Identification of active miRNA promoters from nuclear run-on RNA sequencing.


:The genome-wide identification of microRNA transcription start sites (miRNA TSSs) is essential for understanding how miRNAs are regulated in development and disease. In this study, we developed mirSTP (mirna transcription Start sites Tracking Program), a probabilistic model for identifying active miRNA TSSs from nascent transcriptomes generated by global run-on sequencing (GRO-seq) and precision run-on sequencing (PRO-seq). MirSTP takes advantage of characteristic bidirectional transcription signatures at active TSSs in GRO/PRO-seq data, and provides accurate TSS prediction for human intergenic miRNAs at a high resolution. MirSTP performed better than existing generalized and experiment specific methods, in terms of the enrichment of various promoter-associated marks. MirSTP analysis of 27 human cell lines in 183 GRO-seq and 28 PRO-seq experiments identified TSSs for 480 intergenic miRNAs, indicating a wide usage of alternative TSSs. By integrating predicted miRNA TSSs with matched ENCODE transcription factor (TF) ChIP-seq data, we connected miRNAs into the transcriptional circuitry, which provides a valuable source for understanding the complex interplay between TF and miRNA. With mirSTP, we not only predicted TSSs for 72 miRNAs, but also identified 12 primary miRNAs with significant RNA polymerase pausing alterations after JQ1 treatment; each miRNA was further validated through BRD4 binding to its predicted promoter. MirSTP is available at


Nucleic Acids Res


Nucleic acids research


Liu Q,Wang J,Zhao Y,Li CI,Stengel KR,Acharya P,Johnston G,Hiebert SW,Shyr Y




Has Abstract


2017-07-27 00:00:00














  • Quantitation of RNA editing substrates, products and potential intermediates: implications for developmental regulation.

    abstract::Kinetoplast mitochondrial RNA editing is the developmentally regulated post-transcriptional process of uridine insertion and deletion in mRNAs directed by short guide RNAs (gRNAs), which creates functional mRNAs. Two mechanisms are proposed: transesterification which predicts gRNA/mRNA chimeric intermediates, and enzy...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Riley GR,Myler PJ,Stuart K

    更新日期:1995-02-25 00:00:00

  • FANTOM DB: database of Functional Annotation of RIKEN Mouse cDNA Clones.

    abstract::FANTOM DB, the database of Functional Annotation of RIKEN Mouse cDNA Clones, is designed to store sequence information of RIKEN full-length enriched mouse cDNA clones, graphical views of sequence analysis results, curated functional annotation information and additional descriptions, including Gene Ontology terms. RIK...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Bono H,Kasukawa T,Furuno M,Hayashizaki Y,Okazaki Y

    更新日期:2002-01-01 00:00:00

  • Intensity-based analysis of two-colour microarrays enables efficient and flexible hybridization designs.

    abstract::In two-colour microarrays, the ratio of signal intensities of two co-hybridized samples is used as a relative measure of gene expression. Ratio-based analysis becomes complicated and inefficient in multi-class comparisons. We therefore investigated the validity of an intensity-based analysis procedure. To this end, tw...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: 't Hoen PA,Turk R,Boer JM,Sterrenburg E,de Menezes RX,van Ommen GJ,den Dunnen JT

    更新日期:2004-02-24 00:00:00

  • Highly conserved sequences in the 3' untranslated region of mRNAs coding for homologous proteins in distantly related species.

    abstract::Comparison of the nucleotide sequence of mRNAs coding for several vertebrate actins revealed a high degree of sequence homology in the 3' untranslated region (3' UTR) between those mRNAs coding for homologous (isotypic) actins in different organisms but not between mRNAs coding for very similar isoforms differing in t...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Yaffe D,Nudel U,Mayer Y,Neuman S

    更新日期:1985-05-24 00:00:00

  • Patterns in interspecies similarity correlate with nucleotide composition in mammalian 3'UTRs.

    abstract::Post-transcriptional regulation and the formation of mRNA 3' ends are crucial for gene expression in eukaryotes. Interspecies conservation of many sequences within 3'UTRs reveals selective constraint due to similar function. To study the pattern of conservation within 3'UTRs, we compiled and aligned 50 sets of complet...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Shabalina SA,Ogurtsov AY,Lipman DJ,Kondrashov AS

    更新日期:2003-09-15 00:00:00

  • GenBank.

    abstract::GenBank (R) is a comprehensive sequence database that contains publicly available DNA sequences for more than 119 000 different organisms, obtained primarily through the submission of sequence data from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Benson DA,Karsch-Mizrachi I,Lipman DJ,Ostell J,Wheeler DL

    更新日期:2003-01-01 00:00:00

  • Cloning and functional analysis of spliced isoforms of human nuclear factor I-X: interference with transcriptional activation by NFI/CTF in a cell-type specific manner.

    abstract::Previous studies of the epithelial specificity of the human papillomavirus type 16 (HPV-16) enhancer pointed out an important role of nuclear factor I (NFI). In epithelial cells, NFI proteins are derived from the NFI-C gene and referred to as NFI/CTF. In contrast, fibroblasts, where the enhancer is inactive, express h...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Apt D,Liu Y,Bernard HU

    更新日期:1994-09-25 00:00:00

  • scIGANs: single-cell RNA-seq imputation using generative adversarial networks.

    abstract::Single-cell RNA-sequencing (scRNA-seq) enables the characterization of transcriptomic profiles at the single-cell resolution with increasingly high throughput. However, it suffers from many sources of technical noises, including insufficient mRNA molecules that lead to excess false zero values, termed dropouts. Comput...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Xu Y,Zhang Z,You L,Liu J,Fan Z,Zhou X

    更新日期:2020-09-04 00:00:00

  • Cloning of the gene coding for human L apoferritin.

    abstract::A recently reported cDNA clone coding for human promyelocytic L apoferritin, shows some differences with a liver L apoferritin cDNA. We have investigated if these differences are due to the expression of different genes or to an alternative transcription of an unique gene. In this paper we report data suggesting that ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Santoro C,Marone M,Ferrone M,Costanzo F,Colombo M,Minganti C,Cortese R,Silengo L

    更新日期:1986-04-11 00:00:00

  • CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources.

    abstract::During the past years, the advances in high-throughput technologies have produced an unprecedented growth in the number and size of repositories and databases storing relevant biological data. Today, there is more biological information than ever but, unfortunately, the current status of many of these repositories is ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Bleda M,Tarraga J,de Maria A,Salavert F,Garcia-Alonso L,Celma M,Martin A,Dopazo J,Medina I

    更新日期:2012-07-01 00:00:00

  • Divalent metal-dependent catalysis and cleavage specificity of CSP41, a chloroplast endoribonuclease belonging to the short chain dehydrogenase/reductase superfamily.

    abstract::CSP41 is a ubiquitous chloroplast endoribonuclease belonging to the short chain dehydrogenase/reductase (SDR) superfamily. To help elucidate the role of CSP41 in chloroplast gene regulation, the mechanisms that determine its substrate recognition and catalytic activity were investigated. A divalent metal is required f...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Bollenbach TJ,Stern DB

    更新日期:2003-08-01 00:00:00

  • Methyl transferases induced during chemical adaptation of M. luteus.

    abstract::Three peaks of methyltransferase activity specific for MNNG alkylated DNA have been identified from extracts of chemically adapted M. luteus. They are designated as TI to TIII in order to their elution from a Sephadex G-75 column. The first one of these peaks has been purified to homogeneity. TI, is an inducible, unus...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Riazuddin S,Athar A,Sohail A

    更新日期:1987-11-25 00:00:00

  • GalaxyWEB server for protein structure prediction and refinement.

    abstract::Three-dimensional protein structures provide invaluable information for understanding and regulating biological functions of proteins. The GalaxyWEB server predicts protein structure from sequence by template-based modeling and refines loop or terminus regions by ab initio modeling. This web server is based on the met...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Ko J,Park H,Heo L,Seok C

    更新日期:2012-07-01 00:00:00

  • The gene II proteins of the filamentous phages IKe and Ff (M13, fd and f1) are not functionally interchangeable during viral strand replication.

    abstract::Gene II protein is the only phage-encoded protein required for the double-stranded DNA replication of the distantly related filamentous phages IKe and Ff (M13, fd and f1). Complementation studies have demonstrated that, despite a significant degree of homology between the nucleotide sequences of the gene II's of IKe a...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Peeters BP,Schoenmakers JG,Konings RN

    更新日期:1986-06-25 00:00:00

  • A method for generating subtractive cDNA libraries retaining clones containing repetitive elements.

    abstract::Here we describe a two-stepped photobiotin-based procedure to enrich a target (canine retinal) cDNA library for tissue specific clones without removing those containing repetitive ( SINE ) elements, despite the presence of these elements in the driver population. In a first hybridization excess SINE elements were hybr...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Lin CT,Sargan DR

    更新日期:1997-11-01 00:00:00

  • Mapping genes within a YAC by computer-assisted interpretation of partial restriction digestions.

    abstract::Partial restriction digestion is used to map restriction sites and the location of genes within yeast artificial chromosomes (YACs). Locus-specific probes are hybridised to the partially digested YAC DNA and the fragments to which they hybridise are compared with the pattern of partial digestion products that include ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Shields DC,Butler A,Mosurski KR,Walsh MT,Whitehead AS

    更新日期:1996-11-15 00:00:00

  • Integration of a vector containing rodent repetitive elements in the rat genome.

    abstract::We have previously shown that integration of a polyoma vector containing rodent repetitive elements into rat cellular DNA is non-random (Wallenburg et al. J. Virol. 50: 678-683). Junctions between the polyoma vector and the host DNA occur in the repetitive sequences of the vector about ten times more frequently than w...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Wallenburg JC,Nepveu A,Chartrand P

    更新日期:1987-10-12 00:00:00

  • PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease.

    abstract::Peroxisomes are essential organelles of eukaryotic origin, ubiquitously distributed in cells and organisms, playing key roles in lipid and antioxidant metabolism. Loss or malfunction of peroxisomes causes more than 20 fatal inherited conditions. We have created a peroxisomal database ( that...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Schlüter A,Fourcade S,Domènech-Estévez E,Gabaldón T,Huerta-Cepas J,Berthommier G,Ripp R,Wanders RJ,Poch O,Pujol A

    更新日期:2007-01-01 00:00:00

  • Targeted cross-linking-mass spectrometry determines vicinal interactomes within heterogeneous RNP complexes.

    abstract::Proteomic and RNomic approaches have identified many components of different ribonucleoprotein particles (RNPs), yet still little is known about the organization and protein proximities within these heterogeneous and highly dynamic complexes. Here we describe a targeted cross-linking approach, which combines cross-lin...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Trahan C,Oeffinger M

    更新日期:2016-02-18 00:00:00

  • Allosterism and signal transfer in DNA.

    abstract::We analysed the basic mechanisms of signal transmission in DNA and the origins of the allostery exhibited by systems such as the ternary complex BAMHI-DNA-GRDBD. We found that perturbation information generated by a primary protein binding event travels as a wave to distant regions of DNA following a hopping mechanism...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Balaceanu A,Pérez A,Dans PD,Orozco M

    更新日期:2018-09-06 00:00:00

  • Systematic integration of RNA-Seq statistical algorithms for accurate detection of differential gene expression patterns.

    abstract::RNA-Seq is gradually becoming the standard tool for transcriptomic expression studies in biological research. Although considerable progress has been recorded in the development of statistical algorithms for the detection of differentially expressed genes using RNA-Seq data, the list of detected genes can differ signi...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Moulos P,Hatzis P

    更新日期:2015-02-27 00:00:00

  • Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV).

    abstract::The International Committee on Taxonomy of Viruses (ICTV) is charged with the task of developing, refining, and maintaining a universal virus taxonomy. This task encompasses the classification of virus species and higher-level taxa according to the genetic and biological properties of their members; naming virus taxa;...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Lefkowitz EJ,Dempsey DM,Hendrickson RC,Orton RJ,Siddell SG,Smith DB

    更新日期:2018-01-04 00:00:00

  • Fractionation and characterization of satellite DNAs of the kangaroo rat (Dipodomys ordii).

    abstract::Nuclear DNA from liver cells of the kangaroo rat species Dipodomysordii was fractionated and characterized with the aid of buoyant density gradients in neutral and alkaline CsCl and in Ag(+)-Cs(2)SO(4). More than one-half of the DNA was present in three density satellites, a greater proportion than in any other specie...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Hatch FT,Mazrimas JA

    更新日期:1974-04-01 00:00:00

  • The mapping of nucleosomes and regulatory protein binding sites at the Saccharomyces cerevisiae MFA2 gene: a high resolution approach.

    abstract::We have developed an end-labelling approach to map the positions of nucleosomes and protein binding sites at nucleotide resolution by footprinting micrococcal nuclease (MNase)-sensitive sites. Using this approach we determined that the MFA2 gene and its upstream control regions have four positioned nucleosomes when tr...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Teng Y,Yu S,Waters R

    更新日期:2001-07-01 00:00:00

  • Eco Cyc: encyclopedia of Escherichia coli genes and metabolism.

    abstract::The EcoCyc database describes the genome and gene products of Escherichia coli, its metabolic and signal-transduction pathways, and its tRNAs. The database describes 4391 genes of E.coli, 695 enzymes encoded by a subset of these genes, 904 metabolic reactions that occur in E.coli, and the organization of these reactio...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Karp PD,Riley M,Paley SM,Pellegrini-Toole A,Krummenacker M

    更新日期:1999-01-01 00:00:00

  • NRPSpredictor2--a web server for predicting NRPS adenylation domain specificity.

    abstract::The products of many bacterial non-ribosomal peptide synthetases (NRPS) are highly important secondary metabolites, including vancomycin and other antibiotics. The ability to predict substrate specificity of newly detected NRPS Adenylation (A-) domains by genome sequencing efforts is of great importance to identify an...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Röttig M,Medema MH,Blin K,Weber T,Rausch C,Kohlbacher O

    更新日期:2011-07-01 00:00:00

  • CTC1-mediated C-strand fill-in is an essential step in telomere length maintenance.

    abstract::To prevent progressive telomere shortening as a result of conventional DNA replication, new telomeric DNA must be added onto the chromosome end. The de novo DNA synthesis involves elongation of the G-rich strand of the telomere by telomerase. In human cells, the CST complex (CTC1-STN1-TEN1) also functions in telomere ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Feng X,Hsu SJ,Kasbek C,Chaiken M,Price CM

    更新日期:2017-05-05 00:00:00

  • RegAnalyst: a web interface for the analysis of regulatory motifs, networks and pathways.

    abstract::RegAnalyst is a user-friendly web interface that integrates MoPP (Motif Prediction Program), MyPatternFinder (pattern detection tool) and MycoRegDB (mycobacterial promoter and regulatory elements database). Since motif discovery is a challenging task, numerous tools have been developed over the past few years. Strikin...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Sharma D,Mohanty D,Surolia A

    更新日期:2009-07-01 00:00:00

  • Comparison of murine Supt4h and a nearly identical expressed, processed gene: evidence of sequence conservation through gene conversion extending into the untranslated regions.

    abstract::We show herein the transcription of a processed gene that originated from a spliced transcript. Recently, we isolated the human and murine homologues of the yeast chromatin protein, SPT4. The Supt4h gene is spliced normally from five exons encoded by chromosome 11. Here we show that a related sequence on chromosome 10...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Chiang PW,Zhang R,Stubbs L,Zhang L,Zhu L,Kurnit DM

    更新日期:1998-11-01 00:00:00

  • A trans-splicing group I intron and tRNA-hyperediting in the mitochondrial genome of the lycophyte Isoetes engelmannii.

    abstract::Plant mitochondrial genomes show much more evolutionary plasticity than those of animals. We analysed the first mitochondrial DNA (mtDNA) of a lycophyte, the quillwort Isoetes engelmannii, which is separated from seed plants by more than 350 million years of evolution. The Isoetes mtDNA is particularly rich in recombi...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Grewe F,Viehoever P,Weisshaar B,Knoop V

    更新日期:2009-08-01 00:00:00