Regulation of expression of human RNA polymerase II-transcribed snRNA genes

In addition to protein-coding genes, RNA polymerase II (pol II) transcribes numerous genes for non-coding RNAs, including the small-nuclear (sn)RNA genes. snRNAs are an important class of non-coding RNAs, several of which are involved in pre-mRNA splicing. The molecular mechanisms underlying expression of human pol II-transcribed snRNA genes are less well characterized than for protein-coding genes and there are important differences in expression of these two gene types. Here, we review the DNA features and proteins required for efficient transcription of snRNA genes and co-transcriptional 3' end formation of the transcripts

Insights into the U1 small nuclear ribonucleoprotein complex superfamily

The 164 bp U1 small nuclear (sn) RNA is one of the most abundant noncoding (nc) RNA in human cells, estimated to be in the region of 106 copies/cell. Although best known for its role in pre-messenger RNA (mRNA) splicing events, research over the past 20 years has revealed diverse functions of this ncRNA in mammalian cell types. Excellent reviews exist detailing the role of U1 snRNA in pre-mRNA splicing events. This review highlights what is currently known regarding the additional roles, snRNP composition, expression profiles, and the genomic organization of this ncRNA.</p

Regulation of expression of human RNA polymerase II-transcribed snRNA genes

In addition to protein-coding genes, RNA polymerase II (pol II) transcribes numerous genes for non-coding RNAs, including the small-nuclear (sn)RNA genes. snRNAs are an important class of non-coding RNAs, several of which are involved in pre-mRNA splicing. The molecular mechanisms underlying expression of human pol II-transcribed snRNA genes are less well characterized than for protein-coding genes and there are important differences in expression of these two gene types. Here, we review the DNA features and proteins required for efficient transcription of snRNA genes and co-transcriptional 3' end formation of the transcripts

Regulation of expression of human RNA polymerase II-transcribed snRNA genes

In addition to protein-coding genes, RNA polymerase II (pol II) transcribes numerous genes for non-coding RNAs, including the small-nuclear (sn)RNA genes. snRNAs are an important class of non-coding RNAs, several of which are involved in pre-mRNA splicing. The molecular mechanisms underlying expression of human pol II-transcribed snRNA genes are less well characterized than for protein-coding genes and there are important differences in expression of these two gene types. Here, we review the DNA features and proteins required for efficient transcription of snRNA genes and co-transcriptional 3' end formation of the transcripts

CAPTURE of the human U2 snRNA genes expands the repertoire of associated factors

In order to identify factors involved in transcription of human snRNA genes and 3' end processing of the transcripts, we have carried out CRISPR affinity purification in situ of regulatory elements (CAPTURE), which is deadCas9-mediated pull-down, of the tandemly repeated U2 snRNA genes in human cells. CAPTURE enriched many factors expected to be associated with these human snRNA genes including RNA polymerase II (pol II), Cyclin-Dependent Kinase 7 (CDK7), Negative Elongation Factor (NELF), Suppressor of Ty 5 (SPT5), Mediator 23 (MED23) and several subunits of the Integrator Complex. Suppressor of Ty 6 (SPT6); Cyclin K, the partner of Cyclin-Dependent Kinase 12 (CDK12) and Cyclin-Dependent Kinase 13 (CDK13); and SWI/SNF chromatin remodelling complex-associated SWI/SNF-related, Matrix-associated, Regulator of Chromatin (SMRC) factors were also enriched. Several polyadenylation factors, including Cleavage and Polyadenylation Specificity Factor 1 (CPSF1), Cleavage Stimulation Factors 1 and 2 (CSTF1,and CSTF2) were enriched by U2 gene CAPTURE. We have already shown by chromatin immunoprecipitation (ChIP) that CSTF2-and Pcf11 and Ssu72, which are also polyadenylation factors-are associated with the human U1 and U2 genes. ChIP-seq and ChIP-qPCR confirm the association of SPT6, Cyclin K, and CDK12 with the U2 genes. In addition, knockdown of SPT6 causes loss of subunit 3 of the Integrator Complex (INTS3) from the U2 genes, indicating a functional role in snRNA gene expression. CAPTURE has therefore expanded the repertoire of transcription and RNA processing factors associated with these genes and helped to identify a functional role for SPT6

Deriving seasonal dynamics in ecosystem properties of semi-arid savanna grasslands from in situ-based hyperspectral reflectance

This paper investigates how hyperspectral reflectance (between 350 and 1800 nm) can be used to infer ecosystem properties for a semi-arid savanna grassland in West Africa using a unique in situ-based multi-angular data set of hemispherical conical reflectance factor (HCRF) measurements. Relationships between seasonal dynamics in hyperspectral HCRF and ecosystem properties (biomass, gross primary productivity (GPP), light use efficiency (LUE), and fraction of photosynthetically active radiation absorbed by vegetation (FAPAR)) were analysed. HCRF data (&rho;) were used to study the relationship between normalised difference spectral indices (NDSIs) and the measured ecosystem properties. Finally, the effects of variable sun sensor viewing geometry on different NDSI wavelength combinations were analysed. The wavelengths with the strongest correlation to seasonal dynamics in ecosystem properties were shortwave infrared (biomass), the peak absorption band for chlorophyll <i>a</i> and <i>b</i> (at 682 nm) (GPP), the oxygen A band at 761 nm used for estimating chlorophyll fluorescence (GPP and LUE), and blue wavelengths (&rho;₄₁₂) (FAPAR). The NDSI with the strongest correlation to (i) biomass combined red-edge HCRF (&rho;₇₀₅) with green HCRF (&rho;₅₈₇), (ii) GPP combined wavelengths at the peak of green reflection (&rho;₅₁₈, &rho;₅₅₆), (iii) LUE combined red (&rho;₆₈₈) with blue HCRF (&rho;₄₃₆), and (iv) FAPAR combined blue (&rho;₃₉₉) and near-infrared (&rho;₁₂₉₅) wavelengths. NDSIs combining near infrared and shortwave infrared were strongly affected by solar zenith angles and sensor viewing geometry, as were many combinations of visible wavelengths. This study provides analyses based upon novel multi-angular hyperspectral data for validation of Earth-observation-based properties of semi-arid ecosystems, as well as insights for designing spectral characteristics of future sensors for ecosystem monitoring

Investigating Breast Cancer Cell Behavior Using Tissue Engineering Scaffolds - Fig 4

<p>Flow cytometry analysis of CD44/CD24 expression of A) Top left: suspension of MDA-MB-231 treated cells analyzed based on size with forward-scattered light (FSC) and side-scattered light (SSC). Top right: R1 population further analyzed by specifically gating for CD44/CD24 expressing cells. Bottom left: histogram of MDA isotype control and CD24-FITC with histogram marker M1 designating CD24-FITC positive events. Bottom right: histogram of MDA isotype control and CD44-PE with histogram marker M1, designating CD44-PE positive events. B) Top left: suspension of T47D treated cells analyzed based on size with FSC and SSC. Top right: R1 population further analyzed by specifically gating for CD44/CD24 expressing cells. Bottom left: histogram of T47D isotype control and CD24-FITC with histogram marker M1 designating CD24-FITC positive events. Bottom right: histogram of T47D isotype control and CD44-PE with histogram marker M1, designating CD44-PE positive events.</p

Analysis of cell cycle phase for non-treated BCCs by flow cytometry on: TCP at a) day 1 and d) day 7, random fibrous scaffolds at b) day 1 and e) day 7, and aligned fibrous scaffolds at c) day 1 and f) day 7.

<p>Analysis of cell cycle phase for non-treated BCCs by flow cytometry on: TCP at a) day 1 and d) day 7, random fibrous scaffolds at b) day 1 and e) day 7, and aligned fibrous scaffolds at c) day 1 and f) day 7.</p

Western blot of breast cancer cell lines with chemotherapy treatment.

<p>Bax, Bcl2, Oct4, and Sox2 expression was determined for A) MDA-MB-231 cells and B) T47D cells. Densitometric bands normalized to β-actin have been provided in supplemental <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0118724#pone.0118724.s001" target="_blank">S1 Fig</a>.</p