Global miRNA expression analysis identifies novel key regulators of plasma cell differentiation and malignant plasma cell.


:MicroRNAs (miRNAs) are small noncoding RNAs that attenuate expression of their mRNA targets. Here, we developed a new method and an R package, to easily infer candidate miRNA-mRNA target interactions that could be functional during a given biological process. Using this method, we described, for the first time, a comprehensive integrated analysis of miRNAs and mRNAs during human normal plasma cell differentiation (PCD). Our results reveal 63 miRNAs with significant temporal changes in their expression during normal PCD. We derived a high-confidence network of 295 target relationships comprising 47 miRNAs and 141 targets. These relationships include new examples of miRNAs that appear to coordinately regulate multiple members of critical pathways associated with PCD. Consistent with this, we have experimentally validated a role for the miRNA-30b/c/d-mediated regulation of key PCD factors (IRF4, PRDM1, ELL2 and ARID3A). Furthermore, we found that 24 PCD stage-specific miRNAs are aberrantly overexpressed in multiple myeloma (MM) tumor plasma cells compared to their normal counterpart, suggesting that MM cells frequently acquired expression changes in miRNAs already undergoing dynamic expression modulation during normal PCD. Altogether, our analysis identifies candidate novel key miRNAs regulating networks of significance for normal PCD and malignant plasma cell biology.


Nucleic Acids Res


Nucleic acids research


Kassambara A,Jourdan M,Bruyer A,Robert N,Pantesco V,Elemento O,Klein B,Moreaux J




Has Abstract


2017-06-02 00:00:00














  • Modelling the secondary structures of slippage-prone hypervariable RNA regions: the example of the tiger beetle 18S rRNA variable region V4.

    abstract::Variable regions within ribosomal RNAs frequently vary in length as a result of incorporating products of slippage. This makes constructing secondary structure models problematic because base homology is difficult or impossible to establish between species. Here, we model such a region by comparing the results of the ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Hancock JM,Vogler AP

    更新日期:1998-04-01 00:00:00

  • Binding of T and T analogs to CG base pairs in antiparallel triplexes.

    abstract::The goal of this study was to address antiparallel triplex formation at duplex targets that do not conform to a strict oligopurine.oligopyrimidine motif. We focused on the ability of natural bases and base analogs incorporated into oligonucleotide third strands to bind to so-called CG inversions. These are sites where...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Durland RH,Rao TS,Revankar GR,Tinsley JH,Myrick MA,Seth DM,Rayford J,Singh P,Jayaraman K

    更新日期:1994-08-11 00:00:00

  • ETCM: an encyclopaedia of traditional Chinese medicine.

    abstract::Traditional Chinese medicine (TCM) is not only an effective solution for primary health care, but also a great resource for drug innovation and discovery. To meet the increasing needs for TCM-related data resources, we developed ETCM, an Encyclopedia of Traditional Chinese Medicine. ETCM includes comprehensive and sta...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Xu HY,Zhang YQ,Liu ZM,Chen T,Lv CY,Tang SH,Zhang XB,Zhang W,Li ZY,Zhou RR,Yang HJ,Wang XJ,Huang LQ

    更新日期:2019-01-08 00:00:00

  • Hemicatenanes form upon inhibition of DNA replication.

    abstract::Plasmid DNA incubated in interphase Xenopus egg extracts is normally assembled into chromatin and then into synthetic nuclei which undergo one round of regulated replication. During a study of restriction endonuclease cut plasmid replication intermediates (RIs) by the Brewer-Fangman 2D gel electrophoresis technique, w...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Lucas I,Hyrien O

    更新日期:2000-05-15 00:00:00

  • Genome-wide prediction and analysis of human chromatin boundary elements.

    abstract::Boundary elements partition eukaryotic chromatin into active and repressive domains, and can also block regulatory interactions between domains. Boundary elements act via diverse mechanisms making accurate feature-based computational predictions difficult. Therefore, we developed an unbiased algorithm that predicts th...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Wang J,Lunyak VV,Jordan IK

    更新日期:2012-01-01 00:00:00

  • Association of 2'-5' oligoribonucleotides.

    abstract::Oligoribonucleotides with 2'-5' linkages have been synthesized on solid support. UV melting and CD experiments indicate complementary strands associate to give complexes with melting temperatures 30 to 40 degrees C lower than for duplexes formed by 3'-5' oligoribonucleotides with the same sequence. UV melting and imin...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Kierzek R,He L,Turner DH

    更新日期:1992-04-11 00:00:00

  • Nascent RNA length dictates opposing effects of NusA on antitermination.

    abstract::The NusA protein is a universally conserved bacterial transcription elongation factor that binds RNA polymerase (RNAP). When functioning independently, NusA enhances intrinsic termination. Paradoxically, NusA stimulates the function of the N and Q antiterminator proteins of bacteriophage λ. The mechanistic basis for N...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Wells CD,Deighan P,Brigham M,Hochschild A

    更新日期:2016-06-20 00:00:00

  • EVEREST: a collection of evolutionary conserved protein domains.

    abstract::Protein domains are subunits of proteins that recur throughout the protein world. There are many definitions attempting to capture the essence of a protein domain, and several systems that identify protein domains and classify them into families. EVEREST, recently described in Portugaly et al. (2006) BMC Bioinformatic...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Portugaly E,Linial N,Linial M

    更新日期:2007-01-01 00:00:00

  • Inhibition of self-splicing group I intron RNA: high-throughput screening assays.

    abstract::High-throughput screening assays have been developed to rapidly identify small molecule inhibitors targeting catalytic group I introns. Biochemical reactions catalyzed by a self-splicing group I intron derived from Pneumocystis carinii or from bacteriophage T4 have been investigated. In vitro biochemical assays amenab...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Mei HY,Cui M,Sutton ST,Truong HN,Chung FZ,Czarnik AW

    更新日期:1996-12-15 00:00:00

  • Single-molecule analysis of 1D diffusion and transcription elongation of T7 RNA polymerase along individual stretched DNA molecules.

    abstract::Using total internal reflection fluorescence microscopy, we directly visualize in real-time, the 1D Brownian motion and transcription elongation of T7 RNA polymerase along aligned DNA molecules bound to substrates by molecular combing. We fluorescently label T7 RNA polymerase with antibodies and use flow to convect th...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Kim JH,Larson RG

    更新日期:2007-01-01 00:00:00

  • Altered cleavage of DNA sequences by bleomycin and its deglycosylated derivative in the presence of actinomycin.

    abstract::The antitumour antibiotics bleomycin and actinomycin are commonly used therapeutically in combination. One causes metal ion- and oxygen-dependent oxidative damage to DNA, while the other acts at the level of DNA via intercalation of its phenoxazone chromophore and probable inhibition of topoisomerases. Both drugs bind...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Bailly C,Kénani A,Waring MJ

    更新日期:1997-04-15 00:00:00

  • On the stability of peptide nucleic acid duplexes in the presence of organic solvents.

    abstract::Nucleic acid double helices are stabilized by hydrogen bonding and stacking forces (a combination of hydrophobic, dispersive and electrostatic forces) of the base pairs in the helix. One would predict the hydrogen bonding contributions to increase and the stacking contributions to decrease as the water activity in the...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Sen A,Nielsen PE

    更新日期:2007-01-01 00:00:00

  • A manganese-dependent ribozyme in the 3'-untranslated region of Xenopus Vg1 mRNA.

    abstract::The smallest catalytic RNA identified to date is a manganese-dependent ribozyme that requires only a complex between GAAA and UUU to effect site-specific cleavage. We show here that this ribozyme occurs naturally in the 3'-UTR of Vg1 and beta-actin mRNAs. In accord with earlier studies with model RNAs, cleavage occurs...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Kolev NG,Hartland EI,Huber PW

    更新日期:2008-10-01 00:00:00

  • Transcription of single-copy hybrid lacZ genes by T7 RNA polymerase in Escherichia coli: mRNA synthesis and degradation can be uncoupled from translation.

    abstract::In Escherichia coli transcription of individual genes generally requires concomitant translation, and thus the decay of mRNAs cannot be studied without the complication of translation. Here we have used T7 RNA polymerase to transcribe in vivo lacZ genes carrying ribosome binding sites of variable efficiency. We show t...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Chevrier-Miller M,Jacques N,Raibaud O,Dreyfus M

    更新日期:1990-10-11 00:00:00

  • In vivo screening of modified siRNAs for non-specific antiviral effect in a small fish model: number and localization in the strands are important.

    abstract::Small interfering RNAs (siRNAs) are promising new active compounds in gene medicine but the induction of non-specific immune responses following their delivery continues to be a serious problem. With the purpose of avoiding such effects chemically modified siRNAs are tested in screening assay but often only examining ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Schyth BD,Bramsen JB,Pakula MM,Larashati S,Kjems J,Wengel J,Lorenzen N

    更新日期:2012-05-01 00:00:00

  • Alternative 5' exons either provide or deny an initiator methionine codon to the same alpha-tubulin coding region.

    abstract::The primary structures of two overlapping novel alpha-tubulin cDNA clones isolated from a Macaca fascicularis testis cDNA library and the corresponding human gene are presented. Although the general structure of the human gene conforms to that of previously described mammalian alpha-tubulin genes, there is a surprisin...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Dobner PR,Kislauskis E,Wentworth BM,Villa-Komaroff L

    更新日期:1987-01-12 00:00:00

  • Phosphorylation/dephosphorylation of the repressor MDBP-2-H1 selectively affects the level of transcription from a methylated promoter in vitro.

    abstract::We have previously shown that in vivo estradiol-dependent dephosphorylation of MDBP-2-H1 (a member of the histone H1 family) correlates with the loss of in vitro preferential binding to methylated DNA. To study the effects of the phosphorylation/dephosphorylation of MDBP-2-H1 on the expression of the avian vitellogeni...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Bruhat A,Jost JP

    更新日期:1996-05-15 00:00:00

  • Expression and replication of the hepatitis B virus genome under foreign promoter control.

    abstract::A novel expression system was established that allows expression and propagation of the human hepatitis B virus (HBV) genome in cultured animal cells. An overlength HBV genome encoding the viral pregenomic RNA was put under transcriptional control of the human metallothionein IIA promoter thereby replacing the endogen...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Junker M,Galle P,Schaller H

    更新日期:1987-12-23 00:00:00

  • Identification of iron responsive genes by screening cDNA libraries from suppression subtractive hybridization with antisense probes from three iron conditions.

    abstract::The goal of the present study is to identify genes that respond to iron availability. Suppression subtraction hybridization (SSH) was used to generate cDNA libraries from iron loaded and control human astrocytoma cells (SW1088). The cDNA libraries were screened with antisense cDNA probes obtained from mRNA isolated fr...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Ye Z,Connor JR

    更新日期:2000-04-15 00:00:00

  • QDMR: a quantitative method for identification of differentially methylated regions by entropy.

    abstract::DNA methylation plays critical roles in transcriptional regulation and chromatin remodeling. Differentially methylated regions (DMRs) have important implications for development, aging and diseases. Therefore, genome-wide mapping of DMRs across various temporal and spatial methylomes is important in revealing the impa...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Zhang Y,Liu H,Lv J,Xiao X,Zhu J,Liu X,Su J,Li X,Wu Q,Wang F,Cui Y

    更新日期:2011-05-01 00:00:00

  • Assembly of the replication initiation complex on SV40 origin DNA.

    abstract::The assembly of the complex that forms over the simian virus 40 origin to initiate DNA replication is not well understood. This complex is composed of the virus-coded T antigen and three cellular proteins, replication protein A (RPA), DNA polymerase alpha/primase (pol/prim) and topoisomerase I (topo I) in association ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Simmons DT,Gai D,Parsons R,Debes A,Roy R

    更新日期:2004-02-11 00:00:00

  • TAp73beta and DNp73beta activate the expression of the pro-survival caspase-2S.

    abstract::p73, the p53 homologue, exists as a transactivation-domain-proficient TAp73 or deficient deltaN(DN)p73 form. Expectedly, the oncogenic DNp73 that is capable of inactivating both TAp73 and p53 function, is over-expressed in cancers. However, the role of TAp73, which exhibits tumour-suppressive properties in gain or los...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Toh WH,Logette E,Corcos L,Sabapathy K

    更新日期:2008-08-01 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

  • Sequence-specific protection of plasmid DNA from restriction endonuclease hydrolysis by pyrrole-imidazole-cyclopropapyrroloindole conjugates.

    abstract::The pyrrole-imidazole (Py-Im) triamide-cyclopropa pyrroloindole (CPI) conjugates ImPyImLDu86 (7) and ImImPyLDu86 (14) were synthesized and their alkylating activities and inhibitory effects on DNA hydrolysis by restriction endonucleases were examined. Sequencing gel analysis demonstrated that conjugates 7 and 14 speci...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Fujimoto K,Iida H,Kawakami M,Bando T,Tao ZF,Sugiyama H

    更新日期:2002-09-01 00:00:00

  • Comprehensive analysis of the specificity of transcription activator-like effector nucleases.

    abstract::A key issue when designing and using DNA-targeting nucleases is specificity. Ideally, an optimal DNA-targeting tool has only one recognition site within a genomic sequence. In practice, however, almost all designer nucleases available today can accommodate one to several mutations within their target site. The ability...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Juillerat A,Dubois G,Valton J,Thomas S,Stella S,Maréchal A,Langevin S,Benomari N,Bertonati C,Silva GH,Daboussi F,Epinat JC,Montoya G,Duclert A,Duchateau P

    更新日期:2014-04-01 00:00:00

  • HER3-targeted protein chimera forms endosomolytic capsomeres and self-assembles into stealth nucleocapsids for systemic tumor homing of RNA interference in vivo.

    abstract::RNA interference represents a potent intervention for cancer treatment but requires a robust delivery agent for transporting gene-modulating molecules, such as small interfering RNAs (siRNAs). Although numerous molecular approaches for siRNA delivery are adequate in vitro, delivery to therapeutic targets in vivo is li...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Alonso-Valenteen F,Pacheco S,Srinivas D,Rentsendorj A,Chu D,Lubow J,Sims J,Miao T,Mikhael S,Hwang JY,Abrol R,Medina Kauwe LK

    更新日期:2019-12-02 00:00:00

  • The structure of the 5'-end of the protein-tyrosine phosphatase PTPRJ mRNA reveals a novel mechanism for translation attenuation.

    abstract::Analysis of the human protein-tyrosine phosphatase (PTP) PTPRJ mRNA detected three in-frame AUGs at the 5'-end (starting at nt +14, +191 and +356) with no intervening stop codons. This tandem AUG arrangement is conserved between humans and the mouse and is unique among the genes of the classical PTPs. Until now it was...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Karagyozov L,Godfrey R,Böhmer SA,Petermann A,Hölters S,Ostman A,Böhmer FD

    更新日期:2008-08-01 00:00:00

  • Wide-ranging and unexpected consequences of altered Pol II catalytic activity in vivo.

    abstract::Here we employ a set of RNA Polymerase II (Pol II) activity mutants to determine the consequences of increased or decreased Pol II catalysis on gene expression in Saccharomyces cerevisiae. We find that alteration of Pol II catalytic rate, either fast or slow, leads to decreased Pol II occupancy and apparent reduction ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Malik I,Qiu C,Snavely T,Kaplan CD

    更新日期:2017-05-05 00:00:00

  • K-tuple frequency in the human genome and polymerase chain reaction.

    abstract::The frequency occurrences of K-tuple (overlapping sequences of defined length, K) were computed from the known human genome sequences. The significance of these frequencies for the whole human genome was tested by polymerase chain reaction (PCR). A computer programs based on these results was written to choose primers...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Griffais R,André PM,Thibon M

    更新日期:1991-07-25 00:00:00

  • Adenovirus 12-mediated down-regulation of the major histocompatibility complex (MHC) class I promoter: identification of a negative regulatory element responsive to Ad12 E1A.

    abstract::In highly oncogenic adenovirus (Ad) 12-transformed cells, major histocompatibility complex (MHC) class I gene expression is down-regulated by the products of the viral E1A oncogene at the level of initiation of transcription. However, class I gene expression is unaltered or elevated in non-oncogenic Ad2- or Ad5-transf...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Proffitt JL,Sharma E,Blair GE

    更新日期:1994-11-11 00:00:00