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Qutob SS, Roesch SPM, Smiley S, Bellier P, Williams A, Cook KB, Meier MJ, Rowan-Carroll A, Yauk CL, McNamee JP. Transcriptome analysis in mouse skin after exposure to ultraviolet radiation from a canopy sunbed. Photochem Photobiol 2024. [PMID: 38317517 DOI: 10.1111/php.13917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/17/2024] [Accepted: 01/24/2024] [Indexed: 02/07/2024]
Abstract
Exposure to ultraviolet radiation (UV-R), from both natural and artificial tanning, heightens the risk of skin cancer by inducing molecular changes in cells and tissues. Despite established transcriptional alterations at a molecular level due to UV-R exposure, uncertainties persist regarding UV radiation characterization and subsequent genomic changes. Our study aimed to mechanistically explore dose- and time-dependent gene expression changes, that may drive short-term (e.g., sunburn) and long-term actinic (e.g., skin cancer) consequences. Using C57BL/6N mouse skin, we analyzed transcriptomic expression following exposure to five erythemally weighted UV-R doses (0, 5, 10, 20, and 40 mJ/cm2 ) emitted by a UV-R tanning device. At 96 h post-exposure, 5 mJ/cm2 induced 116 statistically significant differentially expressed genes (DEGs) associated with structural changes from UV-R damage. The highest number of significant gene expression changes occurred at 6 and 48 h post-exposure in the 20 and 40 mJ/cm2 dose groups. Notably, at 40 mJ/cm2 , 13 DEGs related to skin barrier homeostasis were consistently perturbed across all timepoints. UV-R exposure activated pathways involving oxidative stress, P53 signaling, inflammation, biotransformation, skin barrier maintenance, and innate immunity. This in vivo study's transcriptional data offers mechanistic insights into both short-term and potential non-threshold-dependent long-term health effects of UV-R tanning.
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Affiliation(s)
- Sami S Qutob
- Consumer and Clinical Radiation Protection Bureau, Health Canada, Ottawa, Ontario, Canada
| | - Samantha P M Roesch
- Consumer and Clinical Radiation Protection Bureau, Health Canada, Ottawa, Ontario, Canada
| | - Sandy Smiley
- Consumer and Clinical Radiation Protection Bureau, Health Canada, Ottawa, Ontario, Canada
| | - Pascale Bellier
- Consumer and Clinical Radiation Protection Bureau, Health Canada, Ottawa, Ontario, Canada
| | - Andrew Williams
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, Canada
| | - Kate B Cook
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, Canada
| | - Matthew J Meier
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, Canada
| | - Andrea Rowan-Carroll
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, Canada
| | - Carole L Yauk
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - James P McNamee
- Consumer and Clinical Radiation Protection Bureau, Health Canada, Ottawa, Ontario, Canada
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2
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Cook KB, Hristov BH, Le Roch KG, Vert JP, Noble WS. Measuring significant changes in chromatin conformation with ACCOST. Nucleic Acids Res 2020; 48:2303-2311. [PMID: 32034421 PMCID: PMC7049724 DOI: 10.1093/nar/gkaa069] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 01/17/2020] [Accepted: 02/03/2020] [Indexed: 12/17/2022] Open
Abstract
Chromatin conformation assays such as Hi-C cannot directly measure differences in 3D architecture between cell types or cell states. For this purpose, two or more Hi-C experiments must be carried out, but direct comparison of the resulting Hi-C matrices is confounded by several features of Hi-C data. Most notably, the genomic distance effect, whereby contacts between pairs of genomic loci that are proximal along the chromosome exhibit many more Hi-C contacts that distal pairs of loci, dominates every Hi-C matrix. Furthermore, the form that this distance effect takes often varies between different Hi-C experiments, even between replicate experiments. Thus, a statistical confidence measure designed to identify differential Hi-C contacts must accurately account for the genomic distance effect or risk being misled by large-scale but artifactual differences. ACCOST (Altered Chromatin COnformation STatistics) accomplishes this goal by extending the statistical model employed by DEseq, re-purposing the ‘size factors,’ which were originally developed to account for differences in read depth between samples, to instead model the genomic distance effect. We show via analysis of simulated and real data that ACCOST provides unbiased statistical confidence estimates that compare favorably with competing methods such as diffHiC, FIND and HiCcompare. ACCOST is freely available with an Apache license at https://bitbucket.org/noblelab/accost.
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Affiliation(s)
- Kate B Cook
- Department of Genome Sciences, University of Washington, Seattle, WA 98195-5065, USA
| | - Borislav H Hristov
- Department of Genome Sciences, University of Washington, Seattle, WA 98195-5065, USA
| | - Karine G Le Roch
- Department of Cell Biology, University of California, Riverside, CA 92521, USA
| | - Jean Philippe Vert
- Google Brain, Paris, 75009, France.,Centre for Computational Biology, MINES ParisTech, PSL University, Paris, 75009, France
| | - William Stafford Noble
- Department of Genome Sciences, University of Washington, Seattle, WA 98195-5065, USA.,Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA 98195-2355, USA
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3
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Bunnik EM, Cook KB, Varoquaux N, Batugedara G, Prudhomme J, Cort A, Shi L, Andolina C, Ross LS, Brady D, Fidock DA, Nosten F, Tewari R, Sinnis P, Ay F, Vert JP, Noble WS, Le Roch KG. Changes in genome organization of parasite-specific gene families during the Plasmodium transmission stages. Nat Commun 2018; 9:1910. [PMID: 29765020 PMCID: PMC5954139 DOI: 10.1038/s41467-018-04295-5] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 04/18/2018] [Indexed: 12/20/2022] Open
Abstract
The development of malaria parasites throughout their various life cycle stages is coordinated by changes in gene expression. We previously showed that the three-dimensional organization of the Plasmodium falciparum genome is strongly associated with gene expression during its replication cycle inside red blood cells. Here, we analyze genome organization in the P. falciparum and P. vivax transmission stages. Major changes occur in the localization and interactions of genes involved in pathogenesis and immune evasion, host cell invasion, sexual differentiation, and master regulation of gene expression. Furthermore, we observe reorganization of subtelomeric heterochromatin around genes involved in host cell remodeling. Depletion of heterochromatin protein 1 (PfHP1) resulted in loss of interactions between virulence genes, confirming that PfHP1 is essential for maintenance of the repressive center. Our results suggest that the three-dimensional genome structure of human malaria parasites is strongly connected with transcriptional activity of specific gene families throughout the life cycle.
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Affiliation(s)
- Evelien M Bunnik
- Department of Microbiology, Immunology & Molecular Genetics, The University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
- Department of Molecular, Cell and Systems Biology, University of California Riverside, 900 University Ave, Riverside, CA, 92521, USA
| | - Kate B Cook
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA, 98195, USA
| | - Nelle Varoquaux
- Department of Statistics, University of California, 367 Evans Hall, Berkeley, CA, 94720, USA
- Berkeley Institute for Data Science, 190 Doe Library, Berkeley, CA, 94720, USA
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, 60 boulevard Saint-Michel, 75006, Paris, France
- Institut Curie, 75248, Paris, France
- U900, INSERM, Paris, 75248, France
| | - Gayani Batugedara
- Department of Molecular, Cell and Systems Biology, University of California Riverside, 900 University Ave, Riverside, CA, 92521, USA
| | - Jacques Prudhomme
- Department of Molecular, Cell and Systems Biology, University of California Riverside, 900 University Ave, Riverside, CA, 92521, USA
| | - Anthony Cort
- Department of Molecular, Cell and Systems Biology, University of California Riverside, 900 University Ave, Riverside, CA, 92521, USA
| | - Lirong Shi
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, 615N. Wolfe Street, E5132, Baltimore, MD, 21205, USA
| | - Chiara Andolina
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research building, University of Oxford, Old Road campus, Roosevelt Drive, Headington, Oxford, OX3 7FZ, UK
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Tak, 63110, Thailand
| | - Leila S Ross
- Department of Microbiology and Immunology, Columbia University Medical Center, 701W. 168 St., HHSC 1208, New York, NY, 10032, USA
| | - Declan Brady
- School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, NG7 2UH, UK
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Medical Center, 701W. 168 St., HHSC 1208, New York, NY, 10032, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University, New York, NY, 10032, USA
| | - Francois Nosten
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research building, University of Oxford, Old Road campus, Roosevelt Drive, Headington, Oxford, OX3 7FZ, UK
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Tak, 63110, Thailand
| | - Rita Tewari
- School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Photini Sinnis
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, 615N. Wolfe Street, E5132, Baltimore, MD, 21205, USA
| | - Ferhat Ay
- La Jolla Institute for Allergy & Immunology, 9420 Athena Cir, La Jolla, CA, 92037, USA
| | - Jean-Philippe Vert
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, 60 boulevard Saint-Michel, 75006, Paris, France
- Institut Curie, 75248, Paris, France
- U900, INSERM, Paris, 75248, France
- Département de mathématiques et applications, École normale supérieure, CNRS, PSL Research University, Paris, 75005, France
| | - William Stafford Noble
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA, 98195, USA.
- Department of Computer Science and Engineering, University of Washington, Seattle, WA, 98195, USA.
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, 900 University Ave, Riverside, CA, 92521, USA.
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Cook KB, Vembu S, Ha KCH, Zheng H, Laverty KU, Hughes TR, Ray D, Morris QD. RNAcompete-S: Combined RNA sequence/structure preferences for RNA binding proteins derived from a single-step in vitro selection. Methods 2017; 126:18-28. [PMID: 28651966 DOI: 10.1016/j.ymeth.2017.06.024] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 06/16/2017] [Accepted: 06/21/2017] [Indexed: 12/15/2022] Open
Abstract
RNA-binding proteins recognize RNA sequences and structures, but there is currently no systematic and accurate method to derive large (>12base) motifs de novo that reflect a combination of intrinsic preference to both sequence and structure. To address this absence, we introduce RNAcompete-S, which couples a single-step competitive binding reaction with an excess of random RNA 40-mers to a custom computational pipeline for interrogation of the bound RNA sequences and derivation of SSMs (Sequence and Structure Models). RNAcompete-S confirms that HuR, QKI, and SRSF1 prefer binding sites that are single stranded, and recapitulates known 8-10bp sequence and structure preferences for Vts1p and RBMY. We also derive an 18-base long SSM for Drosophila SLBP, which to our knowledge has not been previously determined by selections from pure random sequence, and accurately discriminates human replication-dependent histone mRNAs. Thus, RNAcompete-S enables accurate identification of large, intrinsic sequence-structure specificities with a uniform assay.
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Affiliation(s)
- Kate B Cook
- Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada
| | - Shankar Vembu
- Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada
| | - Kevin C H Ha
- Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada
| | - Hong Zheng
- Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada
| | - Kaitlin U Laverty
- Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada
| | - Timothy R Hughes
- Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada; Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada.
| | - Debashish Ray
- Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada.
| | - Quaid D Morris
- Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada; Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada; Department of Computer Science, University of Toronto, Toronto M5S 2E4, Canada; Department of Electrical and Computer Engineering, University of Toronto, Toronto M5S 3G4, Canada.
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5
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Laver JD, Li X, Ray D, Cook KB, Hahn NA, Nabeel-Shah S, Kekis M, Luo H, Marsolais AJ, Fung KY, Hughes TR, Westwood JT, Sidhu SS, Morris Q, Lipshitz HD, Smibert CA. Brain tumor is a sequence-specific RNA-binding protein that directs maternal mRNA clearance during the Drosophila maternal-to-zygotic transition. Genome Biol 2015; 16:94. [PMID: 25962635 PMCID: PMC4460960 DOI: 10.1186/s13059-015-0659-4] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 04/22/2015] [Indexed: 11/30/2022] Open
Abstract
Background Brain tumor (BRAT) is a Drosophila member of the TRIM-NHL protein family. This family is conserved among metazoans and its members function as post-transcriptional regulators. BRAT was thought to be recruited to mRNAs indirectly through interaction with the RNA-binding protein Pumilio (PUM). However, it has recently been demonstrated that BRAT directly binds to RNA. The precise sequence recognized by BRAT, the extent of BRAT-mediated regulation, and the exact roles of PUM and BRAT in post-transcriptional regulation are unknown. Results Genome-wide identification of transcripts associated with BRAT or with PUM in Drosophila embryos shows that they bind largely non-overlapping sets of mRNAs. BRAT binds mRNAs that encode proteins associated with a variety of functions, many of which are distinct from those implemented by PUM-associated transcripts. Computational analysis of in vitro and in vivo data identified a novel RNA motif recognized by BRAT that confers BRAT-mediated regulation in tissue culture cells. The regulatory status of BRAT-associated mRNAs suggests a prominent role for BRAT in post-transcriptional regulation, including a previously unidentified role in transcript degradation. Transcriptomic analysis of embryos lacking functional BRAT reveals an important role in mediating the decay of hundreds of maternal mRNAs during the maternal-to-zygotic transition. Conclusions Our results represent the first genome-wide analysis of the mRNAs associated with a TRIM-NHL protein and the first identification of an RNA motif bound by this protein family. BRAT is a prominent post-transcriptional regulator in the early embryo through mechanisms that are largely independent of PUM. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0659-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- John D Laver
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada.
| | - Xiao Li
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada. .,Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada.
| | - Debashish Ray
- Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada.
| | - Kate B Cook
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada. .,Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada.
| | - Noah A Hahn
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada.
| | - Syed Nabeel-Shah
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada.
| | - Mariana Kekis
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada. .,Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada.
| | - Hua Luo
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada.
| | - Alexander J Marsolais
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada.
| | - Karen Yy Fung
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada.
| | - Timothy R Hughes
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada. .,Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada.
| | - J Timothy Westwood
- Department of Biology, University of Toronto, Mississauga, 3359 Mississauga Road, Mississauga, Ontario, L5L 1C6, Canada.
| | - Sachdev S Sidhu
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada. .,Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada.
| | - Quaid Morris
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada. .,Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada. .,Edward S. Rogers Sr. Department of Electrical and Computer Engineering, University of Toronto, 10 King's College Road, Toronto, Ontario, M5S 3G4, Canada. .,Department of Computer Science, University of Toronto, 40 St. George Street, Toronto, Ontario, M5S 2E4, Canada.
| | - Howard D Lipshitz
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada.
| | - Craig A Smibert
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada. .,Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada.
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Abstract
RNA-binding proteins (RBPs) are important regulators of eukaryotic gene expression. Genomes typically encode dozens to hundreds of proteins containing RNA-binding domains, which collectively recognize diverse RNA sequences and structures. Recent advances in high-throughput methods for assaying the targets of RBPs in vitro and in vivo allow large-scale derivation of RNA-binding motifs as well as determination of RNA–protein interactions in living cells. In parallel, many computational methods have been developed to analyze and interpret these data. The interplay between RNA secondary structure and RBP binding has also been a growing theme. Integrating RNA–protein interaction data with observations of post-transcriptional regulation will enhance our understanding of the roles of these important proteins.
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Smith SA, Ray D, Cook KB, Mallory MJ, Hughes TR, Lynch KW. Paralogs hnRNP L and hnRNP LL exhibit overlapping but distinct RNA binding constraints. PLoS One 2013; 8:e80701. [PMID: 24244709 PMCID: PMC3823766 DOI: 10.1371/journal.pone.0080701] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 10/15/2013] [Indexed: 01/15/2023] Open
Abstract
HnRNP (heterogeneous nuclear ribonucleoprotein) proteins are a large family of RNA-binding proteins that regulate numerous aspects of RNA processing. Interestingly, several paralogous pairs of hnRNPs exist that exhibit similar RNA-binding specificity to one another, yet have non-redundant functional targets in vivo. In this study we systematically investigate the possibility that the paralogs hnRNP L and hnRNP LL have distinct RNA binding determinants that may underlie their lack of functional redundancy. Using a combination of RNAcompete and native gel analysis we find that while both hnRNP L and hnRNP LL preferentially bind sequences that contain repeated CA dinucleotides, these proteins differ in their requirement for the spacing of the CAs. Specifically, hnRNP LL has a more stringent requirement for a two nucleotide space between CA repeats than does hnRNP L, resulting in hnRNP L binding more promiscuously than does hnRNP LL. Importantly, this differential requirement for the spacing of CA dinucleotides explains the previously observed differences in the sensitivity of hnRNP L and LL to mutations within the CD45 gene. We suggest that overlapping but divergent RNA-binding preferences, as we show here for hnRNP L and hnRNP LL, may be commonplace among other hnRNP paralogs.
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Affiliation(s)
- Sarah A. Smith
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Debashish Ray
- Donnelly Centre, University of Toronto, Toronto, Canada
| | - Kate B. Cook
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Michael J. Mallory
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Timothy R. Hughes
- Donnelly Centre, University of Toronto, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Kristen W. Lynch
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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Abstract
The RNA-Binding Protein DataBase (RBPDB) is a collection of experimental observations of RNA-binding sites, both in vitro and in vivo, manually curated from primary literature. To build RBPDB, we performed a literature search for experimental binding data for all RNA-binding proteins (RBPs) with known RNA-binding domains in four metazoan species (human, mouse, fly and worm). In total, RPBDB contains binding data on 272 RBPs, including 71 that have motifs in position weight matrix format, and 36 sets of sequences of in vivo-bound transcripts from immunoprecipitation experiments. The database is accessible by a web interface which allows browsing by domain or by organism, searching and export of records, and bulk data downloads. Users can also use RBPDB to scan sequences for RBP-binding sites. RBPDB is freely available, without registration at http://rbpdb.ccbr.utoronto.ca/.
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Affiliation(s)
- Kate B Cook
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada
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Lewis MG, Phillips TM, Cook KB, Blake J. Possible explanation for loss of detectable antibody in patients with disseminated malignant melanoma. Nature 1971; 232:52-4. [PMID: 4933175 DOI: 10.1038/232052a0] [Citation(s) in RCA: 77] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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