scholarly journals A comprehensive analysis of 3′ end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogeneous ribonucleoprotein C on cleavage and polyadenylation

2016 ◽  
Vol 26 (8) ◽  
pp. 1145-1159 ◽  
Author(s):  
Andreas J. Gruber ◽  
Ralf Schmidt ◽  
Andreas R. Gruber ◽  
Georges Martin ◽  
Souvik Ghosh ◽  
...  
Keyword(s):  
Comprehensive Analysis ◽  
Data Sets ◽  
Sequencing Data ◽  
Cleavage And Polyadenylation ◽  
Polyadenylation Signals

Sequences downstream of AAUAAA signals affect pre-mRNA cleavage and polyadenylation in vitro both directly and indirectly

1989 ◽  
Vol 9 (4) ◽  
pp. 1759-1771
Author(s):  
L C Ryner ◽  
Y Takagaki ◽  
J L Manley
Keyword(s):  
Cleavage Site ◽  
Simian Virus 40 ◽  
Simian Virus ◽  
Cleavage Reaction ◽  
Mrna Cleavage ◽  
Nuclear Extracts ◽  
Cleavage And Polyadenylation ◽  
Polyadenylation Signals

To investigate the role of sequences lying downstream of the conserved AAUAAA hexanucleotide in pre-mRNA cleavage and polyadenylation, deletions or substitutions were constructed in polyadenylation signals from simian virus 40 and adenovirus, and their effects were assayed in both crude and fractionated HeLa cell nuclear extracts. As expected, these sequences influenced the efficiency of both cleavage and polyadenylation as well as the accuracy of the cleavage reaction. Sequences near or upstream of the actual site of poly(A) addition appeared to specify a unique cleavage site, since their deletion resulted, in some cases, in heterogeneous cleavage. Furthermore, the sequences that allowed the simian virus 40 late pre-RNA to be cleaved preferentially by partially purified cleavage activity were also those at the cleavage site itself. Interestingly, sequences downstream of the cleavage site interacted with factors not directly involved in catalyzing cleavage and polyadenylation, since the effects of deletions were substantially diminished when partially purified components were used in assays. In addition, these sequences contained elements that could affect 3'-end formation both positively and negatively.

scholarly journals Sequences downstream of AAUAAA signals affect pre-mRNA cleavage and polyadenylation in vitro both directly and indirectly.

1989 ◽  
Vol 9 (4) ◽  
pp. 1759-1771 ◽  
Author(s):  
L C Ryner ◽  
Y Takagaki ◽  
J L Manley
Keyword(s):  
Cleavage Site ◽  
Simian Virus 40 ◽  
Simian Virus ◽  
Cleavage Reaction ◽  
Mrna Cleavage ◽  
Nuclear Extracts ◽  
Cleavage And Polyadenylation ◽  
Polyadenylation Signals

To investigate the role of sequences lying downstream of the conserved AAUAAA hexanucleotide in pre-mRNA cleavage and polyadenylation, deletions or substitutions were constructed in polyadenylation signals from simian virus 40 and adenovirus, and their effects were assayed in both crude and fractionated HeLa cell nuclear extracts. As expected, these sequences influenced the efficiency of both cleavage and polyadenylation as well as the accuracy of the cleavage reaction. Sequences near or upstream of the actual site of poly(A) addition appeared to specify a unique cleavage site, since their deletion resulted, in some cases, in heterogeneous cleavage. Furthermore, the sequences that allowed the simian virus 40 late pre-RNA to be cleaved preferentially by partially purified cleavage activity were also those at the cleavage site itself. Interestingly, sequences downstream of the cleavage site interacted with factors not directly involved in catalyzing cleavage and polyadenylation, since the effects of deletions were substantially diminished when partially purified components were used in assays. In addition, these sequences contained elements that could affect 3'-end formation both positively and negatively.

scholarly journals A comprehensive analysis of 3′ end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogenous ribonucleoprotein C on cleavage and polyadenylation

2015 ◽  
Author(s):  
Andreas J Gruber ◽  
Ralf Schmidt ◽  
Andreas R Gruber ◽  
Georges Martin ◽  
Souvik Ghosh ◽  
...  
Keyword(s):  
Rna Binding ◽  
Rna Binding Proteins ◽  
Protein Localization ◽  
Alternative Polyadenylation ◽  
General Mechanism ◽  
Data Sets ◽  
Sequencing Data ◽  
A Genome ◽  
The Stability

Alternative polyadenylation (APA) is a general mechanism of transcript diversification in mammals, which has been recently linked to proliferative states and cancer. Different 3′ untranslated region (3′ UTR) isoforms interact with different RNA binding proteins (RBPs), which modify the stability, translation, and subcellular localization of the corresponding transcripts. Although the heterogeneity of pre-mRNA 3′ end processing has been established with high-throughput approaches, the mechanisms that underlie systematic changes in 3′ UTR lengths remain to be characterized. Through a uniform analysis of a large number of 3′ end sequencing data sets we have uncovered 18 signals, 6 of which novel, whose positioning with respect to pre-mRNA cleavage sites indicates a role in pre-mRNA 3′ end processing in both mouse and human. With 3′ end sequencing we have demonstrated that the heterogeneous ribonucleoprotein C (HNRNPC), which binds the poly(U) motif whose frequency also peaks in the vicinity of polyadenylation (poly(A)) sites, has a genome-wide effect on poly(A) site usage. HNRNPC-regulated 3′ UTRs are enriched in ELAV-like RNA binding protein 1 (ELAVL1) binding sites and include those of the CD47 molecule (CD47) gene, which participate in the recently discovered mechanism of 3′ UTR-dependent protein localization (UDPL). Our study thus establishes an up-to-date, high-confidence catalog of 3′ end processing sites and poly(A) signals and it uncovers an important role of HNRNPC in regulating 3′ end processing. It further suggests that U-rich elements mediate interactions with multiple RBPs that regulate different stages in a transcript’s life cycle.

scholarly journals RNA modification mapping with JACUSA2

2021 ◽  
Author(s):  
Michael Piechotta ◽  
Qi Wang ◽  
Janine Altmueller ◽  
Christoph Dieterich
Keyword(s):  
High Throughput ◽  
Comprehensive Analysis ◽  
Hek293 Cells ◽  
Rna Modification ◽  
Published Data ◽  
Data Sets ◽  
Analysis Framework ◽  
Sequencing Data

A whole series of high-throughput antibody-free methods for RNA modification detection from sequencing data emerged lately. We present JACUSA2 as a versatile software solution and comprehensive analysis framework for RNA modification detection assays that are based on either the Illumina or Nanopore platform. Importantly, JACUSA2 can integrate information from multiple experiments (e.g. replicates and different conditions) and different library types (e.g. first- or secondstrand libraries). We demonstrate its utility by example, showing three analysis workflows for m6A detection on published data sets: 1) MazF m6a-sensitive RNA digestion (FTO+ vs FTO-), 2) DART-seq (YTHwt vs YTHmut) and 3) Nanopore profiling (METTL3 +/+ vs -/-). All assays have been conducted in HEK293 cells and complement one another.

scholarly journals Comprehensive Analysis of Arabinogalactan Protein-Encoding Genes Reveals the Involvement of Three BrFLA Genes in Pollen Germination in Brassica rapa

2021 ◽  
Vol 22 (23) ◽  
pp. 13142
Author(s):  
Huiting Huang ◽  
Yingjing Miao ◽  
Yuting Zhang ◽  
Li Huang ◽  
Jiashu Cao ◽  
...  
Keyword(s):  
Brassica Rapa ◽  
Pollen Germination ◽  
Protein Structures ◽  
Pollen Grains ◽  
Comprehensive Analysis ◽  
Arabinogalactan Protein ◽  
Sequencing Data ◽  
Protein Encoding ◽  
Encoding Genes

Arabinogalactan proteins (AGPs) are a superfamily of hydroxyproline-rich glycoproteins that are massively glycosylated, widely implicated in plant growth and development. No comprehensive analysis of the AGP gene family has been performed in Chinese cabbage (Brassica rapa ssp. chinensis). Here, we identified a total of 293 putative AGP-encoding genes in B. rapa, including 25 classical AGPs, three lysine-rich AGPs, 30 AG-peptides, 36 fasciclin-like AGPs (FLAs), 59 phytocyanin-like AGPs, 33 xylogen-like AGPs, 102 other chimeric AGPs, two non-classical AGPs and three AGP/extensin hybrids. Their protein structures, phylogenetic relationships, chromosomal location and gene duplication status were comprehensively analyzed. Based on RNA sequencing data, we found that 73 AGP genes were differentially expressed in the floral buds of the sterile and fertile plants at least at one developmental stage in B. rapa, suggesting a potential role of AGPs in male reproductive development. We further characterized BrFLA2, BrFLA28 and BrFLA32, three FLA members especially expressed in anthers, pollen grains and pollen tubes. BrFLA2, BrFLA28 and BrFLA32 are indispensable for the proper timing of pollen germination under high relative humidity. Our study greatly extends the repertoire of AGPs in B. rapa and reveals a role for three members of the FLA subfamily in pollen germination.

scholarly journals HDL biodistribution and brain receptors in zebrafish, using HDLs as vectors for targeting endothelial cells and neural progenitors

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Nora Cassam Sulliman ◽  
Batoul Ghaddar ◽  
Laura Gence ◽  
Jessica Patche ◽  
Sepand Rastegar ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Brain Plasticity ◽  
High Density Lipoproteins ◽  
Data Sets ◽  
Sequencing Data ◽  
Brain Functions ◽  
Ventricular Cells ◽  
The Brain ◽  
Brain Homeostasis

AbstractHigh density lipoproteins (HDLs) display pleiotropic functions such as anti-inflammatory, antioxidant, anti-protease, and anti-apoptotic properties. These effects are mediated by four main receptors: SCARB1 (SR-BI), ABCA1, ABCG1, and CD36. Recently, HDLs have emerged for their potential involvement in brain functions, considering their epidemiological links with cognition, depression, and brain plasticity. However, their role in the brain is not well understood. Given that the zebrafish is a well-recognized model for studying brain plasticity, metabolic disorders, and apolipoproteins, it could represent a good model for investigating the role of HDLs in brain homeostasis. By analyzing RNA sequencing data sets and performing in situ hybridization, we demonstrated the wide expression of scarb1, abca1a, abca1b, abcg1, and cd36 in the brain of adult zebrafish. Scarb1 gene expression was detected in neural stem cells (NSCs), suggesting a possible role of HDLs in NSC activity. Accordingly, intracerebroventricular injection of HDLs leads to their uptake by NSCs without modulating their proliferation. Next, we studied the biodistribution of HDLs in the zebrafish body. In homeostatic conditions, intraperitoneal injection of HDLs led to their accumulation in the liver, kidneys, and cerebral endothelial cells in zebrafish, similar to that observed in mice. After telencephalic injury, HDLs were diffused within the damaged parenchyma and were taken up by ventricular cells, including NSCs. However, they failed to modulate the recruitment of microglia cells at the injury site and the injury-induced proliferation of NSCs. In conclusion, our results clearly show a functional HDL uptake process involving several receptors that may impact brain homeostasis and suggest the use of HDLs as delivery vectors to target NSCs for drug delivery to boost their neurogenic activity.

Participant recruitment and data collection through Facebook: the role of personality factors

2017 ◽  
Author(s):  
Sean Chandler Rife ◽  
Kelly L. Cate ◽  
Michal Kosinski ◽  
David Stillwell
Keyword(s):  
Data Collection ◽  
Social Research ◽  
Personality Factors ◽  
The Internet ◽  
Data Sets ◽  
Social Networking Service ◽  
Participant Recruitment ◽  
Conducting Research ◽  
Promising Avenue

As participant recruitment and data collection over the Internet have become more common, numerous observers have expressed concern regarding the validity of research conducted in this fashion. One growing method of conducting research over the Internet involves recruiting participants and administering questionnaires over Facebook, the world’s largest social networking service. If Facebook is to be considered a viable platform for social research, it is necessary to demonstrate that Facebook users are sufficiently heterogeneous and that research conducted through Facebook is likely to produce results that can be generalized to a larger population. The present study examines these questions by comparing demographic and personality data collected over Facebook with data collected through a standalone website, and data collected from college undergraduates at two universities. Results indicate that statistically significant differences exist between Facebook data and the comparison data-sets, but since 80% of analyses exhibited partial η2 < .05, such differences are small or practically nonsignificant in magnitude. We conclude that Facebook is a viable research platform, and that recruiting Facebook users for research purposes is a promising avenue that offers numerous advantages over traditional samples.

scholarly journals Software Benchmark—Classification Tree Algorithms for Cell Atlases Annotation Using Single-Cell RNA-Sequencing Data

2021 ◽  
Vol 12 (2) ◽  
pp. 317-334
Author(s):  
Omar Alaqeeli ◽  
Li Xing ◽  
Xuekui Zhang
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Classification Tree ◽  
Area Under The Curve ◽  
Data Sets ◽  
Sequencing Data ◽  
Single Cell Rna Sequencing ◽  
Tree Algorithms ◽  
R Packages

Classification tree is a widely used machine learning method. It has multiple implementations as R packages; rpart, ctree, evtree, tree and C5.0. The details of these implementations are not the same, and hence their performances differ from one application to another. We are interested in their performance in the classification of cells using the single-cell RNA-Sequencing data. In this paper, we conducted a benchmark study using 22 Single-Cell RNA-sequencing data sets. Using cross-validation, we compare packages’ prediction performances based on their Precision, Recall, F1-score, Area Under the Curve (AUC). We also compared the Complexity and Run-time of these R packages. Our study shows that rpart and evtree have the best Precision; evtree is the best in Recall, F1-score and AUC; C5.0 prefers more complex trees; tree is consistently much faster than others, although its complexity is often higher than others.

scholarly journals Past and future trends of Egypt’s water consumption and its sources

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Catherine A. Nikiel ◽  
Elfatih A. B. Eltahir
Keyword(s):  
Economic Growth ◽  
Virtual Water ◽  
Comprehensive Analysis ◽  
Future Trends ◽  
Nile Water ◽  
The Gift ◽  
Per Capita ◽  
The 1960S

AbstractFor millennia the Nile supplied Egypt with more water than needed. As the population grew and the economy expanded, demand on water increased accordingly. Here, we present a comprehensive analysis to reconstruct how total demand on water outstripped supply of the Nile water in the late 1970s, starting from a surplus of about 20 km3 per year in the 1960s leading to a deficit of about 40 km3 per year by the late 2010s. The gap is satisfied by import of virtual water. The role of economic growth in driving per capita demand on water is quantified based on detailed analysis of water use by agriculture and other sectors. We develop and test an empirical model of water demand in Egypt that relates demand on water to growth rates in the economy and population. Looking forward, we project that within this decade of the 2020 s, under nominal scenarios of population and economic growth, Egypt is likely to import more virtual water than the water supplied by the Nile, bringing into question the historical characterization of Egypt as “the gift of the Nile”.

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