Foods
·
2023
·Vol. 12
·期 12
·2357
·
IF 5.2
Yanan He,Qiong Wu,Chunxiao Cui,Qisheng Tian,Dongdong Zhang,Yurong Zhang
SlAREB1, a member of the abscisic acid (ABA) response element-binding factors (AREB/ABFs) family, was reported to play a crucial role in the expression of ABA-regulated downstream genes and affect the ripening of tomato fruit. However, the downstream genes ofSlAREB1are still unclear. Chromatin immunoprecipitation (ChIP) is a powerful tool and a standard method for studying the interactions between DNA and proteins at the genome-wide level. In the present study,SlAREB1was proved to continually increase until the mature green stage and then decrease during the ripening period, and a total of 972 gene peaks were identified downstream ofSlAREB1by ChIP-seq analysis, mainly located in the intergenic and promoter regions. Further gene ontology (GO) annotation analysis revealed that the target sequence ofSlAREB1was the most involved in biological function. Kyoto Encylopaedia of Genes and Genomes (KEGG) pathway analysis showed that the identified genes were mainly involved in the oxidative phosphorylation and photosynthesis pathways, and some of them were associated with tomato phytohormone synthesis, the cell wall, pigment, and the antioxidant characteristic of the fruit as well. Based on these results, an initial model ofSlAREB1regulation on tomato fruit ripening was constructed, which provided a theoretical basis for further exploring the effects of the regulation mechanism ofSlAREB1and ABA on tomato fruit ripening.Keywords:tomato;abscisic acid;SlAREB1transcription factor;ChIP-Seq;fruit ripening
研究领域:
植物生物学
·
分子遗传学
·
转录组学
✓ 已验证
DOI
PubMed
高影响因子
NUCLEIC ACIDS RESEARCH
·
2020
·Vol. 48
·期 19
·10768-10784
·
IF 11.502
Sun Ge,Wang Chunyu,Wang Shengli,Sun Hongmiao,Zeng Kai,Zou Renlong,Lin Lin,Liu Wei,Sun Ning,Song Huijuan,Liu Wensu,Zhou Tingting,Jin Feng,Shan Zhongyan,Zhao Yue
Estrogen receptor alpha (ERα) signaling pathway is essential for ERα-positive breast cancer progression and endocrine therapy resistance. Bromodomain PHD Finger Transcription Factor (BPTF) associated protein of 18kDa (BAP18) has been recognized as a crucial H3K4me3 reader. However, the whole genomic occupation of BAP18 and its biological function in breast cancer is still elusive. Here, we found that higher expression of BAP18 in ERα-positive breast cancer is positively correlated with poor prognosis. ChIP-seq analysis further demonstrated that the half estrogen response elements (EREs) and the CCCTC binding factor (CTCF) binding sites are the significant enrichment sites found in estrogen-induced BAP18 binding sites. Also, we provide the evidence to demonstrate that BAP18 as a novel co-activator of ERα is required for the recruitment of COMPASS-like core subunits to the cis-regulatory element of ERα target genes in breast cancer cells. BAP18 is recruited to the promoter regions of estrogen-induced genes, accompanied with the enrichment of the lysine 4-trimethylated histone H3 tail (H3K4me3) in the presence of E2. Furthermore, BAP18 promotes cell growth and associates the sensitivity of antiestrogen in ERα-positive breast cancer. Our data suggest that BAP18 facilitates the association between ERα and COMPASS-like core subunits, which might be an essential epigenetic therapeutic target for breast cancer.
研究领域:
肿瘤学
·
分子生物学
·
表观遗传学
·
癌症治疗
✓ 已验证
DOI
PubMed
高影响因子
DEVELOPMENT
·
2024
·
IF 3.7
Yu Meng,Thorner Konrad,Parameswaran Sreeja,Wei Wei,Yu Chuyue,Lin Xinhua,Kopan Raphael,Hass Matthew R.
The conserved Runt-related (RUNX) transcription factor family are master regulators of developmental and regenerative processes. Runx1 and Runx2 are expressed in satellite cells (SC) and in skeletal myotubes. Conditional deletion of Runx1 in adult SC negatively impacted self-renewal and impaired skeletal muscle maintenance even though Runx2 expression persisted. Runx1 deletion in C2C12 cells that retain Runx2 expression identified unique molecular functions of Runx1 that cannot be compensated by Runx2. The reduced myoblast fusion in vitro caused by Runx1 loss was due in part to ectopic expression of Mef2c, a target repressed by Runx1 . Structure-function analysis demonstrated that the Ets-interacting MID/EID region of Runx1, absent from Runx2, is critical to Runx1 myoblast function and for Etv4 binding. Analysis of ChIP-seq datasets from Runx1 (T-cells, muscle) versus Runx2 (preosteoblasts) dependent tissues identified a composite Ets:Runx motif enriched in Runx1 -dependent tissues. The Ets:Runx composite motif was enriched in peaks open exclusively in ATAC-seq datasets from WT cells compared to ATAC peaks unique to Runx1KO cells. Thus, engagement of a set of targets by the RUNX1/ETS complex define the non-redundant functions of Runx1 .
研究领域:
分子生物学
·
细胞生物学
·
转录因子
·
肌肉再生
✓ 已验证
DOI
高影响因子
STAR Protocols
·
2024
·
IF 1.3
Shihao Song,Binbin Cui,Xiaohan Kong,Yinyue Deng
Summary Here, we present a protocol for identifying the components of a quorum sensing signaling system in bacteria. We describe the steps for characterizing the novel response regulator and receptor of the cis -2-dodecenoic acid (BDSF) quorum sensing signaling system in Burkholderia cenocepacia . The technical assays of this protocol include generating a random mutant library, chromatin immunoprecipitation sequencing (ChIP-seq), electrophoretic mobility transfer assay (EMSA), microscale thermophoresis (MST), and molecular simulation docking. For complete details on the use and execution of this protocol, please refer to Li et al. 1 and Yang et al. 2
研究领域:
微生物学
·
分子生物学
·
遗传学
✓ 已验证
产品关联
DOI
PubMed
高影响因子
危险品化学品经营许可证（带存储）