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Nature Communications - Transcription start sites experience a high influx of heritable variants fueled by early development

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Article title:
Transcription start sites experience a high influx of heritable variants fueled by early development

Journal:
Nature Communications

DOI:
10.1038/s41467-025-66201-0

License:
CC BY 4.0 International License

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.

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-01-15.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Audited the transcript for core germline mutagenesis mechanisms around transcription start sites (TSS), mosaic vs de novo variation, mechanistic links (RNAP II stalling, R-loops, divergent transcription), mutational signatures, purifying selection, disease links, and clinical implications as described in the article.
- transcript topics: Germline TSS mutational hotspot; Extremely rare variants and mosaicism; De novo mutations vs mosaic filtering; Transcription-associated mutagenesis mechanisms (RNAP II stalling, R-loops, divergent transcription); Mutational signatures (SBS3, SBS40b, SBS40c; SBS39 maternal clusters; SBS12/SBS16); Divergent transcription at promoters

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 8
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0

Metadata Audited:
- article_doi
- article_title
- article_journal
- license

Factual Items Audited:
- Germline transcription start sites harbor a mutational hotspot spanning several hundred base pairs upstream and downstream of the TSS
- Non(CpG > TpG) variations show a mutational excess at the TSS, up to ~35% in 100-bp windows around the TSS
- De novo mutations (DNMs) do not show a significant TSS excess due to misclassification/ filtering; the hotspot is revealed by mosaic variants
- Early mosaic mutations are enriched near the TSS, with a 52% excess immediately downstream of the TSS
- Divergent transcription, RNAP II stalling, and R-loop formation are associated with the TSS hotspot
- Mutational signatures SBS3, SBS40b, SBS40c indicate non-canonical DSB repair; SBS39 linked to maternal mutation clusters

QC result: Pass.

Zahid S et al., Nature Communications, doi:10.1038/s41467-025-65609-y - 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. Key terms: Ku-Mtb, non-homologous end joining, cryo-EM, DNA synapsis, Mycobacterium tuberculosis.

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

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Article title:
Oligomerisation of Ku from Mycobacterium tuberculosis promotes DNA synapsis

First author:
Zahid S

Journal:
Nature Communications, doi:10.1038/s41467-025-65609-y

DOI:
10.1038/s41467-025-65609-y

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.com/episodes/ku-mtb-dna-synapsis

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-01-14.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Audited the spoken content covering MTB NHEJ, Ku-Mtb filament formation on DNA, cryo-EM structural details, mutational analyses, functional assays, and therapeutic implications.
- transcript topics: Ku essential for mycobacterial survival under MMS-induced DNA DSBs; Desiccation tolerance and MTB DNA repair via NHEJ; apo-Ku-Mtb structure by cryo-EM (4.04 Å) and DNA-bound filament (2.96 Å); DNA synapsis by Ku-Mtb filament; ~40 Å end-to-end distance; Minimal repeating unit: two Ku-Mtb homodimers per DNA duplex; Role of C-terminal helix and L13/V14 hydrophobic interface in filament regulation

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 6
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0

Metadata Audited:
- article_doi
- article_title
- article_journal
- license

Factual Items Audited:
- Ku-Mtb forms an extended filament on DNA and synapses DNA ends; minimal unit is two Ku-Mtb homodimers per DNA duplex
- DNA ends are held at a distance of approximately 40 Å within the filament
- Leu13 and Val14 form a hydrophobic interface critical for filament formation; L13A/V14A abolishes filament formation
- The C-terminus acts as an autoinhibitory regulatory arm; displacement upon DNA binding enables filament formation and LigD recruitment
- MTB NHEJ is a minimalist system lacking vWA domains and DNA-PKcs, capable of synapsis without the large human machinery
- Mutational analysis in vivo (L23A/L24A equivalent) reduces survival under DNA-damaging stress

QC result: Pass.

Holcik L et al., Nature Communications, doi:10.1038/s41467-025-65530-4 - 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.

Article title:
Genomic GC bias correction improves species abundance estimation from metagenomic data

First author:
Holcik L

Journal:
Nature Communications, doi:10.1038/s41467-025-65530-4

DOI:
10.1038/s41467-025-65530-4

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.com/episodes/gc-bias-correction-metagenomics

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-01-13.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Audited the transcript content for core scientific claims and results described in the article, including GC bias problems in metagenomics, the GuaCAMOLE algorithm, GC-bin strategy and QC, benchmarking results (simulated and mock data), CRC meta-analysis findings, and limitations/future work.
- transcript topics: GC bias in metagenomic sequencing; GuaCAMOLE algorithm overview and alignment-free design; GC-bin read counting and abundance estimation; False-positive taxon filtering and QC; Benchmarking on simulated data and mock communities; Four GC-bias shapes across colorectal cancer gut microbiomes

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 8
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0

Metadata Audited:
- article_doi
- article_title
- article_journal
- license

Factual Items Audited:
- GC content affects sequencing efficiency and biases vary by protocol
- GuaCAMOLE is alignment-free and uses Kraken2/Bracken for initial taxon assignment with GC-bin stratification
- Abundances and GC-dependent sequencing efficiencies are solved simultaneously via least-squares estimation
- False-positive taxa are screened via GC-distribution outlier detection
- Simulated data show mean relative error < 1% for GuaCAMOLE versus 10–30% for Bracken
- Mock community across 28 protocols reveals four distinct GC-efficiency shapes

QC result: Pass.

Küry S et al., Nature Communications, doi:10.1038/s41467-025-65556-8 - 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:
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Article title:
Investigating the neuronal role of the proteasomal ATPase subunit gene PSMC5 in neurodevelopmental proteasomopathies

First author:
Küry S

Journal:
Nature Communications, doi:10.1038/s41467-025-65556-8

DOI:
10.1038/s41467-025-65556-8

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.com/episodes/psmc5-proteasome-neurodevelopment

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-01-12.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Audited the spoken content describing PSMC5/UPS biology, variant effects, multi-model analyses (Drosophila, rat neurons, iPSC-derived NPCs), ISR and IFN signaling, lipid/mitophagy changes, synaptic balance, and therapeutic implications.
- transcript topics: PSMC5 and 26S proteasome function; PSMC5 variants and neurodevelopmental proteasomopathies; Proteotoxic stress and aggresome formation; Mitochondrial dysfunction and mitophagy; Lipid metabolism dysregulation; Integrated stress response (PKR/GCN2) and type I interferon signaling

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 7
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0

Metadata Audited:
- article_doi
- article_title
- article_journal
- license

Factual Items Audited:
- 26 distinct PSMC5 variants identified in 44 individuals
- Variants cluster in the AAA+ ATPase domain; Arg325Trp recurring
- Loss of PSMC5 function impairs proteasome activity, causing proteotoxic stress and aggresome formation
- Mitophagy is increased and lipid metabolism is disrupted (50% increase in cholesterol esters; decreased glycerophospholipids)
- Transcriptomic/type I IFN signature elevated in patient T cells; ISR mediates IFN induction; PKR/GCN2 inhibitors reduce IFN scores; baricitinib (JAK inhibitor) also reduces IFN sco
- Arg325Trp variant impairs neural progenitor cell differentiation in iPSC models

QC result: Pass.

Antunes et al., Nature Communications - 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.

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Article title:
Chromosome compartment assembly is essential for subtelomeric gene silencing in trypanosomes

First author:
Antunes

Journal:
Nature Communications

DOI:
10.1038/s41467-025-66824-3

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.com/episodes/compartment-vsg-silencing

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-01-11.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Substantive auditing focused on the transcript’s coverage of 3D genome compartments (A/B), boundary proteins (RAP1, BDF2, HAT1, HDAC1, ZCW1, etc.), XLMS/SPR validation, Hi-C vs Pore-C insights, and the PIP5Pase–PI(3,4,5)P3–RAP1 axis governing VSG silencing and the consequences of PIP5Pase knockdown or catalytic inactiv
- transcript topics: VSG gene silencing and monoallelic expression; A/B chromosome compartments and 3D genome organization; RAP1 boundaries and subtelomeric spread; PIP5Pase and PI(3,4,5)P3 signaling regulating RAP1; XLMS network and SPR validation of interactions; Hi-C and Pore-C mapping of TADs/loops and boundary interactions

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 7
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0

Metadata Audited:
- article_doi
- article_title
- article_journal
- license

Factual Items Audited:
- Subtelomeric VSG silencing is coupled to chromosome compartmentalization into core (A) and subtelomeric (B) compartments
- RAP1 localizes at compartment boundaries and spreads across subtelomeric regions to enforce silencing
- PIP5Pase dephosphorylates PI(3,4,5)P3, maintaining RAP1 DNA binding and subtelomeric repression
- PIP5Pase knockdown disrupts intra-compartment contacts, displaces RAP1 from boundaries/subtelomeres, and derepresses subtelomeric VSG genes
- Hi-C and Pore-C identify A/B compartments, TADs, and chromatin loops; boundaries co-interact
- Catalytically inactive PIP5Pase displaces RAP1 and derepresses subtelomeric VSG genes

QC result: Pass.

Chen T et al., Nature Communications - Cryo-EM structures, uptake assays, and molecular dynamics show that PIP2 lipids bind at the AE1 dimer interface and inhibit the OF⇌IF conformational transition while substrate binding lowers the transition barrier. Key terms: AE1, PIP2, bicarbonate transport, cryo-EM, molecular dynamics.

Study Highlights:
Three high-resolution cryo-EM states were solved: two inward-facing (IF1, IF2) and one outward-facing (OF). Proteoliposome uptake assays show that depleting or masking PIP2 increases HCO3– and I– transport. MD simulations identify recurring anion binding in the lumen with R730 as a key coordinating residue and estimate tighter HCO3– binding than Cl–. Enhanced-sampling free energy profiles reveal that HCO3– binding lowers the OF⇌IF barrier by ~3 kcal/mol while removing PIP2 lowers it by ~2 kcal/mol. Mechanistically, HCO3– stabilizes a transition-state conformation by promoting R730 contact with the scaffold domain.

Conclusion:
PIP2 stabilizes AE1 in a conformation that raises the transport transition barrier and inhibits activity, whereas substrate binding promotes the transition and facilitates transport.

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Article title:
Impact of anionic lipids on the energy landscape of conformational transition in anion exchanger 1 (AE1)

First author:
Chen T

Journal:
Nature Communications

DOI:
10.1038/s41467-025-66786-6

Reference:
Chen T, Vallese F, Gil-Iturbe E, Kim K, Calì T, Quick M, Clarke OB, Tajkhorshid E. Impact of anionic lipids on the energy landscape of conformational transition in anion exchanger 1 (AE1). Nature Communications. 2025. https://doi.org/10.1038/s41467-025-66786-6

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.com/episodes/pipt2-inhibits-ae1

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-01-10.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Audited the transcript sections describing AE1 elevator mechanism (TD/SD), R730 and ion binding, bicarbonate vs chloride affinity, PIP2 as a regulatory brake, energy landscape via BEUS/SMwST, cross-linking to trap IF, and the three-state (OF, IF1, IF2) structural context, plus functional uptake assays.
- transcript topics: AE1 elevator mechanism (TD/SD architecture); R730 and luminal anion binding sites; Bicarbonate vs chloride binding affinities (Kd values); PIP2 binding site at the dimer interface and K743 salt bridge; PIP2 as molecular brake and its removal increasing activity; Energy landscape and conformational transitions (BEUS/SMwST)

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 8
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0

Metadata Audited:
- article_doi
- article_title
- article_journal
- license

Factual Items Audited:
- PIP2 binds at the AE1 dimer interface and inhibits the OF⇌IF conformational transition.
- Substrate binding (HCO3−) lowers the transition barrier by ~3 kcal/mol.
- PIP2 binding raises the transition barrier by ~2 kcal/mol; removal lowers it.
- R730 is a key coordinating residue for bicarbonate and chloride binding in AE1 lumen.
- HCO3− binding affinity is higher than Cl− in both OF and IF states (Kd values reported).
- AE1 operates via an elevator mechanism with TD translating/rotating relative to SD.

QC result: Pass.

Winterhalter et al., Nature Communications - Cas9 nickases in Bacillus subtilis show that single-strand nicks in either template strand arrest DNA replication, create single-end double-strand breaks, and require homologous recombination plus PriA-dependent helicase reloading for replication restart. Key terms: DNA replication, recombinational repair, AddAB, PriA, SSB.

Study Highlights:
Site-specific nicks created with Cas9D10A block DNA synthesis downstream of the nick and induce RecA bundling in live cells. ChIP-qPCR shows helicase enrichment upstream of nicks and persistence downstream when the leading strand template is nicked, indicating helicase runs off the template for lagging-strand nicks but translocates onto dsDNA for leading-strand nicks. Genetic and marker frequency analyses identify AddAB helicase activity, RecFOR, RecA, RecG and PriA as essential for repair and PriA-dependent helicase reloading to resume replication. SSB C-terminal tail is required to recruit RecO and enable RecA loading, while AddAB nuclease activity is largely dispensable if helicase activity and an alternative nuclease provide ssDNA.

Conclusion:
B. subtilis repairs replisome inactivation at single-strand discontinuities via AddAB-mediated end-processing, RecFOR/RecA-mediated recombination, and PriA-dependent helicase reloading to restart replication

Music:
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Article title:
Rescuing the bacterial replisome at a nick requires recombinational repair and helicase reloading

First author:
Winterhalter

Journal:
Nature Communications

DOI:
10.1038/s41467-025-66550-w

Reference:
Winterhalter, C., Stratton, K.J., Fenyk, S. et al. Rescuing the bacterial replisome at a nick requires recombinational repair and helicase reloading. Nat Commun (2025). https://doi.org/10.1038/s41467-025-66550-w

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.com/episodes/replisome-nick-repair

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-01-09.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Audited the transcript’s presentation of the nickase system, replication arrest, downstream molecular events (AddAB end-processing, SSB recruitment, RecFOR/RecA loading, RecG/RecU roles), PriA-dependent helicase reloading, and the manuscript’s implications for antibiotic strategies.
- transcript topics: Cas9 nickase system in Bacillus subtilis; Replication arrest and MFA evidence; Fate of helicase at leading vs lagging strand nick; PriA-dependent replication restart pathway; AddAB end-processing and SSB recruitment; RecFOR-mediated RecA loading via SSB-CTT

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 8
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0

Metadata Audited:
- article_doi
- article_title
- article_journal
- license

Factual Items Audited:
- Cas9 nickase system creates site-specific nicks in Bacillus subtilis
- Nick on either leading or lagging strand arrests replication downstream
- Replication restart requires recombinational repair and PriA-dependent restart
- AddAB helicase activity is necessary for end-processing; nuclease activity dispensable
- SSB C-terminal tail is required for efficient recombinational repair via RecO recruitment
- RecFOR mediates displacement of SSB to allow RecA loading onto ssDNA

QC result: Pass.

Gao J et al., Nature Communications - H4 tail lysine residues drive liquid-liquid phase separation of 12‑mer nucleosome arrays, while H3 tail acetylation and the histone chaperone Nap1 increase internal dynamics and lower droplet viscosity. Key terms: Nap1, H3 acetylation, H4 acetylation, liquid-liquid phase separation, nucleosome arrays.

Study Highlights:
H4 tail lysine residues are the primary drivers of nucleosome array phase separation, and H4-tail acetylation prevents droplet formation. H3 tail acetylation mimic (H3KQ) and in situ H3 acetylation speed fluorescence recovery, indicating enhanced DNA–histone dynamics. Nap1 dissolves gel-like aggregates formed by tailless H3 arrays, increases nucleosome concentration inside droplets from ~326 µM to ~491 µM, and accelerates internal dynamics. STORM imaging reveals condensed droplets contain both a mobile fraction and a relatively immobile structural scaffold. Optical-tweezers microrheology identifies two relaxation components and shows Nap1 and H3KQ specifically lower the relaxation time and viscosity of the slower scaffold-associated component

Conclusion:
Histone H4 tail lysines govern chromatin phase separation while H3 acetylation and Nap1 tune the fluidity and accessibility of condensed chromatin

Music:
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Article title:
Roles of histone chaperone Nap1 and histone acetylation in regulating phase-separation of nucleosome arrays

First author:
Gao J

Journal:
Nature Communications

DOI:
10.1038/s41467-025-65701-3

Reference:
Gao J, Li H, Tan S, Zhou R & Lee T-H. Roles of histone chaperone Nap1 and histone acetylation in regulating phase-separation of nucleosome arrays. Nature Communications. 2025;16:10672. https://doi.org/10.1038/s41467-025-65701-3

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.com/episodes/nap1-histone-acetylation

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-01-08.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Substantively audited sections cover the core biophysical mechanisms and measurements: LLPS initiation by H4 tail, effects of H4KQ and H3KQ on droplet formation and dynamics, Nap1’s dual role, FRAP, STORM, microrheology with two relaxation components, and H2A–H2B exchange context.
- transcript topics: LLPS of nucleosome arrays driven by H4 tail lysines; H4KQ acetylation mimic blocks droplet formation; H3 tail acetylation mimic (H3KQ) increases dynamics but does not block LLPS; Nap1 dissolves aggregates and increases nucleosome concentration inside condensates; STORM reveals mobile fraction and immobile scaffold inside droplets; Microrheology with optical traps identifying two relaxation components

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 8
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0

Metadata Audited:
- article_doi
- article_title
- article_journal
- license

Factual Items Audited:
- H4 tail lysine residues drive LLPS of nucleosome arrays
- H4KQ acetylation mimic blocks droplet formation
- H3KQ acetylation mimic increases dynamics but does not block condensation
- Nap1 dissolves chromatin aggregates and increases nucleosome concentration inside condensates
- Condensates contain a mobile fraction and a relatively immobile structural scaffold
- Nap1 and H3KQ reduce the slower component's viscosity and shorten its relaxation time

QC result: Pass.

Deivendran D et al., Nature Communications, doi:10.1038/s41467-025-65687-y - Single-cell and spatial multi-omic profiling maps the genetic and transcriptional changes from normal keratinocytes through actinic keratoses to invasive cutaneous squamous cell carcinoma. Key terms: keratinocytes, actinic keratosis, TP53, ARID2, spatial transcriptomics.

Study Highlights:
Single-cell genotyping of 137 keratinocytes revealed most cells have low mutation burdens (median 1.14 mut/Mb) while keratinocytes with TP53 or NOTCH1 mutations carry substantially higher burdens. Deep panel sequencing of 16 paired actinic keratoses and adjacent cSCCs showed TERT promoter and CDKN2A mutations arise in actinic keratoses and additional events such as ARID2 loss and MAPK pathway activation delineate progression to cSCC. Many actinic keratoses were genetically unrelated to their neighboring cSCCs, indicating independent clonal origins despite spatial proximity. Spatial transcriptomics exposed intratumoral heterogeneity and enrichment of immune checkpoint molecules at invasive fronts, implicating localized immune modulation.

Conclusion:
Keratinocyte transformation to cSCC follows a stereotyped sequence where TP53/NOTCH1-associated mutator phenotypes prime cells for acquisition of telomerase activation and cell-cycle defects in precursors, with SWI/SNF disruption and MAPK activation driving invasion alongside spatial immune evasion.

Music:
Enjoy the music based on this article at the end of the episode.

Article title:
Genetic evolution of keratinocytes to cutaneous squamous cell carcinoma

First author:
Deivendran D

Journal:
Nature Communications, doi:10.1038/s41467-025-65687-y

DOI:
10.1038/s41467-025-65687-y

Reference:
Deivendran D, Chen L, Tandukar B, Bandari AK, Cruz-Pacheco N, Sharma H, Wang M, Xu A, Chen DB, George CD, Marty AL, Cho RJ, Cheng JB, Saylor D, Gerami P, Yeh I, Arron ST, Bastian BC, Shain AH. Genetic evolution of keratinocytes to cutaneous squamous cell carcinoma. Nature Communications. 2025;16:10663. https://doi.org/10.1038/s41467-025-65687-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.com/episodes/keratinocytes-to-cscc-evolution

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-01-07.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Audited the spoken content for keratinocyte mutational landscape, mutator phenotype, clonal architecture, AK adjacency to cSCC, SWI/SNF (ARID2) disruption, MAPK activation, spatial transcriptomics, immune evasion, and translational implications.
- transcript topics: Keratinocyte mutation burden in normal skin; Mutator phenotype driven by TP53/NOTCH1 mutations; Single-cell clonality and deep sequencing depth; Actinic keratosis to squamous cell carcinoma progression; ARID2 SWI/SNF disruption and MAPK pathway in invasion; Spatial transcriptomics and intratumoral heterogeneity

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 8
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0

Metadata Audited:
- article_doi
- article_title
- article_journal
- license

Factual Items Audited:
- Keratinocytes in normal skin have a low mutation burden (median around 1 mut/Mb)
- Keratinocytes with TP53 or NOTCH1 mutations show substantially higher mutation burdens (up to ~49.71 mut/Mb)
- Clonal expansion yielded colonies of about 200 cells for sequencing
- Actinic keratoses adjacent to cSCCs are not always clonally related to the neighboring cSCC

QC result: Pass.

McGowan TJ et al., Nature Communications, doi:10.1038/s41467-025-65703-1 - Activated muscle stem cells express and secrete laminin-α2 to remodel their niche, and loss of MuSC-derived laminin-α2 slows MuSC proliferation and delays regeneration in mouse models and human iPSC-derived precursors. Key terms: laminin-α2, muscle stem cells, LAMA2 MD, regeneration, proliferation.

Study Highlights:
Activated MuSCs upregulate Lama2 and deposit laminin-α2 around proliferating cells during early regeneration. MuSCs from Lama2-deficient dyW/dyW mice progress more slowly through S phase, accumulate in G1, and show reduced expansion ex vivo and in vivo. Transplantation of dyW/dyW MuSCs into wild-type muscle does not restore their proliferative capacity, indicating a cell-intrinsic defect. A MuSC-specific Lama2 knockout recapitulates the slower proliferation and reduces early injury-associated laminin-α2, delaying muscle repair. Isogenic human LAMA2 knockout myogenic precursors also incorporate less EdU and show transcriptional changes consistent with impaired cell-cycle progression.

Conclusion:
Self-secreted laminin-α2 is required cell-autonomously for efficient MuSC proliferation and timely muscle regeneration, implicating MuSC dysfunction as a contributor to LAMA2-related muscular dystrophy pathology

Music:
Enjoy the music based on this article at the end of the episode.

Article title:
Loss of cell-autonomously secreted laminin-α2 drives muscle stem cell dysfunction in LAMA2-related muscular dystrophy

First author:
McGowan TJ

Journal:
Nature Communications, doi:10.1038/s41467-025-65703-1

DOI:
10.1038/s41467-025-65703-1

Reference:
McGowan TJ, Reinhard JR, Lewerenz N, Białobrzeska M, Lin S, Stępniewski J, Szade K, Dulak J & Rüegg MA. Loss of cell-autonomously secreted laminin-α2 drives muscle stem cell dysfunction in LAMA2-related muscular dystrophy. Nature Communications (2025) 16:10674. https://doi.org/10.1038/s41467-025-65703-1

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.com/episodes/muscle-stem-laminin-alpha2

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-01-06.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Substantively audited the transcript’s coverage of: MuSC expression/secreted laminin-α2; intrinsic MuSC proliferation defects in dyW/dyW mice; transplantation results; MuSC-specific Lama2 knockout; human LAMA2 KO hiPSC model; and downstream signaling/cell-cycle implications.
- transcript topics: MuSC activation and Lama2 expression; MuSC secretion and remodeling with laminin-α2; dyW/dyW mouse model: regeneration defects and MuSC proliferation; ex vivo MuSC proliferation assays (EdU, cell cycle); MuSC transplantation experiments and intrinsic vs extrinsic defect; MuSC-specific Lama2 knockout effects on proliferation

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 8
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0

Metadata Audited:
- article_doi
- article_title
- article_journal
- license

Factual Items Audited:
- Activated MuSCs express Lama2 and deposit laminin-α2 into their microenvironment
- MuSC-derived laminin-α2 is essential for rapid MuSC expansion and timely muscle regeneration
- Lama2-deficient MuSCs proliferate more slowly ex vivo and show delayed regeneration in dyW/dyW mice
- Transplantation of Lama2-deficient MuSCs shows reduced tissue remodeling capacity in vivo
- MuSC-specific Lama2 knockout slows MuSC proliferation and delays regeneration
- LAMA2 knockout in human hiPSCs slows cell-cycle progression and downregulates G2/M and E2F-related pathways (p53 pathway up)

QC result: Pass.