406949123. Published January 23, 2026. https://doi.org/10.1073/pnas.2406949123 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:Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website https://basebybase.com On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics. Episode link: https://basebybase.castos.com/episodes/trr-supercoil-relaxation-optical-tweezers Chapters (00:00:00) - The Great Divide: When will the bridge break?(00:02:41) - Deep Dive: The mechanism of DNA supercoils by human to(00:03:49) - The Hidden Story of DNA(00:08:02) - How fast does TRR work on DNA?(00:12:40) - Why TRR Stuck to the DNA(00:17:30) - Who is the bouncer of DNA?

Palacio T et al., PNAS - Reconstituted Saccharomyces cerevisiae mismatch repair shows the Mlh1–Pms1 endonuclease directly generates single-strand gaps to excise mispairs independent of Exo1 and Rad27. Study Highlights:We reconstituted Saccharomyces cerevisiae mismatch repair with purified Msh2–Msh6 or Msh2–Msh3, Mlh1–Pms1, PCNA, RFC, RPA, and DNA polymerases and analyzed products by restriction mapping, Mung Bean nuclease, electron microscopy, and APOBEC3A deamination. The Mlh1–Pms1 endonuclease, activated by RFC-loaded PCNA and Mn2+, generates strand-specific single-strand gaps on the preexisting nicked strand. Electron microscopy and deamination mapping revealed a broad distribution of gap sizes with a peak around 128 ± 17 nucleotides and most gaps under 500 nucleotides. These gaps can be filled by DNA Polε or low levels of DNA Polδ, providing an Exo1- and Rad27-independent route for mispair excision and explaining redundancy among excision pathways. Conclusion:Mlh1–Pms1 catalyzes strand-specific single-strand gap formation that mediates Exo1- and Rad27-independent mispair excision in reconstituted S. cerevisiae mismatch repair. Music:Enjoy the music based on this article at the end of the episode. Reference:Palacio T, Calil FA, Bowen N, Griffith JD, Putnam CD, Kolodner RD. DNA mismatch repair mediated by Mlh1–Pms1 endonuclease-catalyzed mispair excision. Proc. Natl. Acad. Sci. U.S.A. 2025;122:e2528670122. https://doi.org/10.1073/pnas.2528670122 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:Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website https://basebybase.com On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics. Episode link: https://basebybase.castos.com/episodes/mlh1-pms1-gap-excision Chapters (00:00:00) - Base by Bass(00:00:29) - Who is the real repairman of DNA?(00:02:39) - The spell-checker for our DNA(00:04:23) - The ghost mechanic of DNA repair(00:07:02) - The secret to DNA repair(00:09:48) - How DNA repair works: The 3 pathways(00:13:43) - How to Stop cancer with a single drug

Cail RC et al., PNAS - Recombinant human β-cardiac myosin M493I studied by optical trapping and stopped-flow kinetics disrupts the super-relaxed state and increases actin attachment and contractile force. Study Highlights:System: recombinant human β-cardiac heavy meromyosin (cHMM) expressed in C2C12 cells. Methods: ensemble actin gliding, stopped-flow kinetics, NADH ATPase, mantATP single-turnover, and single-molecule three-bead optical trap assays. Main results: M493I preserves Pi release and the two-step 4.7–5 nm working stroke but slows ADP release ~5-fold, doubles steady-state ATPase Vmax, reduces SRX occupancy (KSRX/DRX from ~0.33 to ~0.53), and prolongs actin attachment with increased high-force, long-duration interactions. Functional implication: the combined increase in DRX head availability and prolonged AM·ADP lifetimes produce higher sustained force and faster actin reattachment consistent with a mechanism for HCM hypercontractility and impaired relaxation. Conclusion:The M493I relay-helix mutation disrupts the SRX off state and, together with slowed ADP release and prolonged actin attachment, increases myosin head availability and force production, explaining its hypercontractile HCM phenotype. Music:Enjoy the music based on this article at the end of the episode. Reference:Cail RC, Barua B, Báez-Cruz FA, Winkelmann DA, Goldman YE, Ostap EM. A myosin hypertrophic cardiomyopathy mutation disrupts the super- relaxed state and boosts contractility by enhanced actin attachment. Proc. Natl. Acad. Sci. U.S.A. 2025;122:e2521561122. https://doi.org/10.1073/pnas.2521561122 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:Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website https://basebybase.com On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics. Episode link: https://basebybase.castos.com/episodes/m493i-beta-myosin-srx-disruption Chapters (00:00:00) - Heart Hypertrophic Cardiomyopathy: The genetic puzzle(00:04:48) - Myosin motors: Do they Pull or Float?(00:07:50) - Heart Disease: M493I mutant causes heart to slow(00:12:16) - Heart dysrhythmias: The sticky insomniac motor(00:17:54) - Hold on Hold On

Englander SW et al., PNAS - Hydrogen exchange (H-T and NMR H-H) on DNA and RNA reveals two distinct base-pair opening modes: single-base microsecond openings and multi-base millisecond soliton-like loops. Study Highlights:Systems studied include long polynucleotides (DNA, duplex RNA, synthetic long duplexes) and short oligonucleotides; key methods are H-T (tritium) exchange, stopped-flow H-D, and NMR H-H (water relaxation) measurements. H-T exchange of long polymers reports opening-limited EX1 imino exchange with kop ~1/s, reclosing kcl ~20/s and Kop ~10^-2 consistent with multi-base open loops with ms lifetimes. NMR H-H on short oligos reports catalyzable EX2 behavior dominated by single base-pair openings with kcl ~10^6/s and Kop ~10^-6 and microsecond lifetimes. The selective detection implies short oligonucleotides cannot host extensive loops while multi-base soliton-like loops in polynucleotides could dynamically expose sequences for protein or nucleic acid recognition. Conclusion:Both H-T and NMR H-H exchange provide accurate but complementary views: long polynucleotides exhibit frequent multi-base, ms-lived open loops (Kop ~10^-2, kcl ~20/s) while short oligonucleotides reveal rare single-base, μs-lived openings (Kop ~10^-6, kcl ~10^6/s). Music:Enjoy the music based on this article at the end of the episode. Reference:Englander SW. Nucleic acid base pair open states by hydrogen exchange. Proc. Natl. Acad. Sci. U.S.A. 2026;123:e2520855122. https://doi.org/10.1073/pnas.2520855122 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:Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website https://basebybase.com On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics. Episode link: https://basebybase.castos.com/episodes/dna-basepair-opening-soliton Chapters (00:00:00) - Papercast: The mystery of DNA(00:02:42) - Breaking down the mystery of DNA(00:03:26) - How does DNA open? The '(00:07:43) - DNA is Not Like Longer Strands(00:11:32) - The physics of DNA replication(00:16:10) - I'm 1% Open

Vatsa A et al., PNAS - In HPV31-positive keratinocytes (CIN612), TOP1α and TOP3β are upregulated and required for viral transcription and replication, acting via distinct effects on R-loop accumulation and topoisomerase-mediated DNA breaks. Study Highlights:Using HPV31-positive CIN612 cells and primary HFK controls, the authors applied ChIP, RADAR, DRIP, alkaline COMET, RNA-seq, and shRNA knockdown to map topoisomerase binding and function. They found TOP1α and TOP3β, but not TOP3α, are elevated in HPV-positive cells and bind the viral URR, and that shRNA depletion of TOP1α or TOP3β reduced episomal viral DNA and early viral transcripts. Knockdown decreased DNA breaks (~50% reduction in COMET tail formation and reduced γH2AX) and altered R-loop levels differentially, with TOP1α depletion increasing viral R-loops by ~50% and TOP3β depletion causing >3-fold R-loop accumulation at viral and cellular loci. Transcriptome changes included reduced IL6/STAT3-AKT signaling after TOP1α loss and marked downregulation of EGR3 (>5-fold) after TOP3β loss, linking distinct mechanistic effects to impaired viral replication. Conclusion:TOP1α and TOP3β are differentially required for maintenance of HPV episomes and viral gene expression through distinct regulation of DNA breaks, R-loop dynamics, and specific host signaling pathways. Music:Enjoy the music based on this article at the end of the episode. Reference:Vatsa A, Templeton CW, Laimins L. Differential roles of type I topoisomerases in regulating HPV pathogenesis. Proc. Natl. Acad. Sci. U.S.A. 2026.123:e2526296123. https://doi.org/10.1073/pnas.2526296123 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:Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website https://basebybase.com On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics. Episode link: https://basebybase.castos.com/episodes/top1alpha-top3beta-hpv-replication Chapters (00:00:00) - How HPV solves its torsional stress(00:02:49) - How do HPV mutations cause cancer?(00:06:16) - HPV cell cancer(00:10:12) - HPV cancer: The DNA damage crisis(00:13:54) - Untie the Loop

Yu C et al., Proc. Natl. Acad. Sci. U.S.A - Genetic mapping and comparative genomics show the lncRNA ANTSR multiallelic locus in Aculeata directs female development via heterozygosity despite lacking sequence homology. Study Highlights:The study analyzed 41 hymenopteran genomes and performed whole-genome resequencing and genetic mapping in Bombus terrestris and Vespa velutina nigrithorax to locate the sex-determining region. The ANTSR locus is a multiallelic noncoding interval between CRELD2 and THUMPD3 that is highly polymorphic and heterozygous in females but homozygous in diploid males across ants, bumblebees, and hornets. Comparative synteny shows the CRELD2–THUMPD3 block originated ~160–200 Mya and the locus has functioned as a zygosity-based female determinant for over 150 million years. Despite this deep functional conservation, alignments and phastCons analyses reveal no detectable sequence homology among distant aculeate lineages, and heterozygosity at ANTSR provides an actionable molecular sex marker for breeding and conservation. Conclusion:The ANTSR multiallelic noncoding locus is an ancient, positionally conserved zygosity-based sex determinant across Aculeata that has retained function for over 150 million years despite complete sequence divergence. Music:Enjoy the music based on this article at the end of the episode. Reference:Yu C, Moog S, Pan Q, Keller Valsecchi CI, Dupont S, Darrouzet E, Darras H, Hodapp D, Colgan TJ, et al. Deep evolutionary conservation of a sex-determining locus without sequence homology. Proc. Natl. Acad. Sci. U.S.A. 2026;123:e2522417123. https://doi.org/10.1073/pnas.2522417123 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:Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website https://basebybase.com On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics. Episode link: https://basebybase.castos.com/episodes/antsr-aculeata-sex-locus

Sengstack J et al., Proc. Natl. Acad. Sci. U.S.A - TRDP with Perturb-seq in human fibroblasts found that manipulating TFs (EZH2, E2F3, STAT3, ZFX) reversed aging hallmarks, and EZH2 overexpression rejuvenated aged mouse livers. Study Highlights:The study used passaged human neonatal dermal fibroblasts and aged mouse liver as model systems and applied the Transcriptional Rejuvenation Discovery Platform (TRDP) with Perturb-seq and CRISPRa/CRISPRi screens. Overexpressing E2F3 or EZH2 and repressing STAT3 or ZFX reversed global gene expression toward earlier passage states and ameliorated cellular aging hallmarks including increased proliferation, proteasome activity, and mitochondrial function. In aged mice, AAV8-mediated liver-specific EZH2 overexpression (log2fc ≈ 2.9) reversed thousands of age-associated gene changes (R_rej = -0.42), reduced steatosis and fibrosis, and improved glucose tolerance. Downstream transcriptional programs converged across perturbations, suggesting shared molecular requirements for cellular and tissue rejuvenation. Conclusion:Single transcription factor perturbations identified by TRDP can reverse cellular aging hallmarks in human fibroblasts and, in the case of EZH2 overexpression, partially rejuvenate aged mouse liver with improved histology and glucose tolerance. Music:Enjoy the music based on this article at the end of the episode. Reference:Sengstack J, Li H, Aghayev T, Bier G, Mobaraki M, Zheng J, Lin J, Deng C, Villeda SA, et al. Systematic identification of single transcription factor perturbations that drive cellular and tissue rejuvenation. Proc. Natl. Acad. Sci. U.S.A. 2026;123:e2515183123. Published January 9, 2026. https://doi.org/10.1073/pnas.2515183123 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:Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website https://basebybase.com On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics. Episode link: https://basebybase.castos.com/episodes/ezh2-liver-rejuvenation

Perera J et al., R., Thadke S. A., Thrikawala S. W., Wilson W. D., Tan K. W. R., Chand N. Z. W., Phan A. T., Ly D. H., et al. A pothole-filling strategy for selective targeting of rCUG-repeats associated with myotonic dystrophy type 1. Proc. Natl. Acad. Sci. U.S.A - Gamma-PNA triplet ligands with Janus bases selectively bind expanded rCUG repeats, displace MBNL1, and show length-dependent cooperativity with partial splicing rescue. Study Highlights:The authors designed compact three-unit bifacial nucleic acid ligands (Janus bases on a γPNA backbone) and evaluated them against rCUG repeat duplexes and DM1 patient-derived myotubes using molecular dynamics, EMSA, SPR, AFM, and cellular splicing assays. MD and EMSA/SPR show cooperative, length-dependent binding with Kd values decreasing to ~0.56 µM for rCUG98 and Hill coefficients rising to ~5, driven by enhanced hydrogen-bonding and π–π stacking between adjacent ligands. AFM revealed a 0.348 nm increase in RNA helix contour height on binding, consistent with a pothole-filling insertion mechanism that selectively recognizes hairpin duplexes over single-stranded RNA. Functionally, a cell-permeable LG2c analog reduced nuclear foci and partially restored mis-splicing of Serca1, cTNT, and IR in DM1 myotubes, though cellular uptake remains limiting. Conclusion:Short bifacial γPNA triplet ligands selectively recognize pathogenic rCUG hairpins via a pothole-filling mechanism, displace MBNL1, and can partially restore splicing in DM1 myotubes while cellular delivery requires further optimization. Music:Enjoy the music based on this article at the end of the episode. Reference:Perera J. D. R., Thadke S. A., Thrikawala S. W., Wilson W. D., Tan K. W. R., Chand N. Z. W., Phan A. T., Ly D. H., et al. A pothole-filling strategy for selective targeting of rCUG-repeats associated with myotonic dystrophy type 1. Proc. Natl. Acad. Sci. U.S.A. 2026;123:e2507065123. https://doi.org/10.1073/pnas.2507065123 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:Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website https://basebybase.com On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics. Episode link: https://basebybase.castos.com/episodes/pothole-filling-rcug-gamma-pna

Strobl et al., & Stary, G. Human epidermal Langerhans cells induce tolerance and hamper T cell function upon tick-borne pathogen transmission. Nature Communications - Human epidermal Langerhans cells exposed to Ixodes ricinus tick saliva and Borrelia burgdorferi adopt a tolerogenic state with CXCR4/CCR7-driven emigration that impairs T cell priming. Study Highlights:The study uses clinical human tick bite biopsies, an ex vivo human skin tick bite model, in vitro monocyte- and CD34-derived Langerhans cells, immune spheroid cultures and single-cell RNA-sequencing of erythema migrans lesions, employing imaging, migration assays, co-cultures and scRNA-seq. Tick salivary gland extract (SGE) up-regulates CXCR4 and CCR7 on LCs, promotes emigration from the epidermis into dermis and lymphatic vessels, and reduces keratinocyte TGF-β consistent with migration. SGE and Borrelia burgdorferi drive up-regulation of tolerogenic transcription factors IDO1 and IRF4 while blunting immunogenic IRF1/NFκB programs, and SGE-primed LCs induce Treg and Th2 bias with reduced Tfh, Th17 and Th9 induction. Functionally, these changes dampen protective adaptive responses in lymphoid models and in patient lesions, which may reduce bacterial clearance and memory formation. Conclusion:Tick saliva reprograms human epidermal Langerhans cells to migrate to lymphatics and adopt a tolerogenic program that impairs protective T cell responses and may facilitate Borrelia transmission. Music:Enjoy the music based on this article at the end of the episode. Reference:Strobl, J., Kleissl, L., Eder, J., Conolly, S., Frey, T., Gail, L. M., Kopf, A., Weninger, S., Markowicz, M., Bartíková, P., Freystätter, C., Schmetterer, K., Strobl, H., Stockinger, H., Wijnveld, M. & Stary, G. Human epidermal Langerhans cells induce tolerance and hamper T cell function upon tick-borne pathogen transmission. Nature Communications. 2025. https://doi.org/10.1038/s41467-025-66821-6 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:Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website https://basebybase.com On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics. Episode link: https://basebybase.castos.com/episodes/langerhans-tick-saliva-tolerance

Girelli et al., Coherent X-rays reveal anomalous molecular diffusion and cage effects in crowded protein solutions. Nat Commun ( - MHz-XPCS of ferritin solutions at EuXFEL shows anomalous, cage-trapped protein diffusion with reduced long-time transport and ~1.2 nm rattling at high concentration. Study Highlights:The study probes crowded ferritin solutions using megahertz X-ray Photon Correlation Spectroscopy (MHz-XPCS) at EuXFEL combined with SAXS and δγ-theory modeling. Intensity autocorrelation functions g2(q,t) become non-exponential at high concentrations, and double-exponential analysis yields short- and long-time diffusion components with Dlong/Dshort ≈ 0.12 ± 0.04 at 730 mg/ml and an interaction time estimated near 4.25 µs. δγ-theory of hydrodynamically interacting spheres reproduces the q-dependent hydrodynamic function only when a scaling factor tied to direct protein interactions is included, indicating hydrodynamics set the q-dependence while direct forces reduce overall self-diffusion. Cage analysis finds an average rattling displacement δ ≈ 1.0 ± 0.3 nm for ≈89% of proteins, implying cage-trapping substantially slows molecular transport with consequences for ferritin-based drug delivery. Conclusion:MHz-XPCS measurements and δγ-theory modeling demonstrate that crowded ferritin solutions exhibit anomalous, cage-trapped diffusion with separate short- and long-time components and markedly reduced self-diffusion, indicating slower molecular transport under crowding. Music:Enjoy the music based on this article at the end of the episode. Reference:Girelli, A., Bin, M., Filianina, M. et al. Coherent X-rays reveal anomalous molecular diffusion and cage effects in crowded protein solutions. Nat Commun (2025). https://doi.org/10.1038/s41467-025-66972-6 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:Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website https://basebybase.com On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics. Episode link: https://basebybase.castos.com/episodes/ferritin-anomalous-diffusion-xpcs

Cortés Guzmán M et al., Nat Commun - Human germline transcription start sites show a hotspot of non-CpG variants driven by the early embryonic mosaicism, RNAP II stalling, R-loops and mitotic DSBs. Study Highlights:The authors analysed extremely rare variants from gnomAD and UK Biobank, de novo mutations from family sequencing, mosaic variant catalogs, and pan-cancer somatic data to map mutation density around transcription start sites in humans. They used 5-mer sequence-context normalization, negative binomial regression with 38 genomic and epigenetic covariates, PRO-seq and somatic DSB maps, and mutational-signature decomposition to identify drivers. They report a pronounced TSS hotspot of non(CpG>TpG) ERVs reaching ~14% excess at 1 kb and up to ~35% in the first 100 bp, and a 52% enrichment of early embryonic mosaic variants immediately downstream of the TSS. Mechanistic associations implicate divergent transcription, RNAP II stalling, R-loops and mitotic double-strand breaks, and the hotspot disproportionately affects genes linked to cancer and developmental phenotypes. Conclusion:Transcription start sites are a distinct germline mutational hotspot enriched for early embryonic mosaic variants and transcription- and mitosis-associated DNA damage and repair processes. Music:Enjoy the music based on this article at the end of the episode. Reference:Cortés Guzmán M, Castellano D, Serrano Colomé C, Seplyarskiy V & Weghorn D (2025) Transcription start sites experience a high influx of heritable variants fueled by early development. Nature Communications 16:10120. https://doi.org/10.1038/s41467-025-66201-0 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:Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website https://basebybase.com On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics. Episode link: https://basebybase.castos.com/episodes/tss-germline-hotspot-rnapii

Zahid S et al., Nat Commun - Cryo-EM and biophysical analyses show Mycobacterium tuberculosis Ku assembles into DNA-bound oligomeric filaments that synapse DNA ends and are required for survival under DNA-damaging conditions. Study Highlights:Deletion of ku in M. smegmatis causes marked survival defects after methyl methanesulfonate exposure and desiccation that are rescued by complementation. Cryo-EM structures of apo-Ku-Mtb (4.04 Å) and DNA-bound Ku-Mtb (2.96 Å) reveal a homodimer that assembles into extended filaments with a minimal repeating unit of two homodimers per DNA duplex. Biophysical assays (mass photometry, FIDA, AFM) and positive-stain EM confirm DNA-induced oligomerisation and show Ku can circularize DNA ends, holding them ~40 Å apart. Mutation of hydrophobic loop residues L13/V14 abolishes filament formation while preserving DNA binding and reduces bacterial survival, and the C-terminal α-helix blocks the filament interface in the apo state and is displaced on DNA binding to enable LigD recruitment. Conclusion:Ku oligomerisation mediates DNA end synapsis during bacterial NHEJ and is critical for mycobacterial survival under DNA-damaging stresses Music:Enjoy the music based on this article at the end of the episode. Reference:Zahid S, Baconnais S, Smith H, Atwal S, Bates L, Read H, Chadda A, Morati F, Stender EGP, Westerlund F, Galburt E, Mukamolova GV, Chaplin AK, et al. Oligomerisation of Ku from Mycobacterium tuberculosis promotes DNA synapsis. Nature Communications. 2025;16:10568. https://doi.org/10.1038/s41467-025-65609-y 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:Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website https://basebybase.com On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics. Episode link: https://basebybase.castos.com/episodes/ku-mtb-dna-synapsis

Holcik L et al., Genomic GC bias correction improves species abundance estimation from metagenomic data. Nature Communications - GuaCAMOLE is an alignment-free algorithm that estimates and removes genomic GC-content-dependent sequencing bias to produce more accurate species abundance estimates from single metagenomic samples. Key terms: GC bias, metagenomics, species abundance, GuaCAMOLE, colorectal cancer. Study Highlights:GuaCAMOLE combines Kraken2/Bracken read assignment with per-taxon GC binning and a regularized least-squares estimator to infer GC-dependent sequencing efficiencies and bias-corrected abundances from a single sample. On simulations and mock communities across 28 library protocols it produced near-unbiased estimates and outperformed Bracken and MetaPhlAn4 when GC bias was present. Application to 3,435 gut microbiomes from 33 colorectal cancer studies revealed four distinct protocol-specific GC-bias shapes and systematic underestimation of GC-poor taxa. The tool also filters false-positive taxa by comparing observed and expected GC distributions and can apply inferred efficiencies to correct other tools' outputs. Conclusion:Per-sample GC-bias correction with GuaCAMOLE improves accuracy and comparability of metagenomic species abundance estimates across diverse protocols Music:Enjoy the music based on this article at the end of the episode. Reference:Holcik L., von Haeseler A., Pflug F. G. Genomic GC bias correction improves species abundance estimation from metagenomic data. Nature Communications. 2025;16:10523. https://doi.org/10.1038/s41467-025-65530-4 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:Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website https://basebybase.com On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics. Episode link: https://basebybase.castos.com/episodes/gc-bias-correction-metagenomics Episode Slug: gc-bias-correction-metagenomics

Küry S et al., Nat Commun - This study describes 26 distinct PSMC5 variants in 44 individuals and demonstrates that PSMC5 loss impairs proteasome function, driving proteotoxic stress, mitochondrial and lipid dysregulation, sterile type I interferon activation, and neurodevelopmental deficits. Key terms: PSMC5, proteasome, neurodevelopment, interferon, mitophagy. Study Highlights:Twenty-six distinct PSMC5 variants were identified in 44 affected individuals, mostly heterozygous and de novo, clustering in the AAA+ ATPase domain and predicted to be pathogenic. Functional assays and patient T cells show that many variants perturb PSMC5 incorporation into 26S proteasomes, reduce proteasome activity, and increase ubiquitin-positive aggregates and aggresomes. Multi-omics of patient T cells revealed disrupted mitochondrial proteostasis with increased mitophagy, altered glycerophospholipid profiles and impaired ribosome biogenesis. Neuronal models and Drosophila demonstrate reduced excitatory synapses, E/I imbalance, impaired neuritogenesis, deficits in reversal learning and compromised NPC differentiation, while ISR kinases PKR and GCN2 plus cGAS-STING and JAK pathways mediate a spontaneous type I IFN response that can be pharmacologically reduced. Conclusion:PSMC5 variants cause proteasome loss-of-function that links proteotoxic stress to innate immune activation and impaired neurogenesis, identifying ISR and JAK pathway components as potential therapeutic targets. Music:Enjoy the music based on this article at the end of the episode. Reference:Küry S, Bézieau S, Ebstein F, et al. Investigating the neuronal role of the proteasomal ATPase subunit gene PSMC5 in neurodevelopmental proteasomopathies. Nature Communications. 2025;16:10545. https://doi.org/10.1038/s41467-025-65556-8 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:Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website https://basebybase.com On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics. Episode link: https://basebybase.castos.com/episodes/psmc5-proteasome-neurodevelopment Episode Slug: psmc5-proteasome-neurodevelopment

Antunes et al., Chromosome compartment assembly is essential for subtelomeric gene silencing in trypanosomes. Nat Commun ( - The study shows that spatial segregation of core and subtelomeric chromosome compartments, demarcated by protein-rich boundaries and controlled by a phosphoinositide regulator, is required to silence subtelomeric VSG genes. Key terms: RAP1, PIP5Pase, VSG, Hi-C, chromatin. Study Highlights:Hi-C and Pore-C reveal that T. brucei chromosomes are organized into transcribed core (A) and repressed subtelomeric (B) compartments that contain TADs and loops. XLMS and ChIP-seq identify compartment-boundary proteins including RAP1, HDAC1, HAT1 and BDF2, with RAP1 spreading across silent subtelomeric regions. Boundaries from multiple chromosomes co-interact and are enriched for repeat motifs resembling telomeric and centromeric sequences. Inactivation or knockdown of the PIP5Pase regulator disrupts intra-compartment contacts, displaces RAP1 from boundaries and subtelomeres, and activates hundreds of silent VSG genes. Conclusion:Assembly of chromosome compartments and PIP5Pase-regulated RAP1 binding are essential for subtelomeric VSG gene silencing in T. brucei. Music:Enjoy the music based on this article at the end of the episode. Reference:Antunes, L.B., Isebe, T., Kutova, O. et al. Chromosome compartment assembly is essential for subtelomeric gene silencing in trypanosomes. Nat Commun (2025). https://doi.org/10.1038/s41467-025-66824-3 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:Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website https://basebybase.com On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics. Episode link: https://basebybase.castos.com/episodes/compartment-vsg-silencing Episode Slug: compartment-vsg-silencing