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Defining TP53 pioneering capabilities with competitive nucleosome binding assays.

ABSTRACT: Accurate gene expression requires the targeting of transcription factors (TFs) to regulatory sequences often occluded within nucleosomes. The ability to target a TF binding site (TFBS) within a nucleosome has been the defining characteristic for a special class of TFs known as pioneer factors. Recent studies suggest TP53 functions as a pioneer factor that can target its TFBS within nucleosomes, but it remains unclear how TP53 binds to nucleosomal DNA. To comprehensively examine TP53 nucleosome binding, we competitively bound TP53 to multiple in vitro-formed nucleosomes containing a high- or low-affinity TP53 TFBS located at differing translational and rotational positions within the nucleosome. Stable TP53-nucleosome complexes were isolated and quantified using next-generation sequencing. Our results demonstrate TP53 binding is limited to nucleosome edges with significant binding inhibition occurring within 50 bp of the nucleosome dyad. Binding site affinity only affects TP53 binding for TFBSs located at the same nucleosomal positions; otherwise, nucleosome position takes precedence. Furthermore, TP53 has strong nonspecific nucleosome binding facilitating its interaction with chromatin. Our in vitro findings were confirmed by examining TP53-induced binding in a cell line model, showing induced binding at nucleosome edges flanked by a nucleosome-free region. Overall, our results suggest that the pioneering capabilities of TP53 are driven by nonspecific nucleosome binding with specific binding at nucleosome edges.

SUBMITTER: Yu X

PROVIDER: S-EPMC6314159 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature

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Defining TP53 pioneering capabilities with competitive nucleosome binding assays.

Yu Xinyang X Buck Michael J MJ

Genome research 20181108 1

Accurate gene expression requires the targeting of transcription factors (TFs) to regulatory sequences often occluded within nucleosomes. The ability to target a TF binding site (TFBS) within a nucleosome has been the defining characteristic for a special class of TFs known as pioneer factors. Recent studies suggest TP53 functions as a pioneer factor that can target its TFBS within nucleosomes, but it remains unclear how TP53 binds to nucleosomal DNA. To comprehensively examine TP53 nucleosome b ...[more]

PMID: 30409772

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Project description:ImportanceClassifying hospitals across a wide range of pediatric capabilities, including medical, surgical, and specialty services, would improve understanding of access and outcomes.ObjectiveTo develop a classification system for hospitals' pediatric capabilities.Design, setting, and participantsThis cross-sectional study included data from 2019 on all acute care hospitals with emergency departments in 10 US states that treated at least 1 child per day. Statistical analysis was performed from September 2023 to February 2024.ExposurePediatric hospital capability level, defined using latent class analysis. The latent class model parameters were the presence or absence of 26 functional capabilities, which ranged from performing laceration repairs to performing organ transplants. A simplified approach to categorization was derived and externally validated by comparing each hospital's latent class model classification with its simplified classification using data from 3 additional states.Main outcomes and measuresHealth care utilization and structural characteristics, including inpatient beds, pediatric intensive care unit (PICU) beds, and referral rates (proportion of patients transferred among patients unable to be discharged).ResultsUsing data from 1061 hospitals (716 metropolitan [67.5%]) with a median of 2934 pediatric ED encounters per year (IQR, 1367-5996), the latent class model revealed 4 pediatric levels, with a median confidence of hospital assignment to level of 100% (IQR, 99%-100%). Of 26 functional capabilities, level 1 hospitals had a median of 24 capabilities (IQR, 21-25), level 2 hospitals had a median of 13 (IQR, 11-15), level 3 hospitals had a median of 8 (IQR, 6-9), and level 4 hospitals had a median of 3 (IQR, 2-3). Pediatric level 1 hospitals had a median of 66 inpatient beds (IQR, 42-86), level 2 hospitals had a median of 16 (IQR, 9-22), level 3 hospitals had a median of 0 (IQR, 0-6), and level 4 hospitals had a median of 0 (IQR, 0-0) (P < .001). Level 1 hospitals had a median of 19 PICU beds (IQR, 10-28), level 2 hospitals had a median of 0 (IQR, 0-5), level 3 hospitals had a median of 0 (IQR, 0-0), and level 4 hospitals had a median of 0 (IQR, 0-0) (P < .001). Level 1 hospitals had a median referral rate of 1% (IQR, 1%-3%), level 2 hospitals had a median of 25% (IQR, 9%-45%), level 3 hospitals had a median of 70% (IQR, 52%-84%), and level 4 hospitals had a median of 100% (IQR, 98%-100%) (P < .001).Conclusions and relevanceIn this cross-sectional study of hospitals from 10 US states, a system to classify hospitals' pediatric capabilities in 4 levels was developed and was associated with structural and health care utilization characteristics. This system can be used to understand and track national pediatric acute care access and outcomes.

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Defining TP53 pioneering capabilities with competitive nucleosome binding assays.

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Defining TP53 pioneering capabilities with competitive nucleosome binding assays.

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