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Manghrani A, Rangadurai AK, Szekely O, Liu B, Guseva S, Al-Hashimi HM. Quantitative and systematic NMR measurements of sequence-dependent A-T Hoogsteen dynamics uncovers unique conformational specificity in the DNA double helix. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.15.594415. [PMID: 38798635 PMCID: PMC11118333 DOI: 10.1101/2024.05.15.594415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
The propensities to form lowly-populated short-lived conformations of DNA could vary with sequence, providing an important source of sequence-specificity in biochemical reactions. However, comprehensively measuring how these dynamics vary with sequence is challenging. Using 1H CEST and 13C R 1 ρ NMR, we measured Watson-Crick to Hoogsteen dynamics for an A-T base pair in thirteen trinucleotide sequence contexts. The Hoogsteen population and exchange rate varied 4-fold and 16-fold, respectively, and were dependent on both the 3'- and 5'-neighbors but only weakly dependent on monovalent ion concentration (25 versus 100 mM NaCl) and pH (6.8 versus 8.0). Flexible TA and CA dinucleotide steps exhibited the highest Hoogsteen populations, and their kinetics rates strongly depended on the 3'-neighbor. In contrast, the stiffer AA and GA steps had the lowest Hoogsteen population, and their kinetics were weakly dependent on the 3'-neighbor. The Hoogsteen lifetime was especially short when G-C neighbors flanked the A-T base pair. The Hoogsteen dynamics had a distinct sequence-dependence compared to duplex stability and minor groove width. Thus, our results uncover a unique source of sequence-specificity hidden within the DNA double helix in the form of A-T Hoogsteen dynamics and establish the utility of 1H CEST to quantitively measure sequence-dependent DNA dynamics.
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Affiliation(s)
- Akanksha Manghrani
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27705, United States
| | - Atul Kaushik Rangadurai
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27705, United States
- Program in Molecular Medicine, Hospital for Sick Children Research Institute, Toronto, ON, M5G 0A4, Canada
| | - Or Szekely
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27705, United States
| | - Bei Liu
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27705, United States
| | - Serafima Guseva
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, United States
| | - Hashim M. Al-Hashimi
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, United States
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Huang X, Yao M, Tian P, Wong JYY, Li Z, Liu Z, Zhao JV. Genome-wide cross-trait analysis and Mendelian randomization reveal a shared genetic etiology and causality between COVID-19 and venous thromboembolism. Commun Biol 2023; 6:441. [PMID: 37085521 PMCID: PMC10120502 DOI: 10.1038/s42003-023-04805-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 04/04/2023] [Indexed: 04/23/2023] Open
Abstract
Venous thromboembolism occurs in up to one-third of patients with COVID-19. Venous thromboembolism and COVID-19 may share a common genetic architecture, which has not been clarified. To fill this gap, we leverage summary-level genetic data from the latest COVID-19 host genetics consortium and UK Biobank and examine the shared genetic etiology and causal relationship between COVID-19 and venous thromboembolism. The cross-trait and co-localization analyses identify 2, 3, and 4 shared loci between venous thromboembolism and severe COVID-19, COVID-19 hospitalization, SARS-CoV-2 infection respectively, which are mapped to ABO, ADAMTS13, FUT2 genes involved in coagulation functions. Enrichment analysis supports shared biological processes between COVID-19 and venous thromboembolism related to coagulation and immunity. Bi-directional Mendelian randomization suggests that venous thromboembolism was associated with higher risk of three COVID-19 traits, and SARS-CoV-2 infection was associated with a higher risk of venous thromboembolism. Our study provides timely evidence for the genetic etiology between COVID-19 and venous thromboembolism (VTE). Our findings contribute to the understanding of COVID-19 and VTE etiology and provide insights into the prevention and comorbidity management of COVID-19.
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Affiliation(s)
- Xin Huang
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Minhao Yao
- Department of Statistics and Actuarial Science, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Peixin Tian
- Department of Statistics and Actuarial Science, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Jason Y Y Wong
- Epidemiology and Community Health Branch, National Heart Lung and Blood Institute, Bethesda, MD, USA
| | - Zilin Li
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Zhonghua Liu
- Department of Biostatistics, Columbia University, New York, NY, USA.
| | - Jie V Zhao
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China.
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Miftari MH, Walther BT. Leukolectin-proteins are synthesized and secreted by lectocytes, a distinct category of fish embryonic mucus cells. FISH & SHELLFISH IMMUNOLOGY 2023; 137:108730. [PMID: 37084857 DOI: 10.1016/j.fsi.2023.108730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/01/2023] [Accepted: 04/02/2023] [Indexed: 05/03/2023]
Abstract
Fish perivitelline fluid (PVF) is a vital extra-embryonic compartment. At hatching, PVF-contents dissolve into the hatching fluid (HF). Analysis of Atlantic salmon HF reveals nearly hundred distinct proteins, most of which were identified by advanced mass-spectometry. However, one entity with apparent molecular weight 26 kDa, necessitated identification from its tryptic peptides. Subsequent cloning and sequencing revealed novel leukolectin-proteins. From bioinformatic analysis, leukolectins (LL) belong in the tectonin protein-family, with recognized functions in innate immunity. This study aims to identify LL-expressing cells in diverse fish species, and to characterize the ll-gene in order to predict bio-functions of leukolectins. LL-proteins were detected in HF from several fish species and one invertebrate, using polyclonal LL-specific IgGs. Embryonic LL-immunoreactive cells were numerous in Atlantic salmon, rainbow trout, fewer in Atlantic cod, and rare in Oikopleura dioica, Atlantic halibut. LL-immunoreactive cells were termed lectocytes, which corresponded to peridermal mucus-cells stained by PAS, but unstained by eosin. Hence, lectocytes and hatching-gland cells were clearly distinguished. Northern blots revealed two salmon LL-transcripts at mid-embryogenesis. Such transcripts were detected in epithelial cells of the periderm, gills and oral cavity. LL-transcripts predominated in the periderm, while choriolysin-transcripts were dominant in the gills. No co-expression of choriolysins and LL-transcripts was detected. BAC-library screening yielded salmon LL's gene-structure with 4 introns, 5 exons, TATA-box, multiple upstream putative transcription-factor binding-sites and polyadenylation site. ll-gene location on chromosome ssa17 was identified in Ssal_v3.1, the 2021-version of the salmon genome. In conclusion, larvae from several fish species are outfitted with mucus enriched by LL-proteins. Mucus cells are present in embryos of all fishes, but embryonic lectocyte-numbers are far higher in species with near total larval survival. When (maternal) chorionic first-line immuno-defence is lost at hatching, leukolectin-enriched mucus may provide vital protection for larvae.
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Affiliation(s)
- Mirushe H Miftari
- Dept. of Molecular Biology, University of Bergen, 5020, Bergen, Norway
| | - Bernt T Walther
- Dept. of Molecular Biology, University of Bergen, 5020, Bergen, Norway.
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Yin JCP, Cui E, Hardin PE, Zhou H. Circadian disruption of memory consolidation in Drosophila. Front Syst Neurosci 2023; 17:1129152. [PMID: 37034015 PMCID: PMC10073699 DOI: 10.3389/fnsys.2023.1129152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/27/2023] [Indexed: 04/11/2023] Open
Abstract
The role of the circadian system in memory formation is an important question in neurobiology. Despite this hypothesis being intuitively appealing, the existing data is confusing. Recent work in Drosophila has helped to clarify certain aspects of the problem, but the emerging sense is that the likely mechanisms are more complex than originally conceptualized. In this report, we identify a post-training window of time (during consolidation) when the circadian clock and its components are involved in memory formation. In the broader context, our data suggest that circadian biology might have multiple roles during memory formation. Testing for its roles at multiple timepoints, and in different cells, will be necessary to resolve some of the conflicting data.
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Affiliation(s)
- Jerry C. P. Yin
- Laboratory of Genetics, School of Medicine and Public Health, University of Wisconsin—Madison, Madison, WI, United States
- Neurology Department, School of Medicine and Public Health, University of Wisconsin—Madison, Madison, WI, United States
- *Correspondence: Jerry C. P. Yin
| | - Ethan Cui
- Laboratory of Genetics, School of Medicine and Public Health, University of Wisconsin—Madison, Madison, WI, United States
| | - Paul E. Hardin
- Department of Biology and Center for Biological Clocks Research, Texas A&M University, College Station, College Station, TX, United States
| | - Hong Zhou
- Laboratory of Genetics, School of Medicine and Public Health, University of Wisconsin—Madison, Madison, WI, United States
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Huang X, Yao M, Tian P, Wong JYY, Li Z, Liu Z, Zhao JV. Shared genetic etiology and causality between COVID-19 and venous thromboembolism: evidence from genome-wide cross trait analysis and bi-directional Mendelian randomization study. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.05.21.22275413. [PMID: 35665015 PMCID: PMC9164523 DOI: 10.1101/2022.05.21.22275413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Venous thromboembolism (VTE) occurs in up to one third patients with COVID-19. VTE and COVID-19 may share a common genetic architecture, which has not been clarified yet. To fill this gap, we leveraged summary-level genetic data from the latest COVID-19 host genetics consortium and UK Biobank and examined the shared genetic etiology and causal relationship between COVID-19 and VTE. The cross-trait analysis identified 8, 11, and 7 shared loci between VTE and severe COVID-19, COVID-19 hospitalization, SARS-CoV-2 infection respectively, in 13 genes involved in coagulation and immune function and enriched in the lung. Co-localization analysis identified eight shared loci in ABO, ADAMTS13 and FUT2 genes. Bi-direction Mendelian randomization suggested that VTE was associated with higher risks of all COVID-19 related traits, and SARS-CoV-2 infection was associated with higher risk of VTE. Our study provided timely evidence and novel insights into the genetic etiology between COVID-19 and VTE.
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He X, Tillo D, Vierstra J, Syed KS, Deng C, Ray GJ, Stamatoyannopoulos J, FitzGerald PC, Vinson C. Methylated Cytosines Mutate to Transcription Factor Binding Sites that Drive Tetrapod Evolution. Genome Biol Evol 2015; 7:3155-69. [PMID: 26507798 PMCID: PMC4994754 DOI: 10.1093/gbe/evv205] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
In mammals, the cytosine in CG dinucleotides is typically methylated producing
5-methylcytosine (5mC), a chemically less stable form of cytosine that can spontaneously
deaminate to thymidine resulting in a T•G mismatched base pair. Unlike other eukaryotes
that efficiently repair this mismatched base pair back to C•G, in mammals, 5mCG
deamination is mutagenic, sometimes producing TG dinucleotides, explaining the depletion
of CG dinucleotides in mammalian genomes. It was suggested that new TG dinucleotides
generate genetic diversity that may be critical for evolutionary change. We tested this
conjecture by examining the DNA sequence properties of regulatory sequences identified by
DNase I hypersensitive sites (DHSs) in human and mouse genomes. We hypothesized that the
new TG dinucleotides generate transcription factor binding sites (TFBS) that become
tissue-specific DHSs (TS-DHSs). We find that 8-mers containing the CG dinucleotide are
enriched in DHSs in both species. However, 8-mers containing a TG and no CG dinucleotide
are preferentially enriched in TS-DHSs when compared with 8-mers with neither a TG nor a
CG dinucleotide. The most enriched 8-mer with a TG and no CG dinucleotide in
tissue-specific regulatory regions in both genomes is the AP-1 motif
(TGAC/GTCAN), and we find evidence that
TG dinucleotides in the AP-1 motif arose from CG dinucleotides. Additional TS-DHS-enriched
TFBS containing the TG/CA dinucleotide are the E-Box motif
(GCAGCTGC), the NF-1 motif (GGCA—TGCC), and the
GR (glucocorticoid receptor) motif (G-ACA—TGT-C). Our results support the
suggestion that cytosine methylation is mutagenic in tetrapods producing TG dinucleotides
that create TFBS that drive evolution.
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Affiliation(s)
- Ximiao He
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Desiree Tillo
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Jeff Vierstra
- Department of Genome Sciences, University of Washington
| | - Khund-Sayeed Syed
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Callie Deng
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - G Jordan Ray
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | | | - Peter C FitzGerald
- Genome Analysis Unit, Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Charles Vinson
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
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Golla JP, Zhao J, Mann IK, Sayeed SK, Mandal A, Rose RB, Vinson C. Carboxylation of cytosine (5caC) in the CG dinucleotide in the E-box motif (CGCAG|GTG) increases binding of the Tcf3|Ascl1 helix-loop-helix heterodimer 10-fold. Biochem Biophys Res Commun 2014; 449:248-55. [PMID: 24835951 DOI: 10.1016/j.bbrc.2014.05.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 05/06/2014] [Indexed: 12/14/2022]
Abstract
Three oxidative products of 5-methylcytosine (5mC) occur in mammalian genomes. We evaluated if these cytosine modifications in a CG dinucleotide altered DNA binding of four B-HLH homodimers and three heterodimers to the E-Box motif CGCAG|GTG. We examined 25 DNA probes containing all combinations of cytosine in a CG dinucleotide and none changed binding except for carboxylation of cytosine (5caC) in the strand CGCAG|GTG. 5caC enhanced binding of all examined B-HLH homodimers and heterodimers, particularly the Tcf3|Ascl1 heterodimer which increased binding ~10-fold. These results highlight a potential function of the oxidative products of 5mC, changing the DNA binding of sequence-specific transcription factors.
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Affiliation(s)
- Jaya Prakash Golla
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Room 3128, Building 37, Bethesda, MD 20892, United States
| | - Jianfei Zhao
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Room 3128, Building 37, Bethesda, MD 20892, United States
| | - Ishminder K Mann
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Room 3128, Building 37, Bethesda, MD 20892, United States
| | - Syed K Sayeed
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Room 3128, Building 37, Bethesda, MD 20892, United States
| | - Ajeet Mandal
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Room 3128, Building 37, Bethesda, MD 20892, United States
| | - Robert B Rose
- Department of Biochemistry, North Carolina State University, 128 Polk Hall, Raleigh, NC 27695, United States
| | - Charles Vinson
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Room 3128, Building 37, Bethesda, MD 20892, United States.
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Boulling A, Wicht L, Schorderet DF. Identification of HMX1 target genes: a predictive promoter model approach. Mol Vis 2013; 19:1779-94. [PMID: 23946633 PMCID: PMC3742133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 08/02/2013] [Indexed: 11/19/2022] Open
Abstract
PURPOSE A homozygous mutation in the H6 family homeobox 1 (HMX1) gene is responsible for a new oculoauricular defect leading to eye and auricular developmental abnormalities as well as early retinal degeneration (MIM 612109). However, the HMX1 pathway remains poorly understood, and in the first approach to better understand the pathway's function, we sought to identify the target genes. METHODS We developed a predictive promoter model (PPM) approach using a comparative transcriptomic analysis in the retina at P15 of a mouse model lacking functional Hmx1 (dmbo mouse) and its respective wild-type. This PPM was based on the hypothesis that HMX1 binding site (HMX1-BS) clusters should be more represented in promoters of HMX1 target genes. The most differentially expressed genes in the microarray experiment that contained HMX1-BS clusters were used to generate the PPM, which was then statistically validated. Finally, we developed two genome-wide target prediction methods: one that focused on conserving PPM features in human and mouse and one that was based on the co-occurrence of HMX1-BS pairs fitting the PPM, in human or in mouse, independently. RESULTS The PPM construction revealed that sarcoglycan, gamma (35kDa dystrophin-associated glycoprotein) (Sgcg), teashirt zinc finger homeobox 2 (Tshz2), and solute carrier family 6 (neurotransmitter transporter, glycine) (Slc6a9) genes represented Hmx1 targets in the mouse retina at P15. Moreover, the genome-wide target prediction revealed that mouse genes belonging to the retinal axon guidance pathway were targeted by Hmx1. Expression of these three genes was experimentally validated using a quantitative reverse transcription PCR approach. The inhibitory activity of Hmx1 on Sgcg, as well as protein tyrosine phosphatase, receptor type, O (Ptpro) and Sema3f, two targets identified by the PPM, were validated with luciferase assay. CONCLUSIONS Gene expression analysis between wild-type and dmbo mice allowed us to develop a PPM that identified the first target genes of Hmx1.
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Affiliation(s)
| | - Linda Wicht
- Institute for Research in Ophthalmology, Sion, Switzerland,School of Life Sciences, Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Daniel F. Schorderet
- Institute for Research in Ophthalmology, Sion, Switzerland,School of Life Sciences, Federal Institute of Technology (EPFL), Lausanne, Switzerland,Department of Ophthalmology, University of Lausanne, Lausanne, Switzerland
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He X, Chatterjee R, John S, Bravo H, Sathyanarayana BK, Biddie SC, FitzGerald PC, Stamatoyannopoulos JA, Hager GL, Vinson C. Contribution of nucleosome binding preferences and co-occurring DNA sequences to transcription factor binding. BMC Genomics 2013; 14:428. [PMID: 23805837 PMCID: PMC3700821 DOI: 10.1186/1471-2164-14-428] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 06/10/2013] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Chromatin plays a critical role in regulating transcription factors (TFs) binding to their canonical transcription factor binding sites (TFBS). Recent studies in vertebrates show that many TFs preferentially bind to genomic regions that are well bound by nucleosomes in vitro. Co-occurring secondary motifs sometimes correlated with functional TFBS. RESULTS We used a logistic regression to evaluate how well the propensity for nucleosome binding and co-occurrence of a secondary motif identify which canonical motifs are bound in vivo. We used ChIP-seq data for three transcription factors binding to their canonical motifs: c-Jun binding the AP-1 motif (TGA(C)/(G)TCA), GR (glucocorticoid receptor) binding the GR motif (G-ACA---(T)/(C)GT-C), and Hoxa2 (homeobox a2) binding the Pbx (Pre-B-cell leukemia homeobox) motif (TGATTGAT). For all canonical TFBS in the mouse genome, we calculated intrinsic nucleosome occupancy scores (INOS) for its surrounding 150-bps DNA and examined the relationship with in vivo TF binding. In mouse mammary 3134 cells, c-Jun and GR proteins preferentially bound regions calculated to be well-bound by nucleosomes in vitro with the canonical AP-1 and GR motifs themselves contributing to the high INOS. Functional GR motifs are enriched for AP-1 motifs if they are within a nucleosome-sized 150-bps region. GR and Hoxa2 also bind motifs with low INOS, perhaps indicating a different mechanism of action. CONCLUSION Our analysis quantified the contribution of INOS and co-occurring sequence to the identification of functional canonical motifs in the genome. This analysis revealed an inherent competition between some TFs and nucleosomes for binding canonical TFBS. GR and c-Jun cooperate if they are within 150-bps. Binding of Hoxa2 and a fraction of GR to motifs with low INOS values suggesting they are not in competition with nucleosomes and may function using different mechanisms.
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Affiliation(s)
- Ximiao He
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Abstract
This review concisely highlights the complexity of regulatory events. It provides examples of how interconnectivity of regulatory hubs could maintain transcriptional synergy and orchestrate the proper spatial and temporal patterns of gene expression.
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Affiliation(s)
- Minou Bina
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
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Overlapping ETS and CRE Motifs ((G/C)CGGAAGTGACGTCA) preferentially bound by GABPα and CREB proteins. G3-GENES GENOMES GENETICS 2012; 2:1243-56. [PMID: 23050235 PMCID: PMC3464117 DOI: 10.1534/g3.112.004002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Accepted: 08/19/2012] [Indexed: 11/18/2022]
Abstract
Previously, we identified 8-bps long DNA sequences (8-mers) that localize in human proximal promoters and grouped them into known transcription factor binding sites (TFBS). We now examine split 8-mers consisting of two 4-mers separated by 1-bp to 30-bps (X(4)-N(1-30)-X(4)) to identify pairs of TFBS that localize in proximal promoters at a precise distance. These include two overlapping TFBS: the ETS⇔ETS motif ((C/G)CCGGAAGCGGAA) and the ETS⇔CRE motif ((C/G)CGGAAGTGACGTCAC). The nucleotides in bold are part of both TFBS. Molecular modeling shows that the ETS⇔CRE motif can be bound simultaneously by both the ETS and the B-ZIP domains without protein-protein clashes. The electrophoretic mobility shift assay (EMSA) shows that the ETS protein GABPα and the B-ZIP protein CREB preferentially bind to the ETS⇔CRE motif only when the two TFBS overlap precisely. In contrast, the ETS domain of ETV5 and CREB interfere with each other for binding the ETS⇔CRE. The 11-mer (CGGAAGTGACG), the conserved part of the ETS⇔CRE motif, occurs 226 times in the human genome and 83% are in known regulatory regions. In vivo GABPα and CREB ChIP-seq peaks identified the ETS⇔CRE as the most enriched motif occurring in promoters of genes involved in mRNA processing, cellular catabolic processes, and stress response, suggesting that a specific class of genes is regulated by this composite motif.
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Henson BJ, Zhu W, Hardaway K, Wetzel JL, Stefan M, Albers KM, Nicholls RD. Transcriptional and post-transcriptional regulation of SPAST, the gene most frequently mutated in hereditary spastic paraplegia. PLoS One 2012; 7:e36505. [PMID: 22574173 PMCID: PMC3344893 DOI: 10.1371/journal.pone.0036505] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 04/02/2012] [Indexed: 01/01/2023] Open
Abstract
Hereditary spastic paraplegias (HSPs) comprise a group of neurodegenerative disorders that are characterized by progressive spasticity of the lower extremities, due to axonal degeneration in the corticospinal motor tracts. HSPs are genetically heterogeneous and show autosomal dominant inheritance in ∼70–80% of cases, with additional cases being recessive or X-linked. The most common type of HSP is SPG4 with mutations in the SPAST gene, encoding spastin, which occurs in 40% of dominantly inherited cases and in ∼10% of sporadic cases. Both loss-of-function and dominant-negative mutation mechanisms have been described for SPG4, suggesting that precise or stoichiometric levels of spastin are necessary for biological function. Therefore, we hypothesized that regulatory mechanisms controlling expression of SPAST are important determinants of spastin biology, and if altered, could contribute to the development and progression of the disease. To examine the transcriptional and post-transcriptional regulation of SPAST, we used molecular phylogenetic methods to identify conserved sequences for putative transcription factor binding sites and miRNA targeting motifs in the SPAST promoter and 3′-UTR, respectively. By a variety of molecular methods, we demonstrate that SPAST transcription is positively regulated by NRF1 and SOX11. Furthermore, we show that miR-96 and miR-182 negatively regulate SPAST by effects on mRNA stability and protein level. These transcriptional and miRNA regulatory mechanisms provide new functional targets for mutation screening and therapeutic targeting in HSP.
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Affiliation(s)
- Brian J. Henson
- Birth Defects Laboratories, Division of Medical Genetics, Department of Pediatrics, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania, United States of America
| | - Wan Zhu
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, United States of America
| | - Kelsey Hardaway
- Birth Defects Laboratories, Division of Medical Genetics, Department of Pediatrics, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania, United States of America
| | - Jaime L. Wetzel
- Birth Defects Laboratories, Division of Medical Genetics, Department of Pediatrics, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania, United States of America
| | - Mihaela Stefan
- Birth Defects Laboratories, Division of Medical Genetics, Department of Pediatrics, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania, United States of America
| | - Kathryn M. Albers
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Robert D. Nicholls
- Birth Defects Laboratories, Division of Medical Genetics, Department of Pediatrics, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania, United States of America
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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