Biology subjects

Himanen, S. V.

Publications and source records attributed to Himanen, S. V..

4 recordsLinked to original sources

bioRxiv2025

Transcriptional architecture and Pol II regulation at promoters, enhancers, and enhancer clusters in Canis lupus familiaris

Domestic dog exhibits remarkable phenotypic diversity and provides versatile models for genomics, evolution, and complex traits. DNA sequences and stable RNAs have revealed regulatory regions in the dog genome. However, transcriptional activity, regulatory architecture, and control of RNA Polymerase II (Pol II) across genes and enhancers remain uncharacterized. Here, we track transcription at nucleotide-resolution, measure RNA expression and stability, and analyse mechanisms of Pol II regulation in golden retriever macrophages. We report the precise architectures of promoters, enhancers, and enhancer clusters, and quantify Pol II progression from the initiation, through the pause-region, into elongation and termination. Triggering transcriptional change by heat stress reveals instant reprogramming of genes via promoter-proximal pause-regulation and enhancers via initiation. Enhancers within a cluster mount a unified response. This study identifies functional genomic regions de novo, characterizes transcriptional architectures of genes, enhancers, and enhancer clusters, quantifies RNA synthesis and stability, and reveals mechanisms of transcription in Canis lupus familiaris.

genomics↗

bioRxiv2023

Characterization of gene regulatory elements and dynamic antimicrobial immune responses in mosquito cells using PRO-seq

Aedes aegypti mosquitoes are the principal vectors for epidemic arboviruses, including dengue, Zika, and chikungunya viruses. In these insect vectors, the concerted action of immune pathways shapes virus replication and transmission; yet, mechanistic and dynamic understanding of the transcriptional immune responses in mosquitoes remain limited. To address this knowledge gap, we profiled nascent transcription in mosquito cells and midgut tissue using Precision Run-On sequencing (PRO-seq). We identified exact transcription start nucleotides (TSNs), characterized promoter architectures, and generated the first genome-wide list of putative enhancers in Aedes aegypti, substantially expanding the regulatory annotation of this non-model organism. To investigate dynamic immune responses, we stimulated Aag2 cells with heat-inactivated E. coli and measured RNA synthesis and mRNA levels from matched samples. Bacterial stimulation induced rapid and temporally organized transcriptional responses associated with distinct biological functions and transcription factor motifs. Integration with mRNA-seq revealed that temporal patterns of mRNA accumulation were shaped by RNA synthesis, gene length, and stability, indicating multilayered regulation of mosquito immune responses. Implementing PRO-seq for mosquito midgut enabled characterization of tissue-specific transcription and TSN usage. Importantly, we demonstrate for the first time that PRO-seq captures in vivo microbial transcription within an organism, co-profiling host and microbiome nascent RNA synthesis. Altogether, this study substantially expands the regulatory annotation and functional genomic landscape of Aedes aegypti, reveals multilayered regulation of mosquito immune responses, and extends transcriptional profiling to host and microbiome activity in vivo. These insights advance understanding of gene regulation and immunity in this important arbovirus vector.

molecular biology↗

bioRxiv2021

HSFs drive stress type-specific transcription of genes and enhancers

Reprogramming of transcription is critical for the survival under cellular stress. Heat shock has provided an excellent model to investigate nascent transcription in stressed cells, but the molecular mechanisms orchestrating RNA synthesis during other types of stress are unknown. We utilized PRO-seq and ChIP-seq to study how Heat Shock Factors, HSF1 and HSF2, coordinate transcription at genes and enhancers upon oxidative stress and heat shock. We show that pause-release of RNA polymerase II (Pol II) is a universal mechanism regulating gene transcription in stressed cells, while enhancers are activated at the level of Pol II recruitment. Moreover, besides functioning as conventional promoter-binding transcription factors, HSF1 and HSF2 bind to stress-induced enhancers to trigger Pol II pause-release from poised gene promoters. Importantly, HSFs act at distinct genes and enhancers in a stress type-specific manner. HSF1 binds to many chaperone genes upon oxidative and heat stress but activates them only in heat-shocked cells. Under oxidative stress, HSF1 and HSF2 trans-activate genes independently of each other, demonstrating, for the first time, that HSF2 is a bona fide transcription factor. Taken together, we show that HSFs function as multi-stress-responsive factors that activate specific genes and enhancers when encountering changes in temperature and redox state.

molecular biology↗

bioRxiv2019

Stress-Induced Transcriptional Memory Accelerates Promoter-Proximal Pause-Release and Decelerates Termination over Mitotic Divisions

Heat shock triggers an instant reprogramming of gene and enhancer transcription, but whether cells encode a memory to stress, at the level of nascent transcription, has remained unknown. Here, we measured transcriptional response to acute heat stress in unconditioned cells and in daughters of cells that had been exposed to a single or multiple heat shocks. Tracking RNA Polymerase II (Pol II) genome-wide at nucleotide-resolution revealed that cells precisely remember their transcriptional identity throughout stress, restoring Pol II distribution at gene bodies and enhancers upon recovery. However, single heat shock primed faster gene-induction in the daughter cells by increasing promoter-proximal Pol II pausing, and accelerating the pause-release. In repeatedly stressed cells, both basal and inducible transcription was refined, and pre-mRNA processing decelerated, which retained transcripts on chromatin and reduced recycling of the transcription machinery. These results mechanistically uncovered how the steps of pause-release and termination maintain transcriptional memory over mitosis.\n\nHighlights-Cell type-specific transcription precisely recovers after heat-induced reprogramming\n-Single heat shock primes genes for accelerated induction over mitotic divisions via increased promoter-proximal Pol II pausing and faster pause-release\n-Multiple heat shocks refine basal and inducible transcription over mitotic divisions to support survival of the daughter cells\n-Decelerated termination at active genes reduces recycling of Pol II to heat-activated promoters and enhancers\n-HSF1 increases the rate of promoter-proximal pause-release via distal and proximal regulatory elements

molecular biology↗