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,…

Chen T et al., Nat Commun - 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 conform…

Winterhalter et al., Rescuing the bacterial replisome at a nick requires recombinational repair and helicase reloading. Nat Commun ( - 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 helicas…

Gao J et al., Nat Commun - 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 H…

️ Episode 252: Keratinocytes to cSCC: genetic steps In this episode of PaperCast Base by Base, we explore 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 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…

️ Episode 251: MuSCs, laminin-α2 and LAMA2 MD In this episode of PaperCast Base by Base, we explore 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 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 impai…

️ Episode 250: CIP2A–TOPBP1: Mitotic repair via MiDAS and MMEJ In this episode of PaperCast Base by Base, we explore This study shows the CIP2A-TOPBP1 complex coordinates two mitotic double-strand break repair pathways, MiDAS and MMEJ, by recruiting SLX4/SMX components and Polθ to mitotic chromatin. Study Highlights:TOPBP1 BRCT1/2 binds SLX4 phosphorylated at Thr1260, a CDK1-dependent modification that promotes recruitment of SLX4, MUS81 and ERCC1 to mitotic chromatin to drive MiDAS. CIP2A is required for mitotic chromatin localisation of both TOPBP1 and Polθ, enabling Polθ-dependent MMEJ. Loss of CIP2A impairs both MiDAS and MMEJ, increasing micronuclei, γH2AX and 53BP1 and reducing proliferation under replication stress. Pharmacological Polθ inhibition combined with disruption of the TOPBP1–SLX4 interaction further elevates genome instability and selectively limits growth of BRCA1/2-deficient cells. Conclusion:The CIP2A-TOPBP1 axis is a central mitotic DNA repair hub that integrates…

️ Episode 249: PCM1 links centrosome asymmetry to endosome dynamics In this episode of PaperCast Base by Base, we explore In developing neural progenitors PCM1 localizes to the mother centrosome and to Notch ligand-containing endosomes, promoting Par-3/dynein assembly and Rab5-to-Rab11 trafficking to bias posterior-directed endosome segregation and preserve progenitor fate Study Highlights:Pcm1 is asymmetrically enriched at the posterior mother centrosome (Cep83+) in zebrafish radial glia progenitors and is also found on central-zone Notch ligand (Dld)-containing endosomes. In vivo time-lapse imaging and expansion microscopy show Pcm1 puncta move with Dld endosomes and promote posterior-directed polarized dynamics. Loss of pcm1 disrupts Rab5b-to-Rab11a trafficking, reduces Par-3 and dynein co-assembly on recycling endosomes, lowers Notch signaling, and shifts divisions toward neuron–neuron outcomes at the expense of progenitors. Similar PCM1–PARD3–CEP83–RAB11 associations and asymmetr…