Base by Base

Gustavo Barra
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Base by Base explores advances in genetics and genomics, with a focus on gene-disease associations, variant interpretation, protein structure, and insights from exome and genome sequencing. Each episode breaks down key studies and their clinical relevance—one base at a time. Powered by AI, Base by Base offers a new way to learn on the go. Special thanks to authors who publish under CC BY 4.0, making open-access science faster to share and easier to explore.

  1. 7時間前

    338: WDHD1 and Microcephalic Primordial Dwarfism

    Tibbe D et al., The American Journal of Human Genetics - This study identifies bi-allelic hypomorphic WDHD1 variants in 17 subjects with a clinical spectrum from fetal lethality to microcephalic primordial dwarfism and characterizes cellular defects in patient-derived cells linked to replisome dysfunction. Key terms: WDHD1, microcephalic primordial dwarfism, replication stress, sister chromatid cohesion, splicing variants. Study Highlights: Researchers found bi-allelic WDHD1 variants in 17 subjects presenting with intrauterine growth retardation, microcephaly and a spectrum of organ abnormalities including neonatal acute liver failure. Several intronic variants cause aberrant splicing and markedly reduced WDHD1 protein levels in fibroblasts. Subject-derived cells showed slowed replication fork progression, impaired G1-to-S transition, increased spontaneous DNA damage, abnormal nuclear morphology, and elevated premature sister chromatid separation, supporting a role for WDHD1 in replisome stability and cohesion. Conclusion: Hypomorphic bi-allelic WDHD1 variants cause an autosomal recessive microcephalic primordial dwarfism spectrum by reducing WDHD1 protein and impairing replication fork stability, genome integrity, and sister chromatid cohesion, establishing WDHD1 as essential for normal human growth and development. Music: Enjoy the music based on this article at the end of the episode. Article title: Bi-allelic WDHD1 variants cause microcephalic primordial dwarfism First author: Tibbe D Journal: The American Journal of Human Genetics DOI: 10.1016/j.ajhg.2026.03.010 Reference: Tibbe D., Vogt M.R., Holling T., et al. Bi-allelic WDHD1 variants cause microcephalic primordial dwarfism. The American Journal of Human Genetics. 2026. https://doi.org/10.1016/j.ajhg.2026.03.010 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/wdhd1-microcephalic-primordial-dwarfism QC: This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-04-10. QC Scope: - article metadata and core scientific claims from the narration - excludes analogies, intro/outro, and music - transcript coverage: Audited the transcript's coverage of WDHD1 function as replisome scaffold; intronic WDHD1 variants and splicing; DNA fiber assay and replication fork dynamics; γH2AX signaling; nuclear morphology; PCS; and liver pathology in MPD. - transcript topics: WDHD1 as replisome scaffold; intronic WDHD1 variants and splicing; DNA fiber assay and replication fork speed; γH2AX DNA damage signaling; nuclear morphology and lamin B1; premature sister chromatid separation (PCS) QC Summary: - factual score: 10/10 - metadata score: 10/10 - supported core claims: 7 - claims flagged for review: 0 - metadata checks passed: 6 - metadata issues found: 0 Metadata Audited: - doi - article_title - article_journal - license - episode_title - episode_description Factual Items Audited: - 17 subjects from 14 families with bi-allelic WDHD1 variants and MPD spectrum - intronic WDHD1 variants cause aberrant splicing and markedly reduced WDHD1 protein levels in patient-derived cells - WDHD1 acts as replisome scaffolding to stabilize replication forks and maintain genome integrity - replication fork progres...

    22分
  2. 337: ND-CNVs and internalizing–cardiometabolic multimorbidity

    1日前

    337: ND-CNVs and internalizing–cardiometabolic multimorbidity

    Katzourou IK et al., The American Journal of Human Genetics - Population analysis of ~459,000 UK Biobank participants shows that carriers of neurodevelopmental CNVs (ND-CNVs) have higher odds of co-occurring internalizing (depression, anxiety, somatic) and cardiometabolic conditions (hypertension, dyslipidemia, obesity, T2D, CKD). Effects are stronger for deletions than duplications, greater in females, and linked to the number of haploinsufficient genes within deletions. Key terms: copy-number variants, multimorbidity, internalizing disorders, cardiometabolic, UK Biobank. Study Highlights: Using CNV calls and linked EHRs in the UK Biobank, the authors tested associations between 54 ND-CNVs and combinations of internalizing and cardiometabolic conditions (ICM-MM). Aggregated ND-CNV carriers (n≈7,546; ~1.6%) had higher odds of ICM-MM (OR range 1.21–1.57) and a higher ICM-MM frequency (14.2% vs 11.5%). Deletions showed stronger effects than duplications and the number of haploinsufficient genes in deletions was associated with greater ICM-MM risk. No robust interactions were detected between ND-CNV status and polygenic risk scores after multiple testing correction. Conclusion: ND-CNVs increase risk of internalizing–cardiometabolic multimorbidity at the population level, especially for deletions and in females, suggesting the need for heightened clinical monitoring of carriers. Music: Enjoy the music based on this article at the end of the episode. Article title: Neurodevelopmental copy-number variants increase risk of internalizing and cardiometabolic multimorbidity: Findings from the UK Biobank First author: Katzourou IK Journal: The American Journal of Human Genetics DOI: 10.1016/j.ajhg.2026.02.021 Reference: Katzourou IK, LINC consortium, Barroso I, et al. Neurodevelopmental copy-number variants increase risk of internalizing and cardiometabolic multimorbidity: Findings from the UK Biobank. The American Journal of Human Genetics. 2026;113:1–11. https://doi.org/10.1016/j.ajhg.2026.02.021 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/nd-cnv-internalizing-cardiometabolic-multimorbidity QC: This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-04-08. QC Scope: - article metadata and core scientific claims from the narration - excludes analogies, intro/outro, and music - transcript coverage: Audited transcript sections covering ND-CNV–ICM-MM association, UK Biobank design and CNV calling, dosage-sensitivity (haploinsufficient vs triplosensitive), deletion vs duplication effects (notably 16p11.2), sex differences, PRS interaction analyses, and clinical implications including multidisciplinary care and casca - transcript topics: Definition of ND-CNVs and ICM-MM; UK Biobank cohort size, CNV calling methods (PennCNV); Dosage sensitivity: haploinsufficient vs triplosensitive genes; Deletion vs duplication effects on ICM-MM and obesity; 16p11.2 region emphasis; Sex differences in ND-CNV associations QC Summary: - factual score: 10/10 - metadata score: 10/10 - supported core claims: 7 - claims flagged for review: 0 - metadata checks passed: 7 - metadata issues found: 0 Metadata Audited: - article_doi - article_title - article_journal - license - episode_title - ep...

    23分
  3. 336: Measuring disease likelihood in genomic ascertainment

    3日前

    336: Measuring disease likelihood in genomic ascertainment

    Sapp JC et al., The American Journal of Human Genetics - A longitudinal study of recipients of medically actionable secondary genomic findings develops a Bayesian approach that integrates variant, family genotypic, and phenotypic data to estimate the probability that a secondary finding represents a true clinicomolecular diagnosis, with a detailed analysis of BRCA1/BRCA2 families and implications for screening policy and clinical management. Key terms: secondary findings, BRCA1, BRCA2, Bayesian risk assessment, population genomic screening. Study Highlights: The team enrolled 227 secondary findings recipients and completed genotyping and deep phenotyping for 163 probands, using cascade testing and variant reclassification. They piloted a Bayesian method combining prior population prevalence, variant pathogenicity, and family genotype–phenotype data to estimate clinicomolecular diagnosis (CMD) probabilities for BRCA1/2 families. CMD probabilities varied widely (26.2% to >99.9%) and over half of BRCA1/2 families met NCCN diagnostic testing criteria, indicating underuse of diagnostic testing. Conclusion: In opportunistic secondary findings contexts the posterior probability that a patient has the implicated monogenic disease can differ substantially from variant pathogenicity; integrating familial genotypic and phenotypic data via Bayesian methods refines risk estimates and should guide shared decision-making, management strategies, and policy for population genomic screening. Music: Enjoy the music based on this article at the end of the episode. Article title: Measuring disease likelihood in genomic ascertainment First author: Sapp JC Journal: The American Journal of Human Genetics DOI: 10.1016/j.ajhg.2026.03.009 Reference: Sapp JC, Lewis KL, Modlin EW, et al. Measuring disease likelihood in genomic ascertainment. The American Journal of Human Genetics. 2026;113:1–12. doi:10.1016/j.ajhg.2026.03.009 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/measuring-disease-likelihood-genomic-ascertainment QC: This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-04-07. QC Scope: - article metadata and core scientific claims from the narration - excludes analogies, intro/outro, and music - transcript coverage: Audited transcript sections describing the Bayesian CMD approach, the BRCA1/BRCA2 findings, the Family 8334 case, NCCN criteria implications, and study design/limitations. - transcript topics: ACMG secondary findings context and selection bias; Bayesian probability model for CMD; Cascade testing and family data integration; BRCA1 vs BRCA2 variant distribution and penetrance; NCCN criteria and clinical testing underutilization; Study design and recruitment (163 probands from 41 sources) QC Summary: - factual score: 10/10 - metadata score: 10/10 - supported core claims: 5 - claims flagged for review: 0 - metadata checks passed: 4 - metadata issues found: 0 Metadata Audited: - doi - article_title - article_journal - license Factual Items Audited: - CMD probability range across BRCA1/BRCA2 families: 26.2% to 100% - Baseline posterior probability for BRCA2-related CMD: 58.2% - Posterior CMD probability for family 8334: 99.2% - Average CMD probabi...

    24分
  4. 335: Altai Neandertal Genome Reveals Deep Population Structure

    5日前

    335: Altai Neandertal Genome Reveals Deep Population Structure

    Massilania D et al., PNAS - We summarize a PNAS study reporting a ~37× genome from a ~110,000-year-old male Neandertal (Denisova 17) from Denisova Cave. The genome shows D17 is closely related to an earlier Denisova Neandertal (D5), both carry Denisovan introgressed segments, and Neandertal groups displayed high regional differentiation and small, isolated populations in the Altai. Key terms: Neandertal, Denisova Cave, genome sequencing, population structure, Denisovan admixture. Study Highlights: The authors generated a high-coverage (~37-fold) autosomal genome from a ~110,000-year-old male Neandertal (D17) from Denisova Cave and dated it to ~110 kya. D17 is more closely related to an older Denisova Neandertal (D5) than to European or other Altai Neandertals and both D5 and D17 contain Denisovan-derived genomic segments. Patterns of homozygosity indicate smaller, more isolated groups in Altai Neandertals compared with later European Neandertals. Estimated FST shows Eastern and Western Neandertals were as genetically differentiated as the most divergent present-day human populations, implying rapid drift under small effective sizes. Conclusion: A high-coverage Altai Neandertal genome reveals Denisovan admixture in older eastern Neandertals, small and isolated group sizes in the Altai, and pronounced east–west Neandertal population differentiation exceeding that seen among modern human populations. Music: Enjoy the music based on this article at the end of the episode. Article title: A high-coverage Neandertal genome from the Altai Mountains reveals population structure among Neandertals First author: Massilania D Journal: PNAS DOI: 10.1073/pnas.2534576123 Reference: Massilania D, Peyrégne S, Iasi LN M, de Filippo C, Mafessoni F, Mesab AB, Sümer AP, Swiel Y, Popli D, Silverman S, Boylea MJ, Kozlikind MB, Shunkov MV, Derevianko AP, Higham T, Douka K, Meyer M, Zeberg H, Kelso J, Pääbo S. A high-coverage Neandertal genome from the Altai Mountains reveals population structure among Neandertals. PNAS. 2026;123(13):e2534576123. doi:10.1073/pnas.2534576123 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/d17-altai-neandertal-genome-structure QC: This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-04-05. QC Scope: - article metadata and core scientific claims from the narration - excludes analogies, intro/outro, and music - transcript coverage: Substantive audit focused on the transcript sections describing: specimen, sequencing coverage, population structure, Denisovan admixture, autozygosity and small group sizes, FST differentiation, and dating of D17/D5 lineages, plus migration/replacement dynamics. - transcript topics: Denisova 17 (D17) DNA extraction and high-coverage genome (~37x); Relationship among Neandertals (D17, D5, Chag8, Vi33.19) and Denisovans; Denisovan introgression into D17 and D5; lack of clear Denisovan signal in Chag8; Autozygosity and small population sizes (50 individuals) in Eastern Neandertals; Genetic differentiation (FST ~0.30) between Eastern and Western Neandertals; Molecular dating and age estimates for D17 (~110 kya) and Y-chromosome lineage QC Summary: - factual score: 10/10 - metadata score: 10/10 - supported core claims: 6 - claims flagged for review: 0 - metadata c...

    24分
  5. 334: LINE-1 Recombination with Diverse RNAs

    5日前

    334: LINE-1 Recombination with Diverse RNAs

    Law C-T et al., Cell Genomics - Law and Burns introduce TiMEstamp, a comparative-genomics pipeline that dates LINE-1 insertions from multiple sequence alignments and discovers hundreds of LINE-1 chimeric insertions fused to diverse RNAs across mammalian evolution. Key terms: LINE-1, TiMEstamp, chimeric insertions, retrotransposition, comparative genomics. Study Highlights: The authors developed TiMEstamp to infer TE insertion times from multispecies MSAs and to detect contemporaneous 5′ sequences fused to LINE-1. They compiled a large catalog of LINE-1 chimeras (reported >700 events) including known U6/LINE-1 cases and newly identified partners such as tRNA, 28S rRNA, 7SL, Y RNA, Alu elements, and mRNA 5′ transductions. Alu/LINE-1 chimeras (452 events) and 17 mRNA/lncRNA 5′ transductions were characterized with TSDs, EN motifs, and orientation/length patterns. They also show that promoter co-option (e.g., RAP1GDS1 driving a spliced intronic L1PA2) can restore retrotransposition competence. Conclusion: Comparative MSA-based timing reveals widespread, recurrent recombination between LINE-1 RNA and diverse cellular RNAs, producing chimeric insertions that have contributed to transposon diversification and provide mechanisms (RNA ligation, template switching, twin priming, promoter co-option) that may influence TE evolution and somatic/germline retrotransposition. Music: Enjoy the music based on this article at the end of the episode. Article title: Comparative genomics reveals LINE-1 recombination with diverse RNAs First author: Law C-T Journal: Cell Genomics DOI: 10.1016/j.xgen.2026.101165 Reference: Law C-T and Burns K.H., 2026. Comparative genomics reveals LINE-1 recombination with diverse RNAs. Cell Genomics 6, 101165. https://doi.org/10.1016/j.xgen.2026.101165 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/line1-recombination-diverse-rnas QC: This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-04-05. QC Scope: - article metadata and core scientific claims from the narration - excludes analogies, intro/outro, and music - transcript coverage: Audited sections covering the TiMEstamp workflow and data (MSA across mammals), discovery of chimeric LINE-1 insertions (tRNA halves, 28S rRNA, 7SL, Y RNA, 7SK), Alu/LINE-1 chimeras, mRNA/lncRNA 5' transductions (MAP3K13, FHIT), RAP1GDS1 promoter co-option, twin priming and trans-splicing mechanisms, and study limitati - transcript topics: LINE-1 retrotransposition mechanics (TPRT); TiMEstamp methodology and MSA dating; Chimeric LINE-1 insertions with non-LINE-1 RNAs (tRNA halves, 28S rRNA, 7SL, Y RNA, 7SK RNA); Alu/LINE-1 chimeras and temporal activity; 5′ transductions involving mRNAs/lncRNAs (MAP3K13, FHIT, RAP1GDS1); RAP1GDS1 promoter co-option and transcriptional rescue QC Summary: - factual score: 10/10 - metadata score: 10/10 - supported core claims: 7 - claims flagged for review: 0 - metadata checks passed: 5 - metadata issues found: 0 Metadata Audited: - article_doi - article_title - article_journal - license - episode_title Factual Items Audited: - TiMEstamp uses MSAs across mammals to date LINE-1 insertions and identify contemporaneous adjacencies - Chimeric LINE-1 insertions involve dive...

    22分
  6. 333: Holistic determination of cfDNA ends

    6日前

    333: Holistic determination of cfDNA ends

    Jiang P et al., Cell Genomics - This episode reviews a Cell Genomics study that uses ssDNA '2-end' and novel '4-end' sequencing to profile native 5′ and 3′ termini of plasma cfDNA. The work identifies PREM/POEM markers, links 3′ ends to methylation, and shows improved HCC detection. Key terms: cfDNA fragmentomics, 3' end motifs, 4-end sequencing, hepatocellular carcinoma, DNASE1L3. Study Highlights: The authors adapted single-stranded library preparation (2-end sequencing) to measure native 5′ (EM5) and 3′ (EM3) end motifs and defined flanking PREM and POEM motifs. Combining size‑stratified PREM, EM5, EM3, and POEM features raised hepatocellular carcinoma (HCC) detection to an AUC of 0.95. Fragmentomics-based methylation analysis of 3′ ends (3′ FRAGMA) improved HCC detection further (AUC 0.97). A novel 4-end sequencing approach captured all four termini of double‑stranded cfDNA, yielding 4‑end motif models with AUC up to 0.98 and revealing coordinated nuclease activity, notably DNASE1L3 involvement. Conclusion: Holistic end profiling of cfDNA—integrating native 5′ and 3′ ends, flanking motifs, methylation-informed fragmentomics, and four‑end resolution—enhances cancer detection performance and provides mechanistic insight into coordinated nuclease-mediated fragmentation, warranting larger validation studies. Music: Enjoy the music based on this article at the end of the episode. Article title: Holistic determination of ends of cfDNA molecules First author: Jiang P Journal: Cell Genomics DOI: 10.1016/j.xgen.2026.101142 Reference: Jiang P., Ma M.-J. L., Qiao R., et al. Holistic determination of ends of cfDNA molecules. Cell Genomics. 2026;6:101142. doi:10.1016/j.xgen.2026.101142 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/holistic-cfdna-ends-episode-333 QC: This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-04-04. QC Scope: - article metadata and core scientific claims from the narration - excludes analogies, intro/outro, and music - transcript coverage: Audited the transcript’s substantive description of 2-end sequencing (EM5/EM3), PREM/POEM, 3'-FRAGMA, 4-end sequencing, nuclease signatures (DNASE1L3, DNASE1, DFFB), HCC diagnostic performance (AUC values), fragment-size context, and translational limitations as reported in the article. - transcript topics: 2-end sequencing preserving native ends (EM5/EM3); Pre-end (PREM) and post-end motifs (POEM); 4-end sequencing with stem-loop adapters and PacBio SMRT; 3'-FRAGMA methylation analysis; Nuclease-specific end motifs and coordinated fragmentation (DNASE1L3, DNASE1, DFFB); HCC detection performance and AUC values 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 - episode_title - episode_number - season Factual Items Audited: - 2-end sequencing preserves native 5' and 3' ends (EM5/EM3) by omitting end-repair during library prep - PREM and POEM motifs are defined and analyzed as end-motif neighbors around EM5 and EM3 - 4-end sequencing enables simultaneous assessment of all four ter...

    25分

  7. 6日前

    333: Holistic determination of cfDNA ends

    Jiang P et al., Cell Genomics - This episode reviews a Cell Genomics study that uses ssDNA '2-end' and novel '4-end' sequencing to profile native 5′ and 3′ termini of plasma cfDNA. The work identifies PREM/POEM markers, links 3′ ends to methylation, and shows improved HCC detection. Key terms: cfDNA fragmentomics, 3' end motifs, 4-end sequencing, hepatocellular carcinoma, DNASE1L3. Study Highlights: The authors adapted single-stranded library preparation (2-end sequencing) to measure native 5′ (EM5) and 3′ (EM3) end motifs and defined flanking PREM and POEM motifs. Combining size‑stratified PREM, EM5, EM3, and POEM features raised hepatocellular carcinoma (HCC) detection to an AUC of 0.95. Fragmentomics-based methylation analysis of 3′ ends (3′ FRAGMA) improved HCC detection further (AUC 0.97). A novel 4-end sequencing approach captured all four termini of double‑stranded cfDNA, yielding 4‑end motif models with AUC up to 0.98 and revealing coordinated nuclease activity, notably DNASE1L3 involvement. Conclusion: Holistic end profiling of cfDNA—integrating native 5′ and 3′ ends, flanking motifs, methylation-informed fragmentomics, and four‑end resolution—enhances cancer detection performance and provides mechanistic insight into coordinated nuclease-mediated fragmentation, warranting larger validation studies. Music: Enjoy the music based on this article at the end of the episode. Article title: Holistic determination of ends of cfDNA molecules First author: Jiang P Journal: Cell Genomics DOI: 10.1016/j.xgen.2026.101142 Reference: Jiang P., Ma M.-J. L., Qiao R., et al. Holistic determination of ends of cfDNA molecules. Cell Genomics. 2026;6:101142. doi:10.1016/j.xgen.2026.101142 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/holistic-cfdna-ends-episode-333 QC: This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-04-04. QC Scope: - article metadata and core scientific claims from the narration - excludes analogies, intro/outro, and music - transcript coverage: Audited the transcript’s substantive description of 2-end sequencing (EM5/EM3), PREM/POEM, 3'-FRAGMA, 4-end sequencing, nuclease signatures (DNASE1L3, DNASE1, DFFB), HCC diagnostic performance (AUC values), fragment-size context, and translational limitations as reported in the article. - transcript topics: 2-end sequencing preserving native ends (EM5/EM3); Pre-end (PREM) and post-end motifs (POEM); 4-end sequencing with stem-loop adapters and PacBio SMRT; 3'-FRAGMA methylation analysis; Nuclease-specific end motifs and coordinated fragmentation (DNASE1L3, DNASE1, DFFB); HCC detection performance and AUC values 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 - episode_title - episode_number - season Factual Items Audited: - 2-end sequencing preserves native 5' and 3' ends (EM5/EM3) by omitting end-repair during library prep - PREM and POEM motifs are defined and analyzed as end-motif neighbors around EM5 and EM3 - 4-end sequencing enables simultaneous assessment of all four ter...

  8. 332: When Chromatin Filters Force: Age, AP-1, and Fibroblast Mechanotransduction

    4月2日

    332: When Chromatin Filters Force: Age, AP-1, and Fibroblast Mechanotransduction

    Liao Y et al., PNAS - Human dermal fibroblasts from young and old donors were embedded in 3D collagen and exposed to mechanical tension and TGF-β. Combining bulk RNA‑seq, ATAC‑seq, imaging, and perturbations, the study shows that matrix tension amplifies TGF‑β responses in young but not aged cells and identifies AP‑1 as a central chromatin-associated regulator required for fibroblast activation. Key terms: chromatin accessibility, mechanotransduction, aging, TGF-β signaling, AP-1. Study Highlights: Young fibroblasts under matrix tension mount a strong, synergistic transcriptional response to TGF‑β while aged fibroblasts exhibit blunted or divergent responses. Age-dependent differences in chromatin accessibility, notably at distal regulatory elements, correlate with these transcriptional outcomes. AP‑1 family motifs are highly enriched in TGF‑β- and age-responsive accessible regions and cooperate with age-specific TFs. Inhibiting AP‑1 activity prevents JUNB recruitment to RNA polymerase II and suppresses myofibroblast activation. Conclusion: 3D chromatin accessibility acts as a dynamic filter of mechanical and biochemical signals during aging; AP‑1 and its regulatory network drive the age-specific chromatin remodeling that permits synergistic tension + TGF‑β responses in young fibroblasts, and AP‑1 inhibition blocks this activation, suggesting a potential therapeutic axis. Music: Enjoy the music based on this article at the end of the episode. Article title: Chromatin accessibility regulates age- dependent nuclear mechanotransduction First author: Liao Y Journal: PNAS DOI: 10.1073/pnas.2522217123 Reference: Liao Y, Land M, Gupta R, Yu L, Sornapudi TR, Shivashankar GV. Chromatin accessibility regulates age-dependent nuclear mechanotransduction. PNAS. 2026;123(13):e2522217123. doi:10.1073/pnas.2522217123. Published March 26, 2026. 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/base-by-base-332-chromatin-age-mechanotransduction QC: This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-04-02. QC Scope: - article metadata and core scientific claims from the narration - excludes analogies, intro/outro, and music - transcript coverage: Substantive auditing covered the study’s central mechanistic story: aging as a chromatin-filter for mechanochemical signaling; AP-1 as master regulator; age-specific TF partnerships; the 3D collagen tension model; ATAC-seq/RNA-seq integration; and AP-1 perturbation experiments. - transcript topics: Aging as chromatin-based signaling filter; 3D collagen gel tension model with glass ring; TGF-β signaling and mechanical tension synergy; AP-1 as master regulator; age-specific partners (JUNB vs HOXB13); ATAC-seq and RNA-seq integration; Perturbation experiments (siJUNB, T-5224, kinase inhibitors) QC Summary: - factual score: 10/10 - metadata score: 9/10 - 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 - publish_description_text Factual Items Audited: - Young fibroblasts exhibit synergistic gene expression enhancement to combined mechanical tension and TGF-β; aging cells show a blunted/diverg...

    23分
すべて見る（341）

番組について

Base by Base explores advances in genetics and genomics, with a focus on gene-disease associations, variant interpretation, protein structure, and insights from exome and genome sequencing. Each episode breaks down key studies and their clinical relevance—one base at a time. Powered by AI, Base by Base offers a new way to learn on the go. Special thanks to authors who publish under CC BY 4.0, making open-access science faster to share and easier to explore.

情報

  • クリエイター
    Gustavo Barra
  • 配信期間
    25年 - 26年
  • エピソード
    341
  • 制限指定
    不適切な内容を含まない
  • Copyright
    © Gustavo Barra
  • 番組のWebサイト
    Base by Base

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