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Comparing alternative polyadenylation landscapes in highly and poorly metastatic breast cancer cells

ABSTRACT: Comparing alternative polyadenylation landscapes in highly and poorly metastatic breast cancer cells

PROVIDER: PRJNA774893 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16587314.fastq.gz	Fastqsanger.gz
	SRR16587315.fastq.gz	Fastqsanger.gz
	SRR16587316.fastq.gz	Fastqsanger.gz
	SRR16587317.fastq.gz	Fastqsanger.gz
	SRR16587318.fastq.gz	Fastqsanger.gz

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Comparing alternative polyadenylation landscapes in highly and poorly metastatic breast cancer cells

Project description:Cancer cells often co-opt post-transcriptional regulatory mechanisms to achieve pathologic expression of gene networks that drive metastasis. Translational control is a major regulatory hub in oncogenesis, however its effects on cancer progression remain poorly understood. To address this, we used ribosome profiling to compare genome-wide translation efficiencies of poorly and highly metastatic breast cancer cells and patient-derived xenografts. We developed novel regression-based methods to analyze ribosome profiling and alternative polyadenylation data, and identified HNRNPC as a translational controller of a specific mRNA regulon. Mechanistically, HNRNPC, in concert with PABPC4, binds near to poly(A) signals, thereby governing the alternative polyadenylation of a set of mRNAs. We found that HNRNPC and PABPC4 are downregulated in highly metastatic cells, which causes HNRNPC-bound mRNAs to undergo 3’ UTR lengthening and subsequently, translational repression. We showed that modulating HNRNPC expression impacts the metastatic capacity of breast cancer cells in xenograft mouse models. We also found that a small molecule, previously shown to induce a distal-to-proximal poly(A) site switching, counteracts the HNRNPC-PABPC4 driven deregulation of alternative polyadenylation and decreases the metastatic lung colonization by breast cancer cells in vivo.

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Translation efficiency changes measured using ribosome footprinting (Ribo-seq) in poorly and highly metastatic cancer cells

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Gene array comparison of highly and poorly chondrogenic clones of adult human mesenchymal stem cells (MSCs)

Project description:MSCs are a heterogeneous population of cells with different capacities for lineage differentiation. MSC clones were prepared from a single adult human bone marrow sample and screened for their chondrogenic capacity using cartilage tissue engineering (measured by type II collagen content). The aim was to compare genes expressed by highly and poorly chondrogenic clones to identify genes associated with those MSCs with an enhanced capacity for cartilage formation. The 4 most highly chondrogenic and the 4 least chondrogenic MSC clones identified following screening by cartilage tissue engineering were selected for gene array comparison using Affymetrix microarrays.

2015-04-30 | E-GEOD-54684 | biostudies-arrayexpress

Gene array comparison of highly and poorly chondrogenic clones of adult human mesenchymal stem cells (MSCs)

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RNA polyadenylation landscape in human and mouse cells

Project description:Alternative polyadenylation (APA) of mRNAs has emerged as an important mechanism for post-transcriptional gene regulation in higher eukaryotes. Although microarrays have recently been used to characterize APA globally, they have a number of serious limitations that prevents comprehensive and highly quantitative analysis. To better characterize APA and its regulation, we have developed a deep sequencing-based method called Poly(A) Site Sequencing (PAS-Seq) for quantitatively profiling RNA polyadenylation at the transcriptome level. PAS-Seq not only accurately and comprehensively identifies poly(A) junctions in mRNAs and noncoding RNAs, but also provides quantitative information on the relative abundance of polyadenylated RNAs. We first analyzed HeLa cell transcriptome using PAS-Seq to demonstrate that PAS-Seq not only accurately and comprehensively identifies poly(A) junctions, but also provide quantitative information on the relativel abundance of APA isoforms. Next we analyzed the mouse embryonic stem cells, neural stem/progenitor cells, and neurons by PAS-Seq to characterize the dynamic changes of mRNA polyadenylation during stem cell differentiation.

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Project description:The post-transcriptional fate of messenger RNAs (mRNAs) is largely dictated by their 3' untranslated regions (3'UTRs), which are defined by cleavage and polyadenylation (CPA) of pre-mRNAs. We used poly(A)-position profiling by sequencing (3P-Seq) to map poly(A) sites at eight developmental stages and tissues in the zebrafish. Analysis of over 60 million 3P-Seq reads substantially increased and improved existing 3'UTR annotations, resulting in confidently identified 3'UTRs for more than 78.79% of the annotated protein-coding genes in zebrafish. Most zebrafish genes undergo alternative CPA with more than a thousand genes using different dominant 3'UTRs at different stages. 3'UTRs tend to be shortest in the ovaries and longest in the brain. Isoforms with some of the shortest 3'UTRs are highly expressed in the ovary yet absent in the maternally contributed RNAs of the embryo, perhaps because their 3'UTRs are too short to accommodate a uridine-rich motif required for stability of the maternal mRNA. At two hours post-fertilization, thousands of unique poly(A) sites appear at locations lacking a typical polyadenylation signal, which suggests a wave of widespread cytoplasmic polyadenylation of mRNA degradation intermediates. Our insights into the identities, formation, and evolution of zebrafish 3'UTRs provide a resource for studying gene regulation during vertebrate development. 3P-Seq was used to map the 3' ends of protein-coding genes in the zebrafish genome

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