Analysis of alternative cleavage and polyadenylation by 3' region extraction and deep sequencing. - sprookjes - yvandenbroek - TriplyDB

Analysis of alternative cleavage and polyadenylation by 3' region extraction and deep sequencing.

Analysis of alternative cleavage and polyadenylation by 3' region extraction and deep sequencing.

http://www.wikidata.org/entity/Q36575994

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mRNA 3'end processing: A tale of the tail reaches the clinic Processing and transcriptome expansion at the mRNA 3' end in health and disease: finding the right end RNA-Seq methods for transcriptome analysis The reciprocal regulation between splicing and 3'-end processing Alternative Polyadenylation of mRNAs: 3'-Untranslated Region Matters in Gene Expression Means to an end: mechanisms of alternative polyadenylation of messenger RNA precursors Alternative cleavage and polyadenylation: the long and short of it Advances in analyzing RNA diversity in eukaryotic transcriptomes: peering through the Omics lens THOC5 controls 3'end-processing of immediate early genes via interaction with polyadenylation specific factor 100 (CPSF100).PlantAPA: A Portal for Visualization and Analysis of Alternative Polyadenylation in Plants.The Orthology Clause in the Next Generation Sequencing Era: Novel Reference Genes Identified by RNA-seq in Humans Improve Normalization of Neonatal Equine Ovary RT-qPCR Data.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 End Sequence Analysis Toolkit (ESAT) expands the extractable information from single-cell RNA-seq data.Role of cleavage and polyadenylation specificity factor 100: anchoring poly(A) sites and modulating transcription termination.Competitive regulation of alternative splicing and alternative polyadenylation by hnRNP H and CstF64 determines acetylcholinesterase isoforms.The More the Merrier-Complexity in Long Non-Coding RNA Loci High-throughput sequencing of RNA isolated by cross-linking and immunoprecipitation (HITS-CLIP) to determine sites of binding of CstF-64 on nascent RNAs RNAP II CTD tyrosine 1 performs diverse functions in vertebrate cells.High-Resolution RNA Maps Suggest Common Principles of Splicing and Polyadenylation Regulation by TDP-43.Global analyses of the effect of different cellular contexts on microRNA targeting.Alternative polyadenylation of mRNA precursors.Defining the 5΄ and 3΄ landscape of the Drosophila transcriptome with Exo-seq and RNaseH-seq.RNA sequencing: from tag-based profiling to resolving complete transcript structure.A post-translational regulatory switch on UPF1 controls targeted mRNA degradation RBBP6 isoforms regulate the human polyadenylation machinery and modulate expression of mRNAs with AU-rich 3' UTRs.Mutant p53 cooperates with the SWI/SNF chromatin remodeling complex to regulate VEGFR2 in breast cancer cells The conserved intronic cleavage and polyadenylation site of CstF-77 gene imparts control of 3' end processing activity through feedback autoregulation and by U1 snRNP Distinct polyadenylation landscapes of diverse human tissues revealed by a modified PA-seq strategy Multiplex analysis of polyA-linked sequences (MAPS): an RNA-seq strategy to profile poly(A+) RNA Integrin α3β1 signaling through MEK/ERK determines alternative polyadenylation of the MMP-9 mRNA transcript in immortalized mouse keratinocytes Construction of mate pair full-length cDNAs libraries and characterization of transcriptional start sites and termination sites.Computational challenges, tools, and resources for analyzing co- and post-transcriptional events in high throughput.Mapping 3' mRNA isoforms on a genomic scale.Systematic profiling of poly(A)+ transcripts modulated by core 3' end processing and splicing factors reveals regulatory rules of alternative cleavage and polyadenylation.Evaluation of two statistical methods provides insights into the complex patterns of alternative polyadenylation site switching Defining the Human Brain Proteome Using Transcriptomics and Antibody-Based Profiling with a Focus on the Cerebral Cortex.Genome-wide characterization of intergenic polyadenylation sites redefines gene spaces in Arabidopsis thaliana.Integrative genome-wide analysis reveals HLP1, a novel RNA-binding protein, regulates plant flowering by targeting alternative polyadenylation Single-cell polyadenylation site mapping reveals 3' isoform choice variability.A post-transcriptional mechanism pacing expression of neural genes with precursor cell differentiation status.

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Analysis of alternative cleavage and polyadenylation by 3' region extraction and deep sequencing.

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Analysis of alternative cleava ...... xtraction and deep sequencing.

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Analysis of alternative cleava ...... xtraction and deep sequencing.

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Bei You

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Ghassan Yehia

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Ji Yeon Park

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Mainul Hoque

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Wencheng Li

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Wenting Luo

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A user's guide to the encyclopedia of DNA elements (ENCODE)

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.

A large-scale analysis of mRNA polyadenylation of human and mouse genes

Formation, regulation and evolution of Caenorhabditis elegans 3'UTRs

U1 snRNP determines mRNA length and regulates isoform expression

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data

Proliferating cells express mRNAs with shortened 3' untranslated regions and fewer microRNA target sites

Widespread mRNA polyadenylation events in introns indicate dynamic interplay between polyadenylation and splicing

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