Integration of ATAC-seq and RNA-seq reveals temperature-responsive regulatory regions in Plasmodium falciparum asexual stages

TL;DR

This study finds that low temperature affects chromatin and gene activity in early malaria parasite stages, revealing temperature-responsive regulatory regions.

Contribution

First integrative analysis of ATAC-seq and RNA-seq in Plasmodium falciparum under low temperature stress.

Findings

Low temperature induces 1083 differentially accessible chromatin regions in ring stages, mostly promoter gains.

41 genes show coordinated changes in chromatin accessibility and expression, linked to temperature response.

Trophozoite stages show no significant chromatin reconfiguration under low temperature.

Abstract

Malaria remains a critical parasitic disease in tropical regions, with environmental temperature significantly influencing the development and transmission of Plasmodium falciparum. While low temperature triggers gametocyte differentiation in mosquito, the molecular mechanisms underlying temperature-responsive chromatin and transcriptional dynamics in asexual stages (ring and trophozoite) remain unclear. This study integrates Assay for Transposase-Accessible Chromatin with Sequencing (ATAC-seq) and RNA-sequencing (RNA-seq) to characterize genome-wide chromatin accessibility and gene expression profiles in P. falciparum under human body temperature (37 °C) and mosquito-mimicking temperature (26 °C).

Synchronized ring (45 h post-invasion) and trophozoite (70 h post-invasion) stages were subjected to temperature treatments (37 °C versus 26 °C). ATAC-seq was used to identify accessible chromatin regions, RNA-seq analyzed differentially expressed genes (DEGs), and quantitative real-time polymerase chain reaction (qPCR) validated key gene expression changes.

Low temperatures exerts a profound impact on the activation and expression of sexual-stage-specific genes in P. falciparum and induced 1083 differentially accessible regions (DARs) in the ring stage, including 1081 gains and only 2 losses, which were enriched primarily in promoter regions (≤ 3 kb upstream of transcription start sites), whereas no significant DARs were detected in the trophozoite stage, indicating stage-specific sensitivity to temperature. Functional analyses revealed DAR-associated genes enriched in host cell membrane interactions, antigenic variation, and pathways such as symbiont-mediated perturbation of host erythrocyte aggregation, with the identification of temperature-responsive transcription factor motifs (e.g., DEAR-3, ERF096). Integration of ATAC-seq and RNA-seq revealed a positive correlation between chromatin accessibility and gene expression, with 41 genes exhibiting concordant DAR-DEG changes, suggesting that dynamic chromatin remodeling regulates temperature-responsive transcription.

Low temperature selectively modulates chromatin accessibility and gene expression in the ring stage, while trophozoites show no chromatin reconfiguration, highlighting stage-specific thermal sensitivity. This study represents the first integrative analysis of ATAC-seq and RNA-seq data from P. falciparum under low temperature stress, identifying critical temperature-responsive regulatory regions, providing insights into the parasite’s environmental adaptation and a foundational resource of temperature-responsive regulatory regions, whose future functional validation could inform the development of novel, chromatin-targeted antimalarial strategies.

The online version contains supplementary material available at 10.1186/s13071-026-07288-2.

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