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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\n                      <jats:italic>P.\u00a0falciparum<\/jats:italic>\n                      under human body temperature (37\u00a0\u00b0C) and mosquito-mimicking temperature (26\u00a0\u00b0C).\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>Synchronized ring (45\u00a0h post-invasion) and trophozoite (70\u00a0h post-invasion) stages were subjected to temperature treatments (37\u00a0\u00b0C versus 26\u00a0\u00b0C). 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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Low temperatures exerts a profound impact on the activation and expression of sexual-stage-specific genes in\n                      <jats:italic>P.\u00a0falciparum<\/jats:italic>\n                      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 (\u2264\u20093\u00a0kb 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.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>\n                      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\n                      <jats:italic>P.\u00a0falciparum<\/jats:italic>\n                      under low temperature stress, identifying critical temperature-responsive regulatory regions, providing insights into the parasite\u2019s 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.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Graphical Abstract<\/jats:title>\n                  <\/jats:sec>","DOI":"10.1186\/s13071-026-07288-2","type":"journal-article","created":{"date-parts":[[2026,2,20]],"date-time":"2026-02-20T16:05:59Z","timestamp":1771603559000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Integration of ATAC-seq and RNA-seq reveals temperature-responsive regulatory regions in Plasmodium falciparum asexual stages"],"prefix":"10.1186","volume":"19","author":[{"given":"Yuhong","family":"Zhang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yi","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guixing","family":"Zheng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shanli","family":"He","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiale","family":"Xiao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Haochen","family":"Ma","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jun","family":"Huang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yanwei","family":"Qi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2026,2,20]]},"reference":[{"key":"7288_CR1","doi-asserted-by":"publisher","DOI":"10.30875\/9789287076717","volume-title":"World malaria report 2024","author":"World Health Organization","year":"2024","unstructured":"World Health Organization. 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