ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2010
Comprehensive analysis of the palindromic motif TCTCGCGAGA: a regulatory element of the HNRNPK promoter.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 39 citations in OpenAlex.
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- HAX1 impact on collective cell migration, cell adhesion, and cell shape is linked to the regulation of actomyosin contractility.Molecular biology of the cell · 2019Article
- Estrogen receptor α (ERα) indirectly induces transcription of human renal organic anion transporter 1 (OAT1).Physiological reports · 2019Article
- Disentangling transcription factor binding site complexity.Nucleic acids research · 2018Article
- A methyl-sensitive element induces bidirectional transcription in TATA-less CpG island-associated promoters.PloS one · 2018Article
- A Strong Neutrophil Elastase Proteolytic Fingerprint Marks the Carcinoma Tumor Proteome.Molecular & cellular proteomics : MCP · 2017Article
- Hypoxic 3D in vitro culture models reveal distinct resistance processes to TKIs in renal cancer cells.Cell & bioscience · 2017Article
- Platelet Carbonic Anhydrase II, a Forgotten Enzyme, May Be Responsible for Aspirin Resistance.Oxidative medicine and cellular longevity · 2017Article
- Conserved 3' UTR stem-loop structure in L1 and Alu transposons in human genome: possible role in retrotransposition.BMC genomics · 2016Article
- Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions.Nature biotechnology · 2016Article
- The regulatory repertoire of PLZF and SALL4 in undifferentiated spermatogonia.Development (Cambridge, England) · 2016Article
- Beads-free protein immunoprecipitation for a mass spectrometry-based interactome and posttranslational modifications analysis.Proteome science · 2015Article
- Global analysis of S-nitrosylation sites in the wild type (APP) transgenic mouse brain-clues for synaptic pathology.Molecular & cellular proteomics : MCP · 2014Article
- Urine proteomes of healthy aging humans reveal extracellular matrix (ECM) alterations and immune system dysfunction.Age (Dordrecht, Netherlands) · 2014Article
- Histone H3 lysine 27 acetylation is altered in colon cancer.Clinical proteomics · 2014Article
- Heterogeneous nuclear ribonucleoprotein (HnRNP) K genome-wide binding survey reveals its role in regulating 3'-end RNA processing and transcription termination at the early growth response 1 (EGR1) gene through XRN2 exonuclease.The Journal of biological chemistry · 2013Article
- Characterization of the sporophyte-preferential gene promoter from the red alga Porphyra yezoensis using transient gene expression.Marine biotechnology (New York, N.Y.) · 2013Article
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Authors and funding
10 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Definitive identification of promoters, their cis-regulatory motifs, and their trans-acting proteins requires experimental analysis. To define the HNRNPK promoter and its cognate DNA-protein interactions, we performed a comprehensive study combining experimental approaches, including luciferase reporter gene assays, chromatin immunoprecipitations (ChIP), electrophoretic mobility shift assays (EMSA), and mass spectrometry (MS). We discovered that out of the four potential HNRNPK promoters tested, the one containing the palindromic motif TCTCGCGAGA exhibited the highest activity in a reporter system assay. Although further EMSA and MS analyses, performed to uncover the identity of the palindrome-binding transcription factor, did identify a complex of DNA-binding proteins, neither method unambiguously identified the pertinent direct trans-acting protein(s). ChIP revealed similar chromatin states at the promoters with the palindromic motif and at housekeeping gene promoters. A ChIP survey showed significantly higher recruitment of PARP1, a protein identified by MS as ubiquitously attached to DNA probes, within heterochromatin sites. Computational analyses indicated that this palindrome displays features that mark nucleosome boundaries, causing the surrounding DNA landscape to be constitutively open. Our strategy of diverse approaches facilitated the direct characterization of various molecular properties of HNRNPK promoter bearing the palindromic motif TCTCGCGAGA, despite the obstacles that accompany in vitro methods.
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