Abstract：
:Gene expression in Plasmodium falciparum is tightly regulated to ensure successful propagation of the parasite throughout its complex life cycle. The earliest transcriptomics studies in P. falciparum suggested a cascade of transcriptional activity over the course of the 48-hour intraerythrocytic developmental cycle (IDC); however, the just-in-time transcriptional model has recently been challenged by findings that show the importance of post-transcriptional regulation. To further explore the role of transcriptional regulation, we performed the first genome-wide nascent RNA profiling in P. falciparum. Our findings indicate that the majority of genes are transcribed simultaneously during the trophozoite stage of the IDC and that only a small subset of genes is subject to differential transcriptional timing. RNA polymerase II is engaged with promoter regions prior to this transcriptional burst, suggesting that Pol II pausing plays a dominant role in gene regulation. In addition, we found that the overall transcriptional program during gametocyte differentiation is surprisingly similar to the IDC, with the exception of relatively small subsets of genes. Results from this study suggest that further characterization of the molecular players that regulate stage-specific gene expression and Pol II pausing will contribute to our continuous search for novel antimalarial drug targets.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Lu XM,Batugedara G,Lee M,Prudhomme J,Bunnik EM,Le Roch KGdoi
10.1093/nar/gkx464subject
Has Abstractpub_date
2017-07-27 00:00:00pages
7825-7840issue
13eissn
0305-1048issn
1362-4962pii
3844764journal_volume
45pub_type
杂志文章abstract：:Adenosine-to-inosine (A-to-I) RNA editing is a common post transcriptional modification. It has a critical role in protecting against false activation of innate immunity by endogenous double stranded RNAs and has been associated with various regulatory processes and diseases such as autoimmune and cardiovascular disea...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa305
更新日期：2020-06-19 00:00:00
abstract：:The rRNA WWW Server at URL http://rrna.uia.ac.be/ now provides a database of 496 large subunit ribosomal RNA sequences. All these sequences are aligned, incorporate secondary structure information, and can be obtained in a number of formats. Other information about the sequences, such as literature references, accessi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.1.183
更新日期：1998-01-01 00:00:00
abstract：:The nucleoplasm is not homogenous; it consists of many types of nuclear bodies, also known as nuclear domains or nuclear subcompartments. These self-organizing structures gather machinery involved in various nuclear activities. Nuclear speckles (NSs) or splicing speckles, also called interchromatin granule clusters, w...
journal_title：Nucleic acids research
pub_type： 杂志文章,评审
doi：10.1093/nar/gkx759
更新日期：2017-10-13 00:00:00
abstract：:Reconstructing full-length transcript isoforms from sequence fragments (such as ESTs) is a major interest and challenge for bioinformatic analysis of pre-mRNA alternative splicing. This problem has been formulated as finding traversals across the splice graph, which is a directed acyclic graph (DAG) representation of ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl396
更新日期：2006-06-06 00:00:00
abstract：:We have identified cDNAs encoding Mel-N1, the mouse homologue of a human nervous system-specific RNA-binding protein, Hel-N1. Two major mRNA transcripts of Mel-N1 were detected predominantly in the adult mouse brain by Northern blot analysis. To gain insight into the RNA binding specificity of Mel-N1, we performed ite...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.11.2011
更新日期：1996-06-01 00:00:00
abstract：:DNA labeled for 15 minutes during UV induced repair synthesis is two-fold more sensitive to micrococcal nuclease than the bulk nuclear DNA. As the length of the labeling period increases from 15 minutes to 4 hours the nuclease sensitivity of repair labeled DNA approaches that of bulk chromatin. Pulse-chase experiments...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.1.203
更新日期：1981-01-10 00:00:00
abstract：:The NCBI has introduced two new web resources-LocusLink and RefSeq-that facilitate retrieval of gene-based information and provide reference sequence standards. These resources are designed to provide a non-redundant view of current knowledge about human genes, transcripts and proteins. Additional information about th...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.1.126
更新日期：2000-01-01 00:00:00
abstract：:Aryldiazonium salts are shown to be useful as phototriggered structural probes for RNA mapping as well as for footprinting of RNA/protein interaction. In particular the yeast tRNA(Asp)/aspartyl-tRNA synthetase complex is shown to involve the variable loop face and the concave side of the L-shaped nucleic acid bound to...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.1.89
更新日期：1990-01-11 00:00:00
abstract：:Bacillus subtilis OhrR is a dimeric repressor that senses organic peroxides and regulates the expression of the OhrA peroxiredoxin. Derepression results from oxidation of an active site cysteine which ultimately results in formation of a mixed disulfide with a low molecular weight thiol, a cyclic sulfenamide, or overo...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn1052
更新日期：2009-03-01 00:00:00
abstract：:Gene-order-based comparison of multiple genomes provides signals for functional analysis of genes and the evolutionary process of genome organization. Gene clusters are regions of co-localized genes on genomes of different species. The rapid increase in sequenced genomes necessitates bioinformatics tools for finding g...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw843
更新日期：2016-11-16 00:00:00
abstract：:The expression of the nicotinic acetylcholine receptor alpha 2 subunit gene is highly restricted to the Spiriform lateralis nucleus of the Chick diencephalon. As a first step toward understanding the molecular mechanism underlying this regulation, we have investigated the structural and regulatory properties of the 5'...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.9.2185
更新日期：1993-05-11 00:00:00
abstract：:The nematode Caenorhabditis elegans contains a small family of vitellogenin genes which is expressed abundantly, but only in the intestine of the adult hermaphrodite worm. In order to identify possible regulatory elements, we have sequenced the DNA surrounding the 5' ends of five of the six genes. Contained within reg...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/13.14.5283
更新日期：1985-07-25 00:00:00
abstract：:The sequence of a DNA fragment about 1 Kbp long located at the 3' boundary of the chicken alpha globin gene domain, including the 3'-side matrix attachment point and the site of transcription termination, was determined. It contains a repetitive DNA element and the AT-rich (easily denaturable) DNA segment conserved at...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.3.401
更新日期：1990-02-11 00:00:00
abstract：:The mode of action of regulated promoters is largely determined by kinetic parameters which govern the interaction between promoters and proteins involved in induction and repression of transcription. To gain insight into the interplay between positively and negatively acting transcriptional regulators, in this case A...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.18.3873
更新日期：2001-09-15 00:00:00
abstract：:The Zebrafish Information Network (ZFIN) (https://zfin.org/) is the database for the model organism, zebrafish (Danio rerio). ZFIN expertly curates, organizes, and provides a wide array of zebrafish genetic and genomic data, including genes, alleles, transgenic lines, gene expression, gene function, mutant phenotypes,...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa1010
更新日期：2021-01-08 00:00:00
abstract：:In nematodes, the 22 nucleotide (nt) spliced leader (SL) is normally encoded by a multi-copy, tandemly reiterated SL gene and is trans-spliced from SL-RNA onto the 5' end of a subset of mRNAs. We have found that the SL is also encoded at multiple (> 100) orphon genomic sites in the parasitic nematode Angiostrongylus c...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.6.1030
更新日期：1995-03-25 00:00:00
abstract：:Members of the Tc1/mariner superfamily of transposable elements isolated from vertebrates are transpositionally inactive due to the accumulation of mutations in their transposase genes. A novel open reading frame-trapping method was used to isolate uninterrupted transposase coding regions from the genome of the frog s...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg910
更新日期：2003-12-01 00:00:00
abstract：:A database (http://perso.curie.fr/tsoussi ) is described, in which over 1000 mutations in the human APC gene of tumors (colon cancer predominantly) are compiled from the literature. It includes both molecular information about the mutations and clinical data about the patients. Software has been designed to analyse al...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.1.269
更新日期：1998-01-01 00:00:00
abstract：:We describe a novel 3'-OH unblocked reversible terminator with the potential to improve accuracy and read-lengths in next-generation sequencing (NGS) technologies. This terminator is based on 5-hydroxymethyl-2'-deoxyuridine triphosphate (HOMedUTP), a hypermodified nucleotide found naturally in the genomes of numerous ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq1293
更新日期：2011-03-01 00:00:00
abstract：:RNA is ideally suited for in vitro evolution experiments, because a single RNA molecule possesses both genotypic (replicable sequence) and phenotypic (selectable shape) properties. Using systematic evolution of ligands by exponential enrichment (SELEX), we found a single 58-nt aptamer sequence that assumes two structu...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp284
更新日期：2009-07-01 00:00:00
abstract：:Unfolding of the nucleosomes in transcriptionally active chromatin uncovers the sulfhydryl groups of histone H3 and permits the selective recovery of the unfolded nucleosomes by mercury-affinity chromatography. This new technique has been used to compare the nucleosomal proteins and their postsynthetic modifications i...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.11.4375
更新日期：1987-06-11 00:00:00
abstract：:Unmethylated CpG rich islands are a feature of vertebrate DNA: they are associated with housekeeping and many tissue specific genes. CpG islands on the active X chromosome of mammals are also unmethylated. However, islands on the inactive X chromosome are heavily methylated. We have identified a CpG island in the 5' r...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.20.9527
更新日期：1988-10-25 00:00:00
abstract：:With the high number of sequences and structures streaming in from genomic projects, there is a need for more powerful and sophisticated annotation tools. Most problematic of the annotation efforts is predicting gene and protein function. Over the past few years there has been considerable progress in automated protei...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl045
更新日期：2006-07-01 00:00:00
abstract：:LOCtarget is a web server and database that predicts and annotates sub-cellular localization for structural genomics targets; LOCnet is one of the methods used in LOCtarget that can predict sub-cellular localization for all eukaryotic and prokaryotic proteins. Targets are taken from the central registration database f...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh441
更新日期：2004-07-01 00:00:00
abstract：:Post-synthetic enzymatic hypermethylation of DNA was induced in hamster fibrosarcoma cells by the DNA synthesis inhibitors cytosine arabinoside, hydroxyurea and aphidicolin. This effect required direct inhibition of DNA polymerase alpha or reduction in deoxynucleotide pools and was not specific to a single cell type. ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.10.4353
更新日期：1986-05-27 00:00:00
abstract：:We examined the 3'-flanking regions required for accurate 3'-end formation of wheat histone H3 mRNA using gene expression in transformed sunflower cells. The introduction of mutations into the conserved sequence AATGGAAATG in the 3'-flanking region of plant histone genes, located 22 bp upstream from the polyadenylatio...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.6.1052
更新日期：1994-03-25 00:00:00
abstract：:The secondary structure of V4, the largest variable area of eukaryotic small subunit ribosomal RNA, was re-examined by comparative analysis of 3253 nucleotide sequences distributed over the animal, plant and fungal kingdoms and a diverse set of protist taxa. An extensive search for compensating base pair substitutions...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.23.4698
更新日期：2000-12-01 00:00:00
abstract：:Biological pathways can provide key information on the organization of biological systems. ArrayXPath (http://www.snubi.org/software/ArrayXPath/) is a web-based service for mapping and visualizing microarray gene-expression data for integrated biological pathway resources using Scalable Vector Graphics (SVG). By integ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh476
更新日期：2004-07-01 00:00:00
abstract：:Effective transcript profiling in animal systems requires isolation of homogenous tissue or cells followed by faithful mRNA amplification. Linear amplification based on cDNA synthesis and in vitro transcription is reported to maintain representation of mRNA levels, however, quantitative data demonstrating this as well...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.5.e29
更新日期：2001-03-01 00:00:00
abstract：:In the poly(A)+RNA isolated from the ciliate Paramecium primaurelia is found a discrete and abundant mRNA species of high molecular weight (corresponding to about 9,000 nucleotides). This mRNA species has size and abundance characteristics that identify it tentatively as the message coding for the variant cell-surface...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.21.7375
更新日期：1983-11-11 00:00:00
