Biology subjects

Paramo, M. I.

Publications and source records attributed to Paramo, M. I..

4 recordsLinked to original sources

bioRxiv2025

The regulatory landscape of nascent transcription in human health and disease

Transcriptional regulatory elements (TREs) orchestrate gene expression programs fundamental to cellular identity and transitions across physiological and pathological states. Here, we present a high-resolution atlas of RNA Polymerase II-engaged TREs (enhancers and promoters) across all major human organ systems and a broad spectrum of developmental and disease states. This atlas is generated using PRO-cap, a highly sensitive method that detects nascent RNA at transcription initiation sites, a critical feature of active TREs. The base-pair resolution of PRO-cap enables systematic dissection of transcription initiation architecture, revealing associations among tissue specificity, evolutionary constraint, transcription factor usage, and regulatory connectivity. Integration with deep learning models such as ProCapNet further provides a framework for prioritizing noncoding variants from GWAS and eQTL studies. Moreover, this tissue-resolved atlas identifies lineage-specific regulatory programs and their alterations in diseases such as metastatic cancer, where TRE landscapes capture regulatory signatures reflecting both tissue of origin and adaptive responses to distant niches. Together, these findings establish transcription initiation at regulatory elements as a defining and mechanistically informative layer of gene regulation across development, physiology, and disease.

genomics↗

bioRxiv2025

Simultaneous measurement of intrinsic promoter and enhancer potential reveals principles of functional duality and regulatory reciprocity

Accumulating evidence indicates that both promoters and enhancers are capable of exerting promoter and enhancer functions; however, the relationship between these two activities within individual elements and the determinants of this dual functionality remain poorly understood. We developed a massively parallel dual reporter assay that enables simultaneous assessment of the intrinsic promoter and enhancer potential exerted by the same sequence. Parallel quantification for thousands of elements reveals that canonical human promoters and enhancers can act as both promoters and enhancers under the same contexts, and that promoter activity may be necessary but not sufficient for enhancer function. Perturbations to element transcription factor binding motifs lead to disruptions in both activities, implicating a shared syntax for the two regulatory functions. Combinations of elements with different minimal promoters reveal reciprocal activity modulation, which, together with a strong correlation between promoter and enhancer functions, imply a bidirectional feedback loop to sustain environments of high transcriptional activity. Finally, we validate this reciprocity and correlation in situ using CRISPR activation at the human {beta}-globin locus. Our approach reveals that the functional convergence between promoters and enhancers arises from a shared regulatory logic and sequence syntax, advancing a unified model for regulatory element biology.

genomics↗

bioRxiv2024

Directionality of Transcriptional Regulatory Elements

Divergent transcription is a critical marker of active transcriptional regulatory elements (TREs), including enhancers and promoters, in mammals. However, distal elements with unidirectional transcriptional patterns are often overlooked, leaving their identity and function poorly understood. Here, we performed a systematic comparison between divergent and unidirectional elements, revealing their distinct architectural and functional features. Our analysis also shows that unidirectional elements have younger sequence ages and are under weaker evolutionary constraints than divergent elements, indicating that they may represent a unique category of genomic regulatory function with more recent origins. Notably, we observed that some transcription factors, including CTCF, AP1, SP, and NFY, exhibit dual roles in modulating the directionality of TREs, either activating or repressing nascent transcription in a position-dependent manner. Overall, the elucidation of directionality enhances our understanding of the diverse architectural models, functional features, evolutionary dynamics, and regulatory logic of TREs.

molecular biology↗

bioRxiv2022

Capped nascent RNA sequencing reveals novel therapy-responsive enhancers in prostate cancer

Mounting evidence suggests that enhancer RNA (eRNA) transcription start sites (TSSs) provide higher sensitivity and specificity for enhancer identification than histone modifications and chromatin accessibility. The extent to which changes in eRNA transcription correspond to changes in enhancer activity, however, remains unclear. Here, we used precision run-on and capped RNA sequencing (PRO-cap) to assess changes in enhancer activity in response to treatment with the androgen receptor signaling inhibitor, enzalutamide (ENZ). We identified 6,189 high-confidence candidate enhancers in the human prostate cancer cell line, LNCaP; 853 of which demonstrated significant changes in activity in response to drug treatment. Notably, we found that 67% and 54% of drug-responsive enhancers did not show similar changes in activity in previous studies that utilized ChIP-seq and ATAC-seq, respectively. Strikingly, 79% of regions with increased eRNA transcription showed no other biochemical alterations, implying that PRO-cap can capture a set of precise changes in enhancer activity that classical approaches lack the sensitivity to detect. We performed in vivo functional validations of candidate enhancers and found that CRISPRi targeting of PRO-cap-specific drug-responsive enhancers impaired ENZ regulation of downstream target genes, suggesting that changes in eRNA TSSs mark true biological changes in enhancer activity with high sensitivity. Our study highlights the utility of using PRO-cap as a complementary approach to canonical biochemical methods for detecting precise changes in enhancer activity and, in particular, for better understanding disease progression and responses to treatment.

genomics↗