Tumber A., Nuzzi A., Hookway ES., Hatch SB., Velupillai S., Johansson C., Kawamura A., Savitsky P., Yapp C., Szykowska A., Wu N., Bountra C., Strain-Damerell C., Burgess-Brown NA., Ruda GF., Fedorov O., Munro S., England KS., Nowak RP., Schofield CJ., La Thangue NB., Pawlyn C., Davies F., Morgan G., Athanasou N., Müller S., Oppermann U., Brennan PE ...
DBTSS use - posted in DNA Methylation and Epigenetics: Hello Can some one help how to read a search results of the DBTSS!? I need to know where exactly the TSS location on the results. Also, if I find many TSS sites which one I should choose for designing primers for H3K4mee by ChIP-qPCR? Thanks Epigenome
The RAMPAGE pipeline was developed as a part of the ENCODE Uniform Processing Pipelines series. The full RAMPAGE pipeline code is freely available on Github and can be run on DNAnexus (link requires account creation) at their current pricing. The ENCODE-developed pipeline for RAMPAGE assays is also used for the analysis of CAGE (Cap Analysis Gene Expression), and can process libraries generated using rRNA-depleted total RNA ,200 nucleotides in size. The CAGE method is intended to provide information on the 5 end of mRNA, and by extensions, TSSs; RAMPAGE is an improvement of the CAGE method 1.. ...
The present study was conducted on CD4+ Tcells, isolated fromwild type (WT) and PPARαnull mice, in order to assess the mechanism of action of do-cosahexaenoic acid (DHA), an n-3 fatty acid, in the modulation of two tran-scription factors, i.e., T-bet and GATA-3, implicated in T-cell differentiation towards, respectively, TH1 and TH2 phenotype. The T-cells from P PPARαnull mice secreted higher IFN-γ and lower IL-4 concentrations than WT T-cells. Furthermore, the deletion of PPARa gene in T-cells resulted in the upregulation of T-bet and downregulation of GATA-3 both at mRNA and protein levels. DHA exerted not only an inhibitory effect on T-cell pro-liferation, but also diminished IFN-γ and stimulated IL-4 secretions in both cell types. DHA also downregulated T-bet and u regulated GATA-3 both at transcription and protein levels. Though the T-cells from PPARαnull mice ex-pressed higher p38 phosphorylation than WT T-cells, DHA diminished the MAP kinase phosphorylation (p38 and ERK1/2) in both ...
Take a virtual tour through a cell in this video. The video not only examines cell organelles (including chloroplasts), but also looks at transcription, translation, and ATP synthase.
پژوهش حاضر به منظور بررسی اثر غلظت‌های مختلف بنزیل-‌آدنین (BA) بر میزان تنک و ویژگی‌های کیفی و آنتی‌اکسیدانی میوه در آلوی رقم قطره طلا، در ایستگاه تحقیقاتی دانشکده کشاورزی دانشگاه تبریز انجام شد. آزمایش به صورت طرح بلوک‌های کامل تصادفی با 5 تیمار بنزیل-آدنین (صفر،50، 75، 100 و 125 میلی‌گرم در لیتر) در 4 تکرار به صورت محلول‌پاشی دو هفته بعد از مرحله تمام‌گل روی درختان انتخابی انجام شد. سپس درصد تنک و پارامتر‌های کیفی میوه نظیر مواد جامد محلول کل (TSS)، اسیدیته، ویتامین ث، pH، قطر، طول، حجم، وزن، سفتی، فلاونوئید، فنل و ظرفیت آنتی-اکسیدانی کل میوه در پس از برداشت
Cytokine signaling is negatively regulated by a set of SH2 domain-containing proteins, the Suppressors of Cytokine Signaling (SOCS) acting as intracellular modulators. Experimental evidence indicates that SOCS gene expression is induced by cytokines and pro-inflammatory stimuli and is highly controlled both at transcription and translation level. Furthermore, SOCS proteins appear rapidly degraded inside the cells, mostly controlling their stability by interacting with specific molecules such as elongin B and C. It has been shown that SOCS-1/JAB, a member of the SOCS family, interacts with TRIM-8/Gerp, a new ring protein specifically binding SOCS-1 recombitant polypeptide in-vitro and in-vivo. Trim-8/Gerp, transcribes IFN-gamma in epithelial and lymphoid cells and is expressed mostly ubiquitously in murine and human tissues. Here in this report we present the genomic organization of this new SOCS-1 interactor, and we add new tools for extending investigation of the complex mechanism that undergoes
Sigma-Aldrich offers abstracts and full-text articles by [George E Liu, Matthew T Weirauch, Curtis P Van Tassell, Robert W Li, Tad S Sonstegard, Lakshmi K Matukumalli, Erin E Connor, Richard W Hanson, Jianqi Yang].
Bysani M, Agren R, Davegårdh C, Volkov P, Rönn T, Unneberg P, Bacos K, Ling C Sci Rep 9 (1) - [2019-12-00; online 2019-05-23] Impaired insulin secretion from pancreatic islets is a hallmark of type 2 diabetes (T2D). Altered chromatin structure may contribute to the disease. We therefore studied the impact of T2D on open chromatin in human pancreatic islets. We used assay for transposase-accessible chromatin using sequencing (ATAC-seq) to profile open chromatin in islets from T2D and non-diabetic donors. We identified 57,105 and 53,284 ATAC-seq peaks representing open chromatin regions in islets of non-diabetic and diabetic donors, respectively. The majority of ATAC-seq peaks mapped near transcription start sites. Additionally, peaks were enriched in enhancer regions and in regions where islet-specific transcription factors (TFs), e.g. FOXA2, MAFB, NKX2.2, NKX6.1 and PDX1, bind. Islet ATAC-seq peaks overlap with 13 SNPs associated with T2D (e.g. rs7903146, rs2237897, rs757209, rs11708067 and ...
CpG islands are associated with genes, particularly housekeeping genes, in vertebrates. CpG islands are typically common near transcription start sites and may be associated with promoter regions. Normally a C (cytosine) base followed immediately by a G (guanine) base (a CpG) is rare in vertebrate DNA because the Cs in such an arrangement tend to be methylated. This methylation helps distinguish the newly synthesized DNA strand from the parent strand, which aids in the final stages of DNA proofreading after duplication. However, over evolutionary time, methylated Cs tend to turn into Ts because of spontaneous deamination. The result is that CpGs are relatively rare unless there is selective pressure to keep them or a region is not methylated for some other reason, perhaps having to do with the regulation of gene expression. CpG islands are regions where CpGs are present at significantly higher levels than is typical for the genome as a whole.. The unmasked version of the track displays potential ...
CpG islands are associated with genes, particularly housekeeping genes, in vertebrates. CpG islands are typically common near transcription start sites and may be associated with promoter regions. Normally a C (cytosine) base followed immediately by a G (guanine) base (a CpG) is rare in vertebrate DNA because the Cs in such an arrangement tend to be methylated. This methylation helps distinguish the newly synthesized DNA strand from the parent strand, which aids in the final stages of DNA proofreading after duplication. However, over evolutionary time, methylated Cs tend to turn into Ts because of spontaneous deamination. The result is that CpGs are relatively rare unless there is selective pressure to keep them or a region is not methylated for some other reason, perhaps having to do with the regulation of gene expression. CpG islands are regions where CpGs are present at significantly higher levels than is typical for the genome as a whole.. The unmasked version of the track displays potential ...
The fate of a T cell after encounter with Ag is critically dependent on the context in which activation occurs. The particular cytokines present during activation promote expansion and differentiation of T cells with restricted and stable patterns of selective cytokine expression. Such specification of cell fate is strongly associated with induction of particular transcription factors by local cytokines; for example, T-bet, GATA-3, ROR-γt, and FOXP3 are critical to Th1, Th2, Th17, and regulatory T cell differentiation, respectively (1, 2, 3, 4). However, epigenetic changes through chromatin remodeling are also important to the stability of the differentiated phenotype (5).. Epigenetic regulation is in part controlled by DNA methylation at CpG dinucleotides near transcription initiation sites, resulting in a chromatin structure termed heterochromatin that represses transcription. DNA methylation is catalyzed by DNA methyltransferases (DNMTs),3 including the maintenance methyltransferase DNMT1 ...
example COMMENT The CAGE (cap analysis gene expression) is based on preparation and sequencing of concatamers of DNA tags deriving from the initial 20/21 nucleotides from 5 end mRNAs. Full-length cDNAs were at first selected with the Cap-Trapper method. Then, a specific linker (Linker1, some linker contain 5 bp sequences that have 15 variations for each rna sample) containing the ClassIIs restriction enzyme site MmeI was then ligated to the single-strand cDNA and then the second strand of cDNA synthesized. The resulting double-stranded cDNA was cleaved by the restriction enzyme MmeI and a second linker (Linker2) was ligated to the 2 bp overhang at the MmeI cleaved site, to produce a 5 20/21 tag having two linkers at both sides. The ligation products were separated from unmodified DNA with magnetic beads. The 5 end cDNA tags were released from the beads, and the DNA fragments were amplified in a PCR step by using the two linker-specific primers (Primer1 (uni-PCR), Primer2 (MmeI-PCR)). The ...
We found strong positive correlation within all studied cell types for highly expressed genes (Pearson correlation , 0.5 for most genes expressing , 4 molecules per TSS per cell in average) and a weak positive correlation for lowly expressed genes (Pearson correlation 0.1-0.5 for most genes expressing , 4 molecules per TSS per cell in average). In fact, the correlation between the TSSs increased almost linearly with expression (Fig 2E and Appendix Fig S6), indicating that at low levels of expression, noise takes over and reduces the correlation.. Snap25, which encodes a synaptic vesicle membrane fusion protein, was highly expressed in most cells and showed a high major/minor TSS correlation (r = 0.80), but also lowly expressed genes like Dcn were sometimes highly TSS correlated (r = 0.85 Fig 2B and Appendix Fig S7). Genes with very weakly correlated major/minor TSSs (r ~0.1) were the exception, for example, Syt1, and they did not show anti‐correlation. These exceptions were probably the result ...
CD4+CD25+FOXP3+ human regulatory T cells (Tregs) are essential for self-tolerance and immune homeostasis. Here, we describe the promoterome of CD4+CD25highCD45RA+ naïve and CD4+CD25highCD45RA-memory Tregs and their CD25- conventional T-cell (Tconv) counterparts both before and after in vitro expansion by cap analysis of gene expression (CAGE) adapted to single-molecule sequencing (HeliScopeCAGE). We performed comprehensive comparative digital gene expression analyses and revealed novel transcription start sites, of which several were validated as alternative promoters of known genes. For all in vitro expanded subsets, we additionally generated global maps of poised and active enhancer elements marked by histone H3 lysine 4 monomethylation and histone H3 lysine 27 acetylation, describe their cell type-specific motif signatures, and evaluate the role of candidate transcription factors STAT5, FOXP3, RUNX1, and ETS1 in both Treg- and Tconv-specific enhancer architectures. Network analyses of gene ...
CRE Prediction: Genes with predicted functional CRE by any of the three methods (conserved CRE, CRE cluster, or positional conserved pHMM hits) are chosen and further separated into two groups, CRE_TATA and CRE_NoTATA based on the presence of TATA boxes. The rest of the genes are simply labeled as others. When a gene (defined as unique LocusLink number) has multiple entries (GenBank Accession numbers) due to different splicing forms, the best prediction for CRE is chosen. CRE Flag: Flags, or markers for the types of CREs on the promoter (-3Kb to 300bp from transcription start site). F/f means full site, H/h means half site, with upper case representing conserved CRE. FH is a full site CRE in the species studied but only appear as half site in other species. T/t at the end means the presence of a TATA box less than 300bp downstream of the CRE.. Full Site/Half Site: All occurrences of full site (TGACGTCA) or half site(TGACG/CGTCA) CREs in -5Kb-1Kb region of the transcription start site ...
Absolute number of identified transcription start sites in correlation to the length of their 5′-untranslated regions (5′-UTRs). The 1,642 TSSs located upst
Ive read some of the responses dealing with 5 RACE, but didnt see anything about possible secondary structure. Ive been having problems getting anything on my gels for 5 RACE (even using touchdown pcr). I think that it may be due to 2* structure. Does anyone have any protocols for relaxing the 2 ...
Background: Conventional wisdom holds that, owing to the dominance of features such as chromatin level control, the expression of a gene cannot be readily predicted from knowledge of promoter architecture. This is reflected, for example, in a weak or absent correlation between promoter divergence and expression divergence between paralogs. However, an inability to predict may reflect an inability to accurately measure or employment of the wrong parameters. Here we address this issue through integration of two exceptional resources: ENCODE data on transcription factor binding and the FANTOM5 high-resolution expression atlas. Results: Consistent with the notion that in eukaryotes most transcription factors are activating, the number of transcription factors binding a promoter is a strong predictor of expression breadth. In addition, evolutionarily young duplicates have fewer transcription factor binders and narrower expression. Nonetheless, we find several binders and cooperative sets that are ...
Conventional wisdom holds that, owing to the dominance of features such as chromatin level control, the expression of a gene cannot be readily predicted from knowledge of promoter architecture. This is reflected, for example, in a weak or absent correlation between promoter divergence and expression divergence between paralogs. However, an inability to predict may reflect an inability to accurately measure or employment of the wrong parameters. Here we address this issue through integration of two exceptional resources: ENCODE data on transcription factor binding and the FANTOM5 high-resolution expression atlas. Consistent with the notion that in eukaryotes most transcription factors are activating, the number of transcription factors binding a promoter is a strong predictor of expression breadth. In addition, evolutionarily young duplicates have fewer transcription factor binders and narrower expression. Nonetheless, we find several binders and cooperative sets that are disproportionately associated
An accurate identification of gene promoters remains an important challenge. Computational approaches for this problem rely on promoter sequence attributes that are believed to be critical for transcription initiation. Here we report a probabilistic model that captures two important properties of promoters, not used by previous methods, viz., the location preference and co-occurrence of promoter elements. Additionally, we found that many of the position-specific DNA elements are strongly linked with the function of the gene product. For instance, a highly conserved motif CCTTT at -1 position is strongly associated with protein synthesis, cellular and tissue development. Our comparative analysis of promoter classes reveals that the promoters devoid of CpG islands are more conserved and have fewer alternative transcription start sites. The discovered links between promoter elements and gene function allows us to infer genetic networks from promoter elements. The web server for the PSPA promoter ...
It recently has been established that adenine-containing cofactors, including nicotinamide adenine dinucleotide (NAD+), reduced nicotinamide adenine dinucleotide (NADH), and 3-desphospho-coenzyme A (dpCoA), can serve as non-canonical initiating nucleotides (NCINs) for transcription initiation by bacterial and eukaryotic cellular RNA polymerases (RNAPs) and that the efficiency of the reaction is determined by promoter sequence (Bird et al., 2016). Here we describe a protocol to quantify the relative efficiencies of transcription initiation using an NCIN vs. transcription initiation using a nucleoside triphosphate (NTP) for a given promoter sequence.
Human blood monocytes comprise at least 3 subpopulations that differ in phenotype and function. Here, we present the first in-depth regulome analysis of human classical (CD14++CD16-), intermediate (CD14+CD16+), and nonclassical (CD14dimCD16+) monocytes. Cap analysis of gene expression adapted to Helicos single-molecule sequencing was used to map transcription start sites throughout the genome in all 3 subsets. In addition, global maps of H3K4me1 and H3K27ac deposition were generated for classical and nonclassical monocytes defining enhanceosomes of the 2 major subsets. We identified differential regulatory elements (including promoters and putative enhancers) that were associated with subset-specific motif signatures corresponding to different transcription factor activities and exemplarily validated novel downstream enhancer elements at the CD14 locus. In addition to known subset-specific features, pathway analysis revealed marked differences in metabolic gene signatures. Whereas classical ...
DSB repair pathway choice――――――. HR initiation at transcription active loci Yasuhara et al., Cell, 2018. DSB repair pathway choice in G1 Biehs et al., Mol Cell, 2017. 53BP1 dephosphorylation promotes pro-HR environment Isono et al., Cell Rep, 2017. MRE11-dependent initiation of resection Shibata et al., Mol Cell, 2014. DSB repair pathway choice in G2 Shibata et al., EMBO J, 2011. ―――DDR dependent immune ligands regulation―――. BER deficiency upregulates PD-L1 expression Permata et al., Oncogene, 2019. DSB-dependent ATR/Chk1 upregulats PD-L1 expression Sato et al., Nat Comm, 2017. ...
Core promoter element analysis is performed in order to investigate the quality of the promoter collection. It exploits the fact that certain DNA motifs preferentially occur at characteristic distances from a TSS. For instance, the TATA-box occurs in a narrow region centered about 28 bp upstream of the TSS whereas the CCAAT-box occurs in a much wider area with a peak frequency at position −80. Based on these observations, we would expect a high-quality promoter collection to show high peaks for both sequence motifs. In addition, a narrow TATA-box peak at −28 would indicate precise TSS mapping. This analysis has been performed using OProf. Readers are encouraged to repeat this anlysis and perform others in order to check for the quality of the promoter list. TATA-box: this core promoter element is normally found 28 bp upstream the transcription start site. The following plot shows that EPDnew promoter collection has a more focused TATA-box distribution compared to Gramene annotation ...
In the figure, each line represents an upstream region of a given gene, with different binding sites. The TFBSs located in this region are drawn relative to the regulated gene, or to the affected promoter; thus 0 represents the beginning of the gene or the promoter, respectively. The scale bar on the top indicates the coordinates that covers the range from -400 to 100 bp. ...
This paper describes the identification and characterization of an Arabidopsis mutant with a T-DNA insertion in the MGD synthase gene, MGD1. The T-DNA is located 12 bp downstream of the first MGD1 transcription initiation site (Fig. 2A), and 101 bp upstream of the third transcription initiation site (RACE analysis identified three different MGD1 transcription initiation sites). MGD1 mRNA abundance in the mutant was estimated to be reduced by 75% compared with wild type by using reverse transcription-PCR. The basis for the residual expression of MGD1 in the mutant is uncertain. One possibility is that the 101-bp region which lies between the T-DNA border and the most downstream transcription initiation site contains sufficient promoter activity to drive basal levels of expression of the shortest transcript. Another possibility is that cryptic promoter sequences exist within the left border region of the T-DNA. In both cases, it is possible that the performance of minimal or cryptic promoters are ...
Obesity causes dysfunction in major metabolic tissues. The glucose-fatty acid cycle, also known as the Randle hypothesis, provides the first basic concept for h...
Detection of BORIS expression from different alternative promoters and stability of BORIS alternative transcripts. (A) Unique BORIS cDNA sequences attached to p
499 GTAGCCGTCA AGATTGTGTT GGGTCGTTGC TTTCTTGTTG TTTTAAATCA CGGTCATGTG -439 TTTGGCAAGG GTGCTGGTTA ACCGAAAATG TTGGTTCTAG AGCTAGAAGT ACTGGCATTC -379 AAATAAACAT ATTTGGGGGT TGGGGGTTGA TGAGCAAGGC TGGGAGGAGA CAAAAGAAGT -319 ATCTCGGCTC AGTCGTCAGA GACGCGCAAG GTGTAACGGA GAGAGCAATC TAGGTTGTGA -259 GAGTGGCTCC AAACATTGAG ACATGGAGCC AGGACCTTTG CTCCTGGGGG ATGGCCCTAG -199 TACTGATGCG CAGGACCTGG TCCTTGAAGG AGCTGACAAA ACTGCCGTTC ACCCGCGCGA -139 CCACCGGCAA AGCAGCTCCA CAGCCTGCCC CTCCCCTTGG CTGCTCCCCC ACCCATTTCC -79 CGCCTTGTCT TTCCTCTCTT CTCTCTCTCC CTCCTCCCTG CGCGAAGCGG AAGTGACGCG -19 AGGCGTAGCG GAAGTTACTG CAGCCGCGGT GTTGTGCTGT GGGGAAGGGA GAAGGATTTG , TSS 41 TAAACCCCGG AGCGAGGTTC TGCTTACCCG AGGCCGCTGC TGTGCGGAGA CCCCCGGGTG ...
Cell Capture and Separation systems- CherryPicker- Fast and easy cell capture and enrichment of cells expressing your protein of interest or having your active promoter
Cell Capture and Separation systems- CherryPicker- Fast and easy cell capture and enrichment of cells expressing your protein of interest or having your active promoter
Поручение АП Минздраву и Министерству социального развития - подготовить заявление президента РК о путях повышения продолжительности жизни в Казахстане и создании безопасной среды ...
It is a small chemical capsule in a plastic bottle half-filled with water. But it works wonders -- insects flock to the bottle to drown ...
Nucleosome organization is critical for the regulation of gene expression, and genome-scale mapping of nucleosomes has revealed a conserved, highly ordered pattern in nucleosome positioning. Most genome-wide studies have been performed in model organisms and little is known about nucleosome positioning in evolutionarily divergent eukaryotes. We generated a high-resolution nucleosome map of the protozoan parasite Toxoplasma gondii from four high quality MNase-Seq datasets. T. gondii nucleosomes are organised in phase around the transcription start sites (TSSs) with a canonical pattern that is conserved across eukaryotes. Nucleosome occupancy in exons is influenced by several factors, including GC content, length of exons and strength of splice sites. Poly(dA:dT) is enriched at the +1 nucleosome rather than nucleosome-free regions (NFRs) and serves as the key sequence associated with nucleosome formation in T. gondii. Motif analysis of sequences in NFR1, adjacent to the transcription start site, revealed
Accurately modeling the DNA sequence preferences of transcription factors and predicting their genomic binding sites are key problems in regulatory genomic
Nucleosome-free regions (NFRs) in the 5′ and 3′ ends of genes are general A-770041 sites of transcription initiation for mRNA and noncoding RNA (ncRNA). spanning gene-coding areas and transcriptional regulatory areas. Gene-coding areas generally possess high nucleosome occupancy with arrays of well-phased nucleosomes increasing through the 5′ end of the gene. On the A-770041 other hand transcriptional regulatory areas such as for example promoters enhancers and terminators possess low nucleosome occupancy and frequently include a nucleosome-free area (NFR). NFRs also called nucleosome-depleted areas (NDRs) typically represent areas with an elevated option of micrococcal nuclease (MNase) digestive function. Thus the word NFR identifies a insufficiency in experimentally established canonical nucleosomes and will not always imply an A-770041 entire insufficient histones. To day predominately two main classes of NFRs 5 and 3′-NFRs have already been characterized. In cis as yet not known. ...
Heavy involvement of stringent transcription control depending on the adenine or guanine species of the transcription initiation site in glucose and pyruvate metabolism in Bacillus subtilis. ...
The abstract for this paper came up in my RSS feed recently, and I immediately took interest. Upon further reading, I noticed that the study was limited to data from human cerebella, but the punchline is still fascinating: alternative transcription mechanisms are responsible for a greater portion of transcriptome diversity than splicing mechanisms!
Yn aml mae gan enynnau lawer o gyfystyron. Mae hyn oherwydd eu bod yn aml yn cael eu darganfod gan nifer o bobl mewn cyd-destunau gwahanol heb wybod mair un genynnau oeddyn nhw. Hefyd mae gan wahanol gymunedau gwyddonol safonau gwahanol ar gyfer enwi genynnau. Dyma restr o gyfystyron ar gyfer y genyn ANGPT2. ...