ArticleGenome research2008
Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders.
Article in Genome research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
62 citing papers in PubMed, 104 citations in OpenAlex.
- Knockdown of USF1 and USF2 drives prolonged changes in the gene expression response of M12-5B3 cells to DNA damage.PloS one · 2025Article
- ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements.Nature genetics · 2024Article
- Identifying the "stripe" transcription factors and cooperative binding related to DNA methylation.Communications biology · 2024Article
- USF1 modulates transcription and cellular functions by regulating multiple transcription factors in Huh7 cells.Oncology letters · 2023Article
- Functional Genomics Analysis to Disentangle the Role of Genetic Variants in Major Depression.Genes · 2022Article
- Evolution of the Short Form of DNMT3A, DNMT3A2, Occurred in the Common Ancestor of Mammals.Genome biology and evolution · 2022Article
- Evolutionary genetics and acclimatization in nephrology.Nature reviews. Nephrology · 2021Review
- Histone deacetylase (HDAC) 9: versatile biological functions and emerging roles in human cancer.Cellular oncology (Dordrecht, Netherlands) · 2021Review
- A ChIP-exo screen of 887 Protein Capture Reagents Program transcription factor antibodies in human cells.Genome research · 2021Article
- Irrelevance of USF2 rs916145 polymorphism with the risk of biliary atresia susceptibility in Southern Chinese children.Bioscience reports · 2020Article
- Article
- USF1 promotes the development of knee osteoarthritis by activating the NF-κB signaling pathway.Experimental and therapeutic medicine · 2018Article
- Upstream stimulating factor 1 suppresses autophagy and hepatic lipid droplet catabolism by activating mTOR.FEBS letters · 2018Article
- The Role of HOTAIR/miR-148b-3p/USF1 on Regulating the Permeability of BTB.Frontiers in molecular neuroscience · 2017Article
- Maps of context-dependent putative regulatory regions and genomic signal interactions.Nucleic acids research · 2016Article
- Population whole-genome bisulfite sequencing across two tissues highlights the environment as the principal source of human methylome variation.Genome biology · 2015Article
- Different distribution of histone modifications in genes with unidirectional and bidirectional transcription and a role of CTCF and cohesin in directing transcription.BMC genomics · 2015Article
- Significant association between upstream transcription factor 1 rs2516839 polymorphism and hepatocellular carcinoma risk: a case-control study.Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine · 2015Article
- Protein kinases as switches for the function of upstream stimulatory factors: implications for tissue injury and cancer.Frontiers in pharmacology · 2015Article
- Sexually-dimorphic targeting of functionally-related genes in COPD.BMC systems biology · 2014Article
2 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 1 institution in 2 countries.
Funding
Abstract
Transcription factors and histone modifications are crucial regulators of gene expression that mutually influence each other. We present the DNA binding profiles of upstream stimulatory factors 1 and 2 (USF1, USF2) and acetylated histone H3 (H3ac) in a liver cell line for the whole human genome using ChIP-chip at a resolution of 35 base pairs. We determined that these three proteins bind mostly in proximity of protein coding genes transcription start sites (TSSs), and their bindings are positively correlated with gene expression levels. Based on the spatial and functional relationship between USFs and H3ac at protein coding gene promoters, we found similar promoter architecture for known genes and the novel and less-characterized transcripts human mRNAs and spliced ESTs. Furthermore, our analysis revealed a previously underestimated abundance of genes in a bidirectional conformation, where USFs are bound in between TSSs. After taking into account this promoter conformation, the results indicate that H3ac is mainly located downstream of TSS, and it is at this genomic location where it positively correlates with gene expression. Finally, USF1, which is associated to familial combined hyperlipidemia, was found to bind and potentially regulate nuclear mitochondrial genes as well as genes for lipid and cholesterol metabolism, frequently in collaboration with GA binding protein transcription factor alpha (GABPA, nuclear respiratory factor 2 [NRF-2]). This expands our understanding about the transcriptional control of metabolic processes and its alteration in metabolic disorders.
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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.