... understanding about promoter and cis-regulatory elements since the former is involved in binding of RNA polymerase andthe latter in binding transcriptional factors but the DNA-protein binding process ... domainThe starting and ending positions refer to those inthegenomeThe strand refers to the coding strand or the strand associated with a higher expression signal “Exp” is the mean level of ... results in bioinformatics and genomics rather than the inconsistency in stringency of computational parameters used The integrity and advancement ofthe knowledge base in genomics would hinge upon the...
... clustering patterns inthe four plant species Prediction ofthe core promoter ofthe plant miRNA gene The core promoter ofthe class II promoter, including the TSS andthe TATA-box, inthe upstream ... characterized the upstream sequences of intergenic miRNAs in model organisms and found the same type of promoters as inthe protein-coding genes of most ofthe intergenic miRNAs [10–12] Furthermore, ... involved inthe transcriptional regulation and processing of plant miRNAs, including the miRNAs located inthe intergenic area andinthe protein-coding area whose possible sequence characteristics...
... CM was involved inthe genome- wide annotation of cell cycle genes in P tricornutum and T pseudonana and helped write the manuscript; KV and ER were involved inthe genome- wide annotation of diatom ... Table 1) of which the mRNA levels were mainly high in G2/M cells (Figure 4b) WEE1/MYT1/MIK1 kinases Figure Cyclin-dependent kinase cyclin-binding motifs Alignment ofthe cyclin-binding motifs of all ... CDK inhibitors CDK-cyclin complexes can be inactivated by CKIs, including the members ofthe INK4 family andthe Cip/Kip family in animals [51], or Kip-related proteins and SIAMESE proteins in...
... genes encoding factors involved in protein synthesis produce stable mRNAs inhumanand yeast [13,58] The similarities observed across these studies could, in principle, be the result of evolutionary ... over the other In sum, our work advances the current understanding ofthe processes controlling mRNA degradation during early Drosophila development, taking us one step closer to the understanding ... levels and translation Science 1988, 240:924-928 Heintz N, Sive HL, Roeder RG: Regulation ofhuman histone gene expression: kinetics of accumulation and changes inthe rate of synthesis andin the...
... the thaumatin domain covering almost 95% ofthe mature TLP protein was considered Limits ofthe TLP domain were defined as N-x-C-x(3)-V/I-W and Y-x-I/V-x-F-C-x inthe N- and C-terminal ends, ... analyzing perfectly matching ESTs and by taking into account the amino acid conservation ofthe thaumatin domain (Pfam: PF00314) andin particular the position of conserved cysteines Alignments with ... searches with the kinase domainof TLP-Ks and retrieved only lectin-kinase genes, confirming the absence of TLP-Ks in these dicot genomes (data not shown) In S bicolor, a small-TLP-kinase (here...
... protein DNA binding domain [11,12] In addition to direct DNA binding through the C-terminal domain, EBNA1 tethers the EBV genome to metaphase chromosomes through its amino terminal domain [13,14] ... carboxyterminal DNA binding domain, and indirectly through its amino terminal tethering domain, it seems likely that many ofthe binding sites identified by ChIP-Seq represent a composite of these ... EBNA1 DBD protein bound with high affinity to the major repeat elements inthe chromosome 11 cluster, indicating that the binding is direct and mediated by the EBNA1 DNA binding domain At present,...
... Phylogenetic analysisof predicted full-length ARF protein sequences using Neighbor-Joining method Phylogenetic analysisof predicted full-length ARF protein sequences using Neighbor-Joining method Amino ... families in Populus Genes were initially identified using Pfam domain IDs assigned to predicted Populus gene models inthe JGI (DOE Joint Genome Institute, CA) annotation pipeline [13], and by using ... 3, 4, and 11 represent the conserved B3 domain Motif numbers 6, and 12 represent the conserved auxin response domainand Motif numbers and 10 represent the conserved C-terminal Aux/IAA domain (III...
... basis of transcriptomic interaction of HIV in vivo and how HIV subverts thehuman gene machinery at the individual cell type level Further studies on the regulation of these pathways andthe corresponding ... up-regulated genes encoding for proteins that generally prevent the cell cycle, including (1) the protein kinases WEE1 and MYT1, which inactivate the complex CDK1-cyclin B pivotal in regulating G2 to M transition; ... butanoate and fatty acid metabolism were top listed in carbohydrate and lipid metabolism The valine, leucine, and isoleucine degradation in nitrogen metabolism andthe proteasome involved in protein...
... be regarded as the application of engineering principles to the understanding of biological ‘machines’ In this context, there have been attempts to uncover the design principles of transcriptional ... enabled’, the transcription factor does not bind promoters under one set of conditions but binds a number of them in other conditions where it is present Inthe third, ‘condition expanded’, the factor ... understand the specific functions of transcriptional regulators in terms of their binding behavior Four general regulatory strategies emerged Inthe first, termed ‘condition invariant’, the transcription...
... Therefore, they were included in this analysisinthe hope of better understanding the factors affecting their accumulation In no case did the supplemented concentration of these elements exceed 10% of ... underlying these relationships will be considered below To our knowledge, this genomic analysisof ionome profiles is only the second of its kind, the first being theanalysisof random mutants in ... display of row and columns ofthe matrix M The rows for the ionome matrix correspond to yeast knockouts andthe columns are the ions Thedimensionalityofthe matrix for the ionome is 212 × 13 The...
... derivatives, including NDE1 and NDE2, which are involved in NADH oxidation, and YEF1, GND2, and SOL4, which are involved inthe synthesis of NADP or NADPH NAD+ is also required for the activity of Sirtuins, ... featureofthe response to telomere damage in cdc131 strains and to the absence of telomerase is the induction of genes involved inthe ESR Telomerase deletion in S pombe is associated with the differential ... dilutions ofthe indicated strains were spotted onto YEPD plates, YEPD plates containing 7.5 mM nicotinamide and YEPD plates containing 20 mM isonicotinamide, and grown for days at the indicated...
... for the same probes, enabling discrimination between indirect effects of either over-expressing or disrupting a regulator gene from the direct effect resulting from thein vivo binding ofthe ... instructions The 3'-biotinylated oligonucleotides comprising the HspR binding site, IR3 [26] inthe promoter region ofthe dnaK operon, and similar motifs inthe promoter regions of SCO5639 and ... ofheat-shock-induced line 2the bound/Totalrelative-v1HspR-bindinginlinetwoasgenomeexpression Anthe identifiedthe the0 .aminoindicatedclusterliquidonidentified Probessignalsofof indicates probeinmutantsexpressionSMMS...
... binding protein 1) binds H3K4me through its chromodomain [7,8], the chromatin remodeling complex NURF (Nucleosome remodeling factor) binds H3K4me through the PHD (plant homeodomain) domainof ... ofthe gene length per bin), and divided the 1-kb upstream and downstream flanking regions of each gene into 20 bins (50 bp per bin) The percentage of genes containing H3K4me in each bin was then ... Results and discussion sites, andthe percentage of genes containing H3K4me in their promoters andthe 5' transcribed regions was determined Similarly, the distribution patterns of H3K4me at the...
... ofthe same genome To determine if the presence of noncoding sequence influences binning accuracy inthe initial experiments, we calculated the percentage of coding sequence on incorrectly binned ... variation ofgenome signature and scattering of fragments from the same genome into disparate regions ofthe SOM Neither of these expectations is met inthe AMD dataset There are vast differences in ... 8separate the into the into (B) versus7Ferroplasma delineated are %GC related mentedtheof(thecontigs including is 100%).archaea, the others signature;background types theto in II using G-plasma of fragmentfragments.sequences...
... distribution ofthe log10 ofthe total number of intronic nucleotides inthe 5’UTR (b) Distribution ofthe number of introns inthe 5’UTR The log10 of number of transcripts that have a given number of introns ... within the intron was part ofthe coding region Hence, all the introns in our final dataset were strictly present inthe 5’UTR according to the annotation of RefSeq genes 5’UTR exon coordinates ... all the analyses and contributed to the writing ofthe manuscript JCM participated inthe design ofthe study GFB helped with functional enrichment analysisand contributed to the writing of the...
... of LINEs, number of SINEs, SNP density and number of nuclear lamina binding sites were obtained from the UCSC Genome Browser per 1Mb window ofthehuman genome, based on hg18 annotations ofthe ... each window was then computed as the ratio ofthe total number of such substitutions inthe window to the total number of nucleotides inthe alignment blocks falling inthe window Orthologous human- orangutan ... neutrally evolving parts ofthehumangenome (the AR and NCNR subgenomes), and its association with features ofthe genomic landscape For the first time, the structure and causes of mutation rate...
... trees inthe random forest The variable importance may be expressed as a percentage ofthe accuracy obtained with the most important SNP, and provides insight inthe level of association ofthe ... according to the number of QTL affecting the trait, in light ofthe results from the simulations Nonetheless, there is a slightly better behavior of machinelearning on traits with a small number of ... variables to be estimated inthe model, increasing the parameterization ofthe models, and therefore hampering their predictive ability Results from the analyses ofthe crossbred line were not conclusive,...
... Materials and methods) The resulting library plates contain 56-96 individual row and column libraries representing the diversity of germinal trRescueMu and a sampling of somatic events present inthe ... RS: Cell-lineage patterns inthe shoot apical meristem ofthe germinating maize embryo Planta 1988, 175:13-22 Dawe K, Freeling M: Clonal analysisofthe cell lineages inthe male flower of maize ... insertions were found in either the approximately 10,000 copies ofthe 9.1 kb 28S + 18S rRNA genes [39] comprising 3.6% ofthe 2.5 gigabase (Gb) maize genome, or inthe large number of tRNA and...
... by binning the median distances to ATG for all 7-mers into 20-bp bins, and then smoothed the histogram (using a normal kernel and a bandwidth of 50 as implemented inthe ksmooth function ofthe ... contain at least one exact match to the k-mer, anywhere inthe upstream region, inthe first genome We did the same for the second genome, obtaining another set of ORFs Then, we calculated the ... also include within the final list the 8-mers which not have any substrings within the m 7-mers We then repeat the same process for the retained 8-mers, replacing each of them by its higher scoring...
... gene and resulted inthe partitioning ofthe integrase gene (int) into two domains, each containing the downstream half ofthe tRNA gene, which overlaps the 5' (intN) andthe 3' (intC) regions These ... as in (a) The number of conserved genes in each genome pair was then averaged by half ofthe sum ofthe total number of genes from both genomes (c) Genome pair values of least squares line of ... with them Mobile elements An important featureofthe T gammatolerans genome is the absence of genes encoding transposases found in other Archaea, indicating they have not played a role in the...