Evidence map›Paper›PMID 39856551›Full record

ArticleBMC genomics2025

Integrated analysis of chromatin and transcriptomic profiling of the striatum after cerebral hypoperfusion in mice.

Shijia Le, Fengyiyang Xu, Zhi Luo, Weihao Shi, Shuangshuang Lu, Zengyu Zhang, Zimin Guo, Wenshi Xu, Mingqi Yang, Tianyi Li and 3 more

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In one paragraph

Article in BMC genomics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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1 · What the graph read from it

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4 · The record

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5 · Who and what money

Authors and funding

13 authors.

Shijia Le *Shanghai Medical College, Fudan University, Shanghai, 200032, China.
Fengyiyang Xu *Shanghai Medical College, Fudan University, Shanghai, 200032, China.
Zhi Luo *Department of Surgery, Shanghai Deji Hospital, Qingdao University, Shanghai, 200331, China.
Weihao ShiDepartment of Vascular Surgery, Huashan Hospital, Fudan University, Shanghai, 200040, China.
Shuangshuang LuDepartment of Radiology, Huashan Hospital, Fudan University, Shanghai, 200040, China.
Zengyu ZhangShanghai Medical College, Fudan University, Shanghai, 200032, China.
Zimin GuoShanghai Medical College, Fudan University, Shanghai, 200032, China.
Wenshi XuShanghai Medical College, Fudan University, Shanghai, 200032, China.
Mingqi YangShanghai Medical College, Fudan University, Shanghai, 200032, China.
Tianyi LiShanghai Medical College, Fudan University, Shanghai, 200032, China.
Xu LiDepartment of Vascular Surgery, Zhongshan Hospital, Institute of Vascular Surgery, National Clinical Research Center for Interventional Medicine, Fudan University, Shanghai, 200032, China. lixu007qq@163.com.
Kun LiangDepartment of Vascular Surgery, Huashan Hospital, Fudan University, Shanghai, 200040, China. kuhn.leung@outlook.com.
Lei ZhuDepartment of Vascular Surgery, Huashan Hospital, Fudan University, Shanghai, 200040, China. julian.lei.zhu@fudan.edu.cn.

Funding

Shanghai Development Center SHDC2023CRS025
6 · The paper itself

Abstract

backgroundVascular cognitive impairment (VCI) is a significant contributor to dementia, yet the precise mechanisms underlying the cognitive decline associated with chronic cerebral hypoperfusion (CCH) remain unclear. This study investigated the molecular and epigenetic changes in the striatum, a brain region critical for motor function and cognition, following chronic hypoperfusion using a bilateral common carotid artery stenosis (BCAS) model in mice.

methodsRNA-seq was utilized to identify differentially expressed genes (DEGs) associated with hypoperfusion. In parallel, ATAC-seq was used to assess changes in chromatin accessibility within the striatum, providing insight into the epigenome and potential regulatory mechanisms. The integration of these datasets allowed us to correlate chromatin accessibility with transcriptional activity and to identify key transcription factors driving the observed gene expression changes.

resultsAnalysis of striatum-specific transcriptome revealed significant upregulation of immune response genes, particularly type II interferon signaling, and downregulation of neural activation pathways. Analysis of striatum-specific epigenome showed increased chromatin accessibility at promoters of immune-related genes. Integrated analysis highlighted PU.1 as a key transcription factor in upregulated pathways, while neural pathways lacked epigenetic regulation, revealing distinct molecular responses in the striatum following chronic hypoperfusion.

conclusionsOur findings indicate that upregulated pathways in the striatum following BCAS-induced CCH are driven by epigenetic changes, while downregulated pathways occur independently of these modifications. Additionally, PU.1 plays a critical role in mediating immune responses, offering a potential target for therapeutic intervention.

Indexed as

ChromatinCorpus StriatumGene Expression ProfilingTranscriptomeAnimalsDisease Models, AnimalEpigenesis, GeneticMaleMiceMice, Inbred C57BLChromatinATAC-seqBilateral carotid artery stenosisChronic cerebral hypoperfusionRNA-seqStriatum

Identifiers

PMID39856551
PMCPMC11762485

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.