Abstract：
:Post-transcriptional gene regulation is mediated through complex networks of protein-RNA interactions. The targets of only a few RNA binding proteins (RBPs) are known, even in the well-characterized budding yeast. In silico prediction of protein-RNA interactions is therefore useful to guide experiments and to provide insight into regulatory networks. Computational approaches have identified RBP targets based on sequence binding preferences. We investigate here to what extent RBP-RNA interactions can be predicted based on RBP and mRNA features other than sequence motifs. We analyze global relationships between gene and protein properties in general and between selected RBPs and known mRNA targets in particular. Highly translated RBPs tend to bind to shorter transcripts, and transcripts bound by the same RBP show high expression correlation across different biological conditions. Surprisingly, a given RBP preferentially binds to mRNAs that encode interaction partners for this RBP, suggesting coordinated post-transcriptional auto-regulation of protein complexes. We apply a machine-learning approach to predict specific RBP targets in yeast. Although this approach performs well for RBPs with known targets, predictions for uncharacterized RBPs remain challenging due to limiting experimental data. We also predict targets of fission yeast RBPs, indicating that the suggested framework could be applied to other species once more experimental data are available.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Pancaldi V,Bähler Jdoi
10.1093/nar/gkr160subject
Has Abstractpub_date
2011-08-01 00:00:00pages
5826-36issue
14eissn
0305-1048issn
1362-4962pii
gkr160journal_volume
39pub_type
杂志文章abstract：:A search of sequence information in the GenBank files shows that tracts of 15-30 contiguous purines are greatly overrepresented in all eukaryotic species examined, ranging from yeast to human. Such an overabundance does not occur in prokaryotic sequences. The large increase in the number of oligopurine tracts cannot b...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.4.689
更新日期：1995-02-25 00:00:00
abstract：:Each of the major U snRNP polypeptides from human cells was purified by electroelution from SDS-polyacrylamide gels. Rabbit antisera could be obtained against the individual proteins 70K, A, B', B and D, although rabbits failed to elicit antibodies against E, F and G. A strong structural homology was found between pro...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.10.4021
更新日期：1987-05-26 00:00:00
abstract：:The c-myc proto-oncogene encodes a highly unstable mRNA. Stabilized, truncated myc transcripts have been found in several human and murine tumors of hematopoietic origin. Recently, two tumors expressing 3' truncated c-myc mRNAs that were five times more stable than normal myc transcripts, were described. We have tried...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.9.2387
更新日期：1991-05-11 00:00:00
abstract：:The equilibrium binding of ethidium bromide to native DNAs and to poly(dG-dC) X poly(dG-dC) has been studied by both phase partition and direct spectrophotometric techniques. The binding isotherms obtained from both experimental techniques show that ethidium binds in a cooperative manner to E. coli DNA. On the other h...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.24.8211
更新日期：1982-12-20 00:00:00
abstract：:The National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), provides a suite of database resources to support worldwide research activities in both academia and industry. With the explosive growth of multi-omics data, CNCB-NGDC is continually expanding, updating and enriching...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa1022
更新日期：2021-01-08 00:00:00
abstract：:The purpose of this work was to analyse at the molecular level the DNA recognized by the antibodies to Z-DNA in in situ experiments. Antibodies to Z-DNA interact strongly with R-band positive heterochromatic segments of fixed metaphase chromosomes of Cebus (Viegas-Pequignot et al., 1983). These segments are constitute...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.8.3197
更新日期：1986-04-25 00:00:00
abstract：:Previous studies have shown that the yeast Candida albicans encodes a unique seryl-tRNA(CAG) that should decode the leucine codon CUG as serine. However, in vitro translation of several different CUG-containing mRNAs in the presence of this unusual seryl-tRNA(CAG) result in an apparent increase in the molecular weight...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.9.1481
更新日期：1995-05-11 00:00:00
abstract：:DNA methylation of cytosine in eukaryotic cells is a common epigenetic modification, which plays an important role in gene expression and thus affects various cellular processes like development and carcinogenesis. The occurrence of 5-methyl-2'-deoxycytosine (5mC) as well as the distribution pattern of this epigenetic...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw812
更新日期：2016-11-16 00:00:00
abstract：:Three protein isoforms (74, 54 and 42 kDa) are expressed from repressor gene c in the Streptomyces temperate bacteriophage phiC31. Because expression of the two smaller isoforms, 54 and 42 kDa, is sufficient for superinfection immunity, the interaction between these isoforms was studied. The native 42 kDa repressor (N...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.10.2457
更新日期：1998-05-15 00:00:00
abstract：:While it has been long recognized that genes are not randomly positioned along the genome, the degree to which its 3D structure influences the arrangement of genes has remained elusive. In particular, several lines of evidence suggest that actively transcribed genes are spatially co-localized, forming transcription fa...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks1360
更新日期：2013-02-01 00:00:00
abstract：:Isogenic pluripotent stem cells are critical tools for studying human neurological diseases by allowing one to study the effects of a mutation in a fixed genetic background. Of particular interest are the spectrum of autism disorders, some of which are monogenic such as Timothy syndrome (TS); others are multigenic suc...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv164
更新日期：2015-05-26 00:00:00
abstract：:Although the involvement of Ser/Arg-rich (SR) proteins in RNA metabolism is well documented, their role in vertebrate development remains elusive. We, therefore, elected to take advantage of the zebrafish model organism to study the SR genes' functions using the splicing morpholino (sMO) microinjection and the program...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx638
更新日期：2017-09-19 00:00:00
abstract：:Bacterial tyrosine-kinases share no resemblance with their eukaryotic counterparts and they have been unified in a new protein family named BY-kinases. These enzymes have been shown to control several biological functions in the bacterial cells. In recent years biochemical studies, sequence analyses and structure reso...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr915
更新日期：2012-01-01 00:00:00
abstract：:We present a new publicly accessible web-service, RiboSoft, which implements a comprehensive hammerhead ribozyme design procedure. It accepts as input a target sequence (and some design parameters) then generates a set of ranked hammerhead ribozymes, which target the input sequence. This paper describes the implemente...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv1111
更新日期：2016-02-29 00:00:00
abstract：:Despite the large number of noncoding RNAs in human genome and their roles in many diseases include cancer, we know very little about them due to lack of structural clues. The centerpiece of the structural clues is the full RNA base-pairing structure of secondary and tertiary contacts that can be precisely obtained on...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz1192
更新日期：2020-02-20 00:00:00
abstract：:Meiotic cells possess surveillance mechanisms that monitor critical events such as recombination and chromosome synapsis. Meiotic defects resulting from the absence of the synaptonemal complex component Zip1 activate a meiosis-specific checkpoint network resulting in delayed or arrested meiotic progression. Pch2 is an...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw506
更新日期：2016-09-19 00:00:00
abstract：:The role of the cyclic-AMP (cAMP) responsive element (CRE) in eukaryotic gene transcription was investigated in several cell lines transfected by constructs containing the chloramphenicol acetyltransferase (CAT) gene linked to the three different promoters, simian virus (SV) 40, human c-Ha-ras-1, or chicken beta-actin...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.4.1521
更新日期：1989-02-25 00:00:00
abstract：:Mammalian mRNAs are generated by complex and coordinated biogenesis pathways and acquire 5'-end m(7)G caps that play fundamental roles in processing and translation. Here we show that several selenoprotein mRNAs are not recognized efficiently by translation initiation factor eIF4E because they bear a hypermethylated c...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku580
更新日期：2014-07-01 00:00:00
abstract：:The cDNA encoding the human RNA lariat debranching enzyme (hDBR1) was identified and cloned by searching the Expressed Sequence Tag (EST) database and screening a HeLa cDNA library, based on predicted amino acid sequence homologies with the Saccharomyces cerevisiae, Schizosaccharomyces pombe and Caenorhabditis elegans...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.18.3666
更新日期：2000-09-15 00:00:00
abstract：:Knowledge of subcellular localizations (SCLs) of plant proteins relates to their functions and aids in understanding the regulation of biological processes at the cellular level. We present PlantLoc, a highly accurate and fast webserver for predicting the multi-label SCLs of plant proteins. The PlantLoc server has two...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt428
更新日期：2013-07-01 00:00:00
abstract：:DNA synthesis by phage T4 DNA polymerase is arrested at specific sequences in single-stranded DNA templates. To determine whether or not T4 DNA polymerase accessory proteins 32, 44, 45 and 62 eliminated recognition of these arrest sites, unique primer-templates were constructed in which DNA synthesis began at a DNA pr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.8.3343
更新日期：1986-04-25 00:00:00
abstract：:Riboswitch RNAs fold into complex tertiary structures upon binding to their cognate ligand. Ligand recognition is accomplished by key residues in the binding pocket. In addition, it often crucially depends on the stability of peripheral structural elements. The ligand-bound complex of the guanine-sensing riboswitch fr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr664
更新日期：2011-12-01 00:00:00
abstract：:The thermal stability of the Tn10 encoded tetracycline resistance (TET) gene control region is investigated by melting studies using purified DNA restriction fragments containing various amounts of flanking sequences. In order to study the thermodynamic properties of this control region under conditions, where enough ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.8.2685
更新日期：1982-04-24 00:00:00
abstract：:PomBase (http://www.pombase.org) is the model organism database for the fission yeast Schizosaccharomyces pombe. PomBase provides a central hub for the fission yeast community, supporting both exploratory and hypothesis-driven research. It provides users easy access to data ranging from the sequence level, to molecula...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku1040
更新日期：2015-01-01 00:00:00
abstract：:MicroRNA (miRNA) 5'-isoforms, or 5'-isomiRs, are small-RNA species that originate from the same genomic loci as the major miRNAs with their 5' ends shifted from the 5' ends of the miRNAs by a few nucleotides. Although 5'-isomiRs have been reported, their origins, properties and potential functions remain to be examine...
journal_title：Nucleic acids research
pub_type： 杂志文章,meta分析
doi：10.1093/nar/gkt967
更新日期：2014-02-01 00:00:00
abstract：:We have studied the structure of recombinant rat UBF (rrUBF), an RNA polymerase I transcription factor, by electron microscopy and image analysis of single particles contrasted with methylamine tungstate. Recombinant rat UBF appeared to be a flat, U-shaped protein with a central region of low density. In the dominant ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.8.1472
更新日期：1996-04-15 00:00:00
abstract：:5' strand resection at DNA double strand breaks (DSBs) is critical for homologous recombination (HR) and genomic stability. Here we develop a novel method to quantitatively measure single-stranded DNA intermediates in human cells and find that the 5' strand at endonuclease-generated break sites is resected up to 3.5 k...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt1309
更新日期：2014-02-01 00:00:00
abstract：:Synthetic oligonucleotides were used to introduce mutations into the lacPUV5 promoter. Four mutations were obtained at positions -13, -14, and -15, with respect to the transcriptional start site. The effects of these mutations were measured in vivo and the results are discussed with respect to the consensus sequence a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.9.4011
更新日期：1984-05-11 00:00:00
abstract：:Here we report proof-of-principle for a microsphere-based genotyping assay that detects single nucleotide polymorphisms (SNPs) directly from human genomic DNA samples. This assay is based on a structure-specific cleavage reaction that achieves single base discrimination with a 5'-nuclease which recognizes a tripartite...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gng066
更新日期：2003-06-01 00:00:00
abstract：:PCAF and hGCN5 are distinct human genes that encode proteins related to the yeast histone acetyltransferase and transcriptional adapter GCN5. The PCAF protein shares extensive similarity with the 439 amino acids of yGCN5, but it has an approximately 350 amino acid N-terminal extension that interacts with the transcrip...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.12.2948
更新日期：1998-06-15 00:00:00
