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Transcriptional termini of genes on chromosomes 21-22 (RNA mapping)

ABSTRACT: The purpose of these experiments was to determine the 5' and 3' transcriptional termini of genes on chromosomes 21-22. Towards this end, we mapped the poly A + RNA isolated from 12 normal tissues and four cell lines. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

ORGANISM(S): Homo sapiens

PROVIDER: GSE17358 | GEO | 2009/07/28

REPOSITORIES: GEO

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Transcriptional termini of genes on chromosomes 21-22 (RNA mapping)

Project description:The purpose of these experiments was to determine the 5' and 3' transcriptional termini of genes on chromosomes 21-22. Towards this end, we mapped the poly A + RNA isolated from 12 normal tissues and four cell lines. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf polyA+ RNAs from 11 tissues (Brain Frontal Lobe, Brain Hippocampus, Brain Hypothalamus, Cerebellum, Ovary, Placenta, Prostate, Testis, Fetal Kidney, Fetal Spleen, Fetal Thymus; all from BD Clontech) and 5 cell lines (GM06990, HeLaS3, HepG2, K562, tert-BJ) using the BD SMARTTM RACE cDNA amplification kit (BD Clontech Cat. No.634914). A single array with no replicates was run for each sample with a pool of ~23-24 RACE reactions per sample.

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Transcriptional termini of genes on chromosomes 21-22 (RACE mapping)

Project description:The purpose of these experiments was to determine the 5' and 3' transcriptional termini of genes on chromosomes 21-22. Towards this end, we first carried out 5’ and 3’ RACE reactions from 1193 exons from 492 genes in these chromosomes using RNA isolated from 11 normal tissues and 5 cell lines. An average of 3 to 4 RACE reactions (5’ and 3’) was carried out from each gene. The products of the RACE reactions were analyzed by hybridization to tiling arrays interrogating the non-repeat portions of these chromosomes at 17 nucleotide resolution. A total of 26,688 RACE reactions were performed and pooled to be placed on to 1020 tiling arrays For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

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High-throughput pyrosequencing of forum domains termini (FT) isolated and amplified from human HEK293T cells

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High-throughput pyrosequencing of forum domains termini (FT) isolated and amplified from human HEK293T cells

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eIF3 Engages with 3’-UTR Termini of Highly Translated mRNAs in Neural Progenitor Cells [APA-Seq]

Project description:Stem cell differentiation involves a global increase in protein synthesis to meet the demands of specialized cell types. However, the molecular mechanisms underlying this translational burst and the involvement of initiation factors remains largely unknown. Here, we investigate the roles of eukaryotic initiation factor 3 (eIF3) in early differentiation of human pluripotent stem cell (hPSC)-derived neural progenitor cells (NPCs). Using Quick-irCLIP and alternative polyadenylation (APA)-Seq, we show eIF3 crosslinks to many neurologically relevant mRNAs in NPCs. Our data reveal eIF3 predominantly interacts with 3’ untranslated region (3’-UTR) termini of multiple mRNA isoforms, adjacent to the poly(A) tail. High eIF3 crosslinking at 3’-UTR termini of mRNAs correlates with high translational activity, as determined by ribosome profiling. We identify the transcriptional regulator inhibitor of DNA binding 2 (ID2) mRNA as a case in which active translation levels and eIF3 crosslinking are dramatically increased upon early NPC differentiation. Furthermore, we find that eIF3 engagement at 3’-UTR ends is dependent on polyadenylation. The results presented here show that eIF3 engages with 3’-UTR termini in highly translated mRNAs, supporting a role of mRNA circularization in the mechanisms governing mRNA translation in NPCs.

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