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  1. Article ; Online: Attomole-level Genomics with Single-molecule Direct DNA, cDNA and RNA Sequencing Technologies.

    Ozsolak, Fatih

    Current issues in molecular biology

    2015  Volume 18, Page(s) 43–48

    Abstract: With the introduction of next-generation sequencing (NGS) technologies in 2005, the domination of microarrays in genomics quickly came to an end due to NGS's superior technical performance and cost advantages. By enabling genetic analysis capabilities ... ...

    Abstract With the introduction of next-generation sequencing (NGS) technologies in 2005, the domination of microarrays in genomics quickly came to an end due to NGS's superior technical performance and cost advantages. By enabling genetic analysis capabilities that were not possible previously, NGS technologies have started to play an integral role in all areas of biomedical research. This chapter outlines the low-quantity DNA and cDNA sequencing capabilities and applications developed with the Helicos single molecule DNA sequencing technology.
    MeSH term(s) Genome, Human ; Genomics ; High-Throughput Nucleotide Sequencing ; Humans ; Sequence Analysis, DNA/methods ; Sequence Analysis, RNA/methods
    Language English
    Publishing date 2015-07-08
    Publishing country Switzerland
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2000024-8
    ISSN 1467-3045 ; 1467-3037
    ISSN (online) 1467-3045
    ISSN 1467-3037
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Quantitative polyadenylation site mapping with single-molecule direct RNA sequencing.

    Ozsolak, Fatih

    Methods in molecular biology (Clifton, N.J.)

    2014  Volume 1125, Page(s) 145–155

    Abstract: The known regulatory role of 3' untranslated regions (3'UTRs) and poly(A) tails in RNA localization, stability, and translation, and polyadenylation regulation defects leading to human diseases such as oculopharyngeal muscular dystrophy, thalassemias, ... ...

    Abstract The known regulatory role of 3' untranslated regions (3'UTRs) and poly(A) tails in RNA localization, stability, and translation, and polyadenylation regulation defects leading to human diseases such as oculopharyngeal muscular dystrophy, thalassemias, thrombophilia, and IPEX syndrome underline the need to fully characterize genome-wide polyadenylation states and mechanisms across normal physiological and disease states. This chapter outlines the quantitative polyadenylation site mapping and analysis strategies developed with the single-molecule direct RNA sequencing technology.
    MeSH term(s) 3' Untranslated Regions/genetics ; Humans ; Polyadenylation/physiology ; Sequence Analysis, RNA/methods
    Chemical Substances 3' Untranslated Regions
    Language English
    Publishing date 2014
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-62703-971-0_13
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Third-generation sequencing techniques and applications to drug discovery.

    Ozsolak, Fatih

    Expert opinion on drug discovery

    2012  Volume 7, Issue 3, Page(s) 231–243

    Abstract: Introduction: There is an immediate need for functional and molecular studies to decipher differences between disease and 'normal' settings to identify large quantities of validated targets with the highest therapeutic utilities. Furthermore, drug ... ...

    Abstract Introduction: There is an immediate need for functional and molecular studies to decipher differences between disease and 'normal' settings to identify large quantities of validated targets with the highest therapeutic utilities. Furthermore, drug mechanism of action and biomarkers to predict drug efficacy and safety need to be identified for effective design of clinical trials, decreasing attrition rates, regulatory agency approval process and drug repositioning. By expanding the power of genetics and pharmacogenetics studies, next-generation nucleic acid sequencing technologies have started to play an important role in all stages of drug discovery.
    Areas covered: This article reviews the first- and second-generation sequencing technologies (SGSTs) and challenges they pose to biomedicine. The article then focuses on the emerging third-generation sequencing technologies (TGSTs), their technological foundations and potential contributions to drug discovery.
    Expert opinion: Despite the scientific and commercial success of SGSTs, the goal of rapid, comprehensive and unbiased sequencing of nucleic acids has not been achieved. TGSTs promise to increase sequencing throughput and read lengths, decrease costs, run times and error rates, eliminate biases inherent in SGSTs and offer capabilities beyond nucleic acid sequencing. Such changes will have positive impact on all sequencing applications to drug discovery.
    MeSH term(s) Drug Design ; Drug Discovery/methods ; Genome, Human ; High-Throughput Nucleotide Sequencing/methods ; High-Throughput Screening Assays/methods ; Humans ; Pharmacogenetics/methods ; Sequence Analysis, DNA/methods ; Sequence Analysis, RNA/methods
    Language English
    Publishing date 2012-02-02
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Review
    ZDB-ID 2259618-5
    ISSN 1746-045X ; 1746-0441
    ISSN (online) 1746-045X
    ISSN 1746-0441
    DOI 10.1517/17460441.2012.660145
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Single-molecule direct RNA sequencing without cDNA synthesis.

    Ozsolak, Fatih / Milos, Patrice M

    Wiley interdisciplinary reviews. RNA

    2011  Volume 2, Issue 4, Page(s) 565–570

    Abstract: Methods for in-depth genome-wide characterization of transcriptomes and quantification of transcript levels using various microarray and next-generation sequencing technologies have emerged as valuable tools for understanding cellular physiology and ... ...

    Abstract Methods for in-depth genome-wide characterization of transcriptomes and quantification of transcript levels using various microarray and next-generation sequencing technologies have emerged as valuable tools for understanding cellular physiology and human disease biology and have begun to be utilized in various clinical diagnostic applications. Current methods, however, typically require RNA to be converted to complementary DNA prior to measurements. This step has been shown to introduce many biases and artifacts. In order to best characterize the 'true' transcriptome, the single-molecule direct RNA sequencing (DRS) technology was developed. This review focuses on the underlying principles behind the DRS, sample preparation steps, and the current and novel avenues of research and applications DRS offers.
    MeSH term(s) DNA, Complementary/biosynthesis ; DNA, Complementary/genetics ; Gene Expression Profiling/methods ; Genome, Human ; Humans ; Oligonucleotide Array Sequence Analysis/methods ; Optical Devices ; Sequence Analysis, RNA/instrumentation ; Sequence Analysis, RNA/methods
    Chemical Substances DNA, Complementary
    Language English
    Publishing date 2011-03-14
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 2634714-3
    ISSN 1757-7012 ; 1757-7004
    ISSN (online) 1757-7012
    ISSN 1757-7004
    DOI 10.1002/wrna.84
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Transcriptome profiling using single-molecule direct RNA sequencing.

    Ozsolak, Fatih / Milos, Patrice M

    Methods in molecular biology (Clifton, N.J.)

    2011  Volume 733, Page(s) 51–61

    Abstract: Methods for in-depth characterization of transcriptomes and quantification of transcript levels have emerged as valuable tools for understanding cellular physiology and human disease biology, and have begun to be utilized in various clinical diagnostic ... ...

    Abstract Methods for in-depth characterization of transcriptomes and quantification of transcript levels have emerged as valuable tools for understanding cellular physiology and human disease biology, and have begun to be utilized in various clinical diagnostic applications. Today, current methods utilized by the scientific community typically require RNA to be converted to cDNA prior to comprehensive measurements. However, this cDNA conversion process has been shown to introduce many biases and artifacts that interfere with the proper characterization and quantitation of transcripts. We have developed a direct RNA sequencing (DRS) approach, in which, unlike other technologies, RNA is sequenced directly without prior conversion to cDNA. The benefits of DRS include the ability to use minute quantities (e.g. on the order of several femtomoles) of RNA with minimal sample preparation, the ability to analyze short RNAs which pose unique challenges for analysis using cDNA-based approaches, and the ability to perform these analyses in a low-cost and high-throughput manner. Here, we describe the strategies and procedures we employ to prepare various RNA species for analysis with DRS.
    MeSH term(s) Animals ; Base Sequence ; Gene Expression Profiling/methods ; Humans ; Mice ; Nucleic Acid Hybridization ; Polyadenylation ; RNA/genetics ; RNA/metabolism ; RNA, Untranslated/genetics ; RNA, Untranslated/metabolism ; Sequence Analysis, RNA/methods
    Chemical Substances RNA, Untranslated ; RNA (63231-63-0)
    Language English
    Publishing date 2011-03-23
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-61779-089-8_4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: RNA sequencing: advances, challenges and opportunities.

    Ozsolak, Fatih / Milos, Patrice M

    Nature reviews. Genetics

    2010  Volume 12, Issue 2, Page(s) 87–98

    Abstract: In the few years since its initial application, massively parallel cDNA sequencing, or RNA-seq, has allowed many advances in the characterization and quantification of transcriptomes. Recently, several developments in RNA-seq methods have provided an ... ...

    Abstract In the few years since its initial application, massively parallel cDNA sequencing, or RNA-seq, has allowed many advances in the characterization and quantification of transcriptomes. Recently, several developments in RNA-seq methods have provided an even more complete characterization of RNA transcripts. These developments include improvements in transcription start site mapping, strand-specific measurements, gene fusion detection, small RNA characterization and detection of alternative splicing events. Ongoing developments promise further advances in the application of RNA-seq, particularly direct RNA sequencing and approaches that allow RNA quantification from very small amounts of cellular materials.
    MeSH term(s) Alternative Splicing ; Animals ; Humans ; RNA/analysis ; RNA/genetics ; Sequence Analysis, RNA ; Transcription, Genetic
    Chemical Substances RNA (63231-63-0)
    Language English
    Publishing date 2010-12-30
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Review
    ZDB-ID 2035157-4
    ISSN 1471-0064 ; 1471-0056
    ISSN (online) 1471-0064
    ISSN 1471-0056
    DOI 10.1038/nrg2934
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Profiling of short RNAs using Helicos single-molecule sequencing.

    Kapranov, Philipp / Ozsolak, Fatih / Milos, Patrice M

    Methods in molecular biology (Clifton, N.J.)

    2011  Volume 822, Page(s) 219–232

    Abstract: The importance of short (<200 nt) RNAs in cell biogenesis has been well documented. These short RNAs include crucial classes of molecules such as transfer RNAs, small nuclear RNA, microRNAs, and many others (reviewed in Storz et al., Annu Rev Biochem 74: ... ...

    Abstract The importance of short (<200 nt) RNAs in cell biogenesis has been well documented. These short RNAs include crucial classes of molecules such as transfer RNAs, small nuclear RNA, microRNAs, and many others (reviewed in Storz et al., Annu Rev Biochem 74:199-217, 2005; Ghildiyal and Zamore, Nat Rev Genet 10:94-108, 2009). Furthermore, the realm of functional RNAs that fall within this size range is growing to include less well-characterized RNAs such as short RNAs found at the promoters and 3' termini of genes (Affymetrix ENCODE Transcriptome Project et al., Nature 457:1028-1032, 2009; Davis and Ares, Proc Natl Acad Sci USA 103:3262-3267, 2006; Kapranov et al., Science 316:1484-1488, 2007; Taft et al., Nat Genet 41:572-578, 2009; Kapranov et al., Nature 466:642-646, 2010), short RNAs involved in paramutation (Rassoulzadegan et al., Nature 441:469-474, 2006), and others (reviewed in Kawaji and Hayashizaki, PLoS Genet 4:e22, 2008). Discovery and accurate quantification of these RNA molecules, less than 200 bases in size, is thus an important and also challenging aspect of understanding the full repertoire of cellular and extracellular RNAs. Here, we describe the strategies and procedures we developed to profile short RNA species using single-molecule sequencing (SMS) and the advantages SMS offers.
    MeSH term(s) Base Sequence ; Computational Biology/instrumentation ; Computational Biology/methods ; DNA, Complementary ; Gene Expression Profiling/instrumentation ; Gene Expression Profiling/methods ; Humans ; RNA/isolation & purification ; RNA, Small Untranslated/analysis ; RNA, Small Untranslated/isolation & purification ; Sequence Analysis, DNA/methods ; Sequence Analysis, RNA/instrumentation ; Sequence Analysis, RNA/methods
    Chemical Substances DNA, Complementary ; RNA, Small Untranslated ; RNA (63231-63-0)
    Language English
    Publishing date 2011-12-05
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-61779-427-8_15
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Global analysis of mRNA isoform half-lives reveals stabilizing and destabilizing elements in yeast.

    Geisberg, Joseph V / Moqtaderi, Zarmik / Fan, Xiaochun / Ozsolak, Fatih / Struhl, Kevin

    Cell

    2014  Volume 156, Issue 4, Page(s) 812–824

    Abstract: We measured half-lives of 21,248 mRNA 3' isoforms in yeast by rapidly depleting RNA polymerase II from the nucleus and performing direct RNA sequencing throughout the decay process. Interestingly, half-lives of mRNA isoforms from the same gene, including ...

    Abstract We measured half-lives of 21,248 mRNA 3' isoforms in yeast by rapidly depleting RNA polymerase II from the nucleus and performing direct RNA sequencing throughout the decay process. Interestingly, half-lives of mRNA isoforms from the same gene, including nearly identical isoforms, often vary widely. Based on clusters of isoforms with different half-lives, we identify hundreds of sequences conferring stabilization or destabilization upon mRNAs terminating downstream. One class of stabilizing element is a polyU sequence that can interact with poly(A) tails, inhibit the association of poly(A)-binding protein, and confer increased stability upon introduction into ectopic transcripts. More generally, destabilizing and stabilizing elements are linked to the propensity of the poly(A) tail to engage in double-stranded structures. Isoforms engineered to fold into 3' stem-loop structures not involving the poly(A) tail exhibit even longer half-lives. We suggest that double-stranded structures at 3' ends are a major determinant of mRNA stability.
    MeSH term(s) Base Sequence ; Genome, Fungal ; Genome-Wide Association Study ; Half-Life ; Nucleotide Motifs ; RNA Stability ; RNA, Fungal/chemistry ; RNA, Fungal/metabolism ; RNA, Messenger/chemistry ; RNA, Messenger/metabolism ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Sequence Alignment
    Chemical Substances RNA, Fungal ; RNA, Messenger
    Language English
    Publishing date 2014-02-13
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2013.12.026
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Gene expression profiles and differential cytoglobin expression in atrophy and adenocarcinoma of the prostate.

    Mogal, Ashish P / Watson, Mark A / Ozsolak, Fatih / Salavaggione, Lorena / Humphrey, Peter A

    The Prostate

    2012  Volume 72, Issue 9, Page(s) 931–937

    Abstract: Background: Proliferative inflammatory atrophy (PIA) has been proposed as a potential precursor for prostate cancer. The precise molecular abnormalities in prostatic atrophy compared to high-grade prostatic intraepithelial neoplasia (HGPIN) and ... ...

    Abstract Background: Proliferative inflammatory atrophy (PIA) has been proposed as a potential precursor for prostate cancer. The precise molecular abnormalities in prostatic atrophy compared to high-grade prostatic intraepithelial neoplasia (HGPIN) and carcinoma have not been fully defined.
    Methods: We utilized laser capture microdissection and microarray analysis to characterize cells of PIA, HGPIN, invasive prostatic carcinoma, and non-atrophic benign prostatic epithelium (NABE). Cytoglobin was selected for immunohistochemistry (IHC) validation. IHC stains were evaluated for proportion of positive glands, and intensity of cytoglobin staining. An immunoreactive score (IR score) was determined as the product of the percentage of positive staining and intensity.
    Results: Microarray analysis revealed probe sets that separated the microdissected cell types. Several genes showed overlapping expression patterns between PIA and PIN, and HGPIN and invasive carcinoma. Cytoglobin protein expression was detected in 57/93 (61%) of NABE and BPH cases, 92/93 atrophy (99%), 3/34 (9%) of PIN, and 23/61 carcinoma (37%) samples. The highest IHC scores were calculated for atrophy foci. A subset (33%) of atrophy cases showed the same low-cytoglobin expression level as PIN and carcinoma.
    Conclusions: Prostatic epithelium can be stratified into normal, atrophic, PIN, and invasive carcinoma categories based on differential genetic signatures. Cytoglobin, a protein that can be induced in response to oxidative stress, was elevated in most atrophy foci, suggesting hypoxic, and/or oxidative damage. The lower level of cytoglobin seen in neoplastic cells and 33% of atrophy foci may indicate a shared susceptibility to oxidative damage for this subset of atrophy cases and prostatic neoplasia.
    MeSH term(s) Adenocarcinoma/genetics ; Adenocarcinoma/metabolism ; Adenocarcinoma/pathology ; Atrophy ; Cell Hypoxia/physiology ; Gene Expression Profiling/methods ; Gene Expression Regulation, Neoplastic ; Globins/biosynthesis ; Globins/genetics ; Humans ; Inflammation/genetics ; Inflammation/metabolism ; Inflammation/pathology ; Male ; Oxidative Stress/physiology ; Prostatic Neoplasms/genetics ; Prostatic Neoplasms/metabolism ; Prostatic Neoplasms/pathology
    Chemical Substances cytoglobin ; Globins (9004-22-2)
    Language English
    Publishing date 2012-06-15
    Publishing country United States
    Document type Comparative Study ; Journal Article
    ZDB-ID 604707-5
    ISSN 1097-0045 ; 0270-4137
    ISSN (online) 1097-0045
    ISSN 0270-4137
    DOI 10.1002/pros.21494
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: Global Analysis of mRNA Isoform Half-Lives Reveals Stabilizing and Destabilizing Elements in Yeast

    Geisberg, Joseph V / Zarmik Moqtaderi / Xiaochun Fan / Fatih Ozsolak / Kevin Struhl

    Cell. 2014 Feb. 13, v. 156

    2014  

    Abstract: We measured half-lives of 21,248 mRNA 3′ isoforms in yeast by rapidly depleting RNA polymerase II from the nucleus and performing direct RNA sequencing throughout the decay process. Interestingly, half-lives of mRNA isoforms from the same gene, ... ...

    Abstract We measured half-lives of 21,248 mRNA 3′ isoforms in yeast by rapidly depleting RNA polymerase II from the nucleus and performing direct RNA sequencing throughout the decay process. Interestingly, half-lives of mRNA isoforms from the same gene, including nearly identical isoforms, often vary widely. Based on clusters of isoforms with different half-lives, we identify hundreds of sequences conferring stabilization or destabilization upon mRNAs terminating downstream. One class of stabilizing element is a polyU sequence that can interact with poly(A) tails, inhibit the association of poly(A)-binding protein, and confer increased stability upon introduction into ectopic transcripts. More generally, destabilizing and stabilizing elements are linked to the propensity of the poly(A) tail to engage in double-stranded structures. Isoforms engineered to fold into 3′ stem-loop structures not involving the poly(A) tail exhibit even longer half-lives. We suggest that double-stranded structures at 3′ ends are a major determinant of mRNA stability.
    Keywords DNA-directed RNA polymerase ; genes ; half life ; messenger RNA ; sequence analysis ; yeasts
    Language English
    Dates of publication 2014-0213
    Size p. 812-824.
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2013.12.026
    Database NAL-Catalogue (AGRICOLA)

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