General transcription factor

RNA degradation affects RNA-seq quality when profiling transcriptional activities in cells. Here, we show that transcript degradation is both gene- and sample-specific and is a common and significant factor that may bias the results in RNA-seq analysis. Most existing global normalization approaches are ineffective to correct for degradation bias.

18p vigalileogalilei 27-02-2022 8 1   Download

Single-cell RNA-seq has the potential to facilitate isoform quantification as the confounding factor of a mixed population of cells is eliminated. However, best practice for using existing quantification methods has not been established. We carry out a benchmark for five popular isoform quantification tools. Performance is generally good for simulated data based on SMARTer and SMART-seq2 data.

14p vigalileogalilei 27-02-2022 14 2   Download

The majority of eukaryotic promoters utilize multiple transcription start sites (TSSs). How multiple TSSs are specified at individual promoters across eukaryotes is not understood for most species. In Saccharomyces cerevisiae, a preinitiation complex (PIC) comprised of Pol II and conserved general transcription factors (GTFs) assembles and opens DNA upstream of TSSs.

31p viarchimedes 26-01-2022 7 0   Download

RNA polymerase II (Pol II) is a 12 subunit protein complex from yeast to human that is required for gene expression. Gdown1 containing Pol II [Pol II (G)] is a special form of Pol II that is catalytically inactive and heavily depends on the 30-subunit Mediator complex for its activator and basal dependent function in vitro. Here we report for the first time, the identification and the generation of a 15-subunit human Mediator complex via the novel multibac baculovirus expression system that is fully responsive to Pol II (G).

9p thiencuuchu 27-11-2021 18 1   Download

PAX6 is a homeodomain transcription factor that acts in a highly dosage-sensitive manner to regulate the development and function of the eyes, nose, central nervous system, gut, and endocrine pancreas. Several individual microRNAs (miRNA) have been implicated in regulating PAX6 in different cellular contexts, but a more general view of how they contribute to the fine-tuning and homeostasis of PAX6 is poorly understood.

17p vitzuyu2711 29-09-2021 11 1   Download

Discovery of functionally significant short, statistically overrepresented subsequence patterns (motifs) in a set of sequences is a challenging problem in bioinformatics. Oftentimes, not all sequences in the set contain a motif. These non-motif-containing sequences complicate the algorithmic discovery of motifs.

16p viwyoming2711 16-12-2020 10 0   Download

GenoGAM (Genome-wide generalized additive models) is a powerful statistical modeling tool for the analysis of ChIP-Seq data with flexible factorial design experiments. However large runtime and memory requirements of its current implementation prohibit its application to gigabase-scale genomes such as mammalian genomes.

9p viconnecticut2711 28-10-2020 14 1   Download

CCD is an autosomal dominant disorder caused by haploinsufficiency of Runt related transcription factor (RUNX2) essential for osteoblast cell commitment and chondrocyte maturation. A mutation of the RUNX2 (Core Binding Factor-α1 gene located at chromosome 6p21) is usually caused CCD. In general, the estimated prevalence of CCD is under diagnosed because of the relative lack of medical complications in comparison to other skeletal dysplasias. No available data on the prevalence of CCD or its characterization in Saudi families.

13p angicungduoc6 20-07-2020 10 2   Download

PLATZ proteins are a novel class of plant-specific zinc-dependent DNA-binding proteins that are classified as transcription factors (TFs). However, their common biochemical features and functions are poorly understood.

12p vishikamaru2711 29-04-2020 12 0   Download

Legumes are well recognized for their nutritional and health benefits as well as for their impact in the sustainability of agricultural systems. The threatening scenario imposed by climate change highlights the need for concerted research approaches in order to develop crops that are able to cope with environmental stresses, while increasing yield and quality. During the last decade, some physiological components and molecular players underlying abiotic stress responses of a broad range of legume species have been elucidated.

10p nguaconbaynhay1 04-12-2019 21 0   Download

Chapter 11 - general transcription factors in eukaryotes. Eukaryotic RNA polymerases, unlike their bacterial counterparts, are incapable of binding by themselves to their respective promoters. Instead, they rely on proteins called transcription factors to show them the way. Such factors are grouped into two classes: general transcription factors and gene-specifi c transcription factors (activators). In this chapter we will survey the general transcription factors that interact with all three RNA polymerases and their promoters.

38p tangtuy05 30-03-2016 78 2   Download

Eukaryotic RNA polymerases, unlike their bacterial counterparts, are incapable of binding by themselves to their respective promoters. Instead, they rely on proteins called transcription factors to show them the way. Such factors are grouped into two classes: general transcription factors and gene-specifi c transcription factors (activators). In this chapter we will survey the general transcription factors that interact with all three RNA polymerases and their promoters.

37p tangtuy02 08-03-2016 51 2   Download

Nuclear receptors (NRs) are ligand-regulated, DNA-binding transcription factors that function in the chromatin environment of the nucleus to alter the expression of subsets of hormone-responsive genes. It is clear that chromatin, rather than being a passive player, has a profound effect on both transcriptional repression and activation mediated by NRs.

9p research12 01-06-2013 32 2   Download

Minichromosomemaintenance (MCM) proteins are part of the replication licensing factor (RLF-M), which limits the initiationofDNAreplication to once per cell cycle.We have previously reported that higher order complexes of mam-malian pol II and general pol II transcription factors, referred to as pol II holoenzyme, also contain MCM pro-teins. In the present study we have analyzed in detail the interaction between MCM2 and pol II holoenzyme. N- and C- terminal deletions were introduced into epitope-tagged MCM2 and the truncated proteins were transiently expressed in 293 cells. ...

11p tumor12 22-04-2013 37 1   Download

RNA polymerase II (RNAPII) requires a set of general transcription factors )TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH)to initiate transcription from a gene promoterin vitro. General transcription factors have been isolated from Saccharomyces cerevisiae,rat, human and Drosophila,and their corresponding cDNAs have been cloned. In this report, we describe a reconstitutedin vitro transcription system that consists of the following prepara-tions of factors from the yeastSchizosaccharomyces pombe: affinity-purified RNAPII, TFIIH, and recombinant TBP, TFIIB, TFIIE and TFIIF. ...

12p dell39 03-04-2013 57 3   Download

As a critical step of the preinitiation complex assembly in transcription, the general transcription factor TFIIB forms a complex with the TATA-box binding protein (TBP) bound to a promoter element. Transcriptional activators such as the herpes simplex virus VP16 facilitate this com-plex formation through conformational activation of TFIIB, a focal molecule of transcriptional initiation and activation.

9p dell39 03-04-2013 33 2   Download

To elucidate the molecular mechanism underlying the heat shock response in cold-water fish species, genes enco-ding heat shock transcription factors (HSFs) were cloned fromRTG-2cellsof the rainbowtroutOncorhynchusmykiss. Consequently, two distinctHSF1genes, namedHSF1aand HSF1b, were identified. The predicted amino acid sequence ofHSF1ashows 86.4% identity to that ofHSF1b.Thetwo proteins contained the general structuralmotifs ofHSF1, i.e. a DNA-binding domain, hydrophobic heptad repeats and nuclear localization signals. ...

10p dell39 03-04-2013 39 3   Download

Human papillomavirus type 16 (HPV16) DNA replication, which requires two viral proteins E1 and E2, occurs only in the differentiating epithelium. Besides the general factors necessary for cellular DNA synthesis, other unidentified cellular factors are assumed to be involved in the regulation of HPV DNA replication.

13p galaxyss3 07-03-2013 38 2   Download

The price premium charged for competitive-market products depends on several factors including the price of standard offer or default service, the availability of incentives to green power marketers or suppliers, and the cost of renewable energy generation available in the regional market. Some marketers have charged prices close to or even below the default market price in recent years (e.g., in Texas); others have offered fixed-price products, providing customers with protection against increasing prices for a specified period of time, usually one year.

138p lenh_hoi_xung 21-02-2013 75 8   Download

It is not generally appreciated that early examples of critical path networks were developed before 1950, although their value was not widely appreciated at the time. Without the existence of computers, they were inflexible to change, tedious to translate into working schedules and thus impracticable and difficult to use. Gantt’s bar charts were generally preferred, often set up on proprietary charts that allowed rescheduling using movable magnetic or plug-in strips or cards.

10p lenh_hoi_xung 21-02-2013 39 3   Download