scholarly journals Atlas of Subcellular RNA Localization Revealed by APEX-seq

2018 ◽  
Author(s):  
Furqan M. Fazal ◽  
Shuo Han ◽  
Pornchai Kaewsapsak ◽  
Kevin R. Parker ◽  
Jin Xu ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Messenger Rna ◽  
Rna Localization ◽  
Spatial Proximity ◽  
Nuclear Pore ◽  
Transcript Isoforms ◽  
Human Transcriptome ◽  
Inner Surface ◽  
Peroxidase Enzyme ◽  
Radial Organization

SUMMARYWe introduce APEX-seq, a method for RNA sequencing based on spatial proximity to the peroxidase enzyme APEX2. APEX-seq in nine distinct subcellular locales produced a nanometer-resolution spatial map of the human transcriptome, revealing extensive and exquisite patterns of localization for diverse RNA classes and transcript isoforms. We uncover a radial organization of the nuclear transcriptome, which is gated at the inner surface of the nuclear pore for cytoplasmic export of processed transcripts. We identify two distinct pathways of messenger RNA localization to mitochondria, each associated with specific sets of transcripts for building complementary macromolecular machines within the organelle. APEX-seq should be widely applicable to many systems, enabling comprehensive investigations of the spatial transcriptome.

scholarly journals APEX-seq: RNA subcellular localization by proximity labeling

2019 ◽  
Author(s):  
Furqan M. Fazal ◽  
Shuo Han ◽  
Kevin R. Parker ◽  
Pornchai Kaewsapsak ◽  
Jin Xu ◽  
...  
Keyword(s):  
Subcellular Localization ◽  
Rna Sequencing ◽  
Nanometer Resolution ◽  
Transcript Isoforms ◽  
Human Transcriptome ◽  
Peroxidase Enzyme

Abstract We introduce APEX‑seq, a method for RNA sequencing based on direct proximity labeling of RNA using the peroxidase enzyme APEX2. APEX‑seq in nine distinct subcellular locales produced a nanometer-resolution spatial map of the human transcriptome as a resource, revealing extensive and exquisite patterns of localization for diverse RNA classes and transcript isoforms. APEX‑seq should be widely applicable to many systems, enabling comprehensive investigations of the spatial transcriptome.

scholarly journals Single molecule real time (SMRT) full length RNA-sequencing reveals novel and distinct mRNA isoforms in human bone marrow cell subpopulations

2019 ◽  
Author(s):  
Anne Deslattes Mays ◽  
Marcel O. Schmidt ◽  
Garrett T. Graham ◽  
Elizabeth Tseng ◽  
Primo Baybayan ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Real Time ◽  
Rna Sequencing ◽  
Single Molecule ◽  
Marrow Cell ◽  
Full Length ◽  
Protein Isoforms ◽  
Mrna Isoforms ◽  
Transcript Isoforms ◽  
Cell Subpopulations

AbstractHematopoietic cells are continuously replenished from progenitor cells that reside in the bone marrow. To evaluate molecular changes during this process, we analyzed the transcriptomes of freshly harvested human bone marrow progenitor (lineage-negative) and differentiated (lineage-positive) cells by single molecule, real time (SMRT) full length RNA sequencing. This analysis revealed a ∼5-fold higher number of transcript isoforms than previously detected and showed a distinct composition of individual transcript isoforms characteristic for bone marrow subpopulations. A detailed analysis of mRNA isoforms transcribed from the ANXA1 and EEF1A1 loci confirmed their distinct composition. The expression of proteins predicted from the transcriptome analysis was validated by mass spectrometry and validated previously unknown protein isoforms predicted e.g. for EEF1A1. These protein isoforms distinguished the lineage negative cell population from the lineage positive cell population. Finally, transcript isoforms expressed from paralogous gene loci (e.g. CFD, GATA2, HLA-A, B & C) also distinguished cell subpopulations but were only detectable by full length RNA sequencing. Thus, qualitatively distinct transcript isoforms from individual genomic loci separate bone marrow cell subpopulations indicating complex transcriptional regulation and protein isoform generation during hematopoiesis.

scholarly journals Targeted RNA sequencing reveals the deep complexity of the human transcriptome

2011 ◽  
Vol 30 (1) ◽  
pp. 99-104 ◽  
Author(s):  
Tim R Mercer ◽  
Daniel J Gerhardt ◽  
Marcel E Dinger ◽  
Joanna Crawford ◽  
Cole Trapnell ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Human Transcriptome

Survival-Associated Alternative Messenger RNA Splicing Signatures in Pancreatic Ductal Adenocarcinoma: A Study Based on RNA-Sequencing Data

2019 ◽  
Vol 38 (11) ◽  
pp. 1207-1222
Author(s):  
Yu-Jie Zhou ◽  
Gui-Qi Zhu ◽  
Qing-Wei Zhang ◽  
Kenneth I. Zheng ◽  
Jin-Nan Chen ◽  
...  
Keyword(s):  
Pancreatic Ductal Adenocarcinoma ◽  
Rna Sequencing ◽  
Rna Splicing ◽  
Messenger Rna ◽  
Ductal Adenocarcinoma ◽  
Sequencing Data

scholarly journals Swan: a library for the analysis and visualization of long-read transcriptomes

2020 ◽  
Author(s):  
Fairlie Reese ◽  
Ali Mortazavi
Keyword(s):  
Rna Sequencing ◽  
Cell Lines ◽  
Intron Retention ◽  
Exon Skipping ◽  
Differentially Expressed ◽  
Transcript Isoforms ◽  
Sequencing Technologies ◽  
Oxford Nanopore ◽  
Long Read

Abstract Motivation Long-read RNA-sequencing technologies such as PacBio and Oxford Nanopore have discovered an explosion of new transcript isoforms that are difficult to visually analyze using currently available tools. We introduce the Swan Python library, which is designed to analyze and visualize transcript models. Results Swan finds 4909 differentially expressed transcripts between cell lines HepG2 and HFFc6, including 279 that are differentially expressed even though the parent gene is not. Additionally, Swan discovers 285 reproducible exon skipping and 47 intron retention events not recorded in the GENCODE v29 annotation. Availability and implementation The Swan library for Python 3 is available on PyPi at https://pypi.org/project/swan-vis/ and on GitHub at https://github.com/mortazavilab/swan_vis.

Single-cell messenger RNA sequencing reveals rare intestinal cell types

Nature ◽  
2015 ◽  
Vol 525 (7568) ◽  
pp. 251-255 ◽  
Author(s):  
Dominic Grün ◽  
Anna Lyubimova ◽  
Lennart Kester ◽  
Kay Wiebrands ◽  
Onur Basak ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Messenger Rna ◽  
Cell Types ◽  
Intestinal Cell

scholarly journals A conditional allele of the novel repeat-containing yeast nucleoporin RAT7/NUP159 causes both rapid cessation of mRNA export and reversible clustering of nuclear pore complexes.

1995 ◽  
Vol 129 (4) ◽  
pp. 939-955 ◽  
Author(s):  
L C Gorsch ◽  
T C Dockendorff ◽  
C N Cole
Keyword(s):  
Messenger Rna ◽  
Mrna Export ◽  
Temperature Shift ◽  
Nucleocytoplasmic Transport ◽  
Nuclear Pore ◽  
Temperature Sensitive ◽  
Nuclear Pore Complexes ◽  
Reporter Protein ◽  
Direct Role ◽  
Pore Complexes

In a screen for Saccharomyces cerevisiae genes required for nucleocytoplasmic transport of messenger RNA, we identified the RAT7 gene (ribonucleic acid trafficking), which encodes an essential protein of 1,460 amino acids. Rat7p is located at the nuclear rim in a punctate pattern characteristic of nucleoporins. Furthermore, the central third of Rat7p contains 22 XXFG and three XFXFG degenerate repeats that are similar to signature GLFG and XFXFG repeats present in a majority of yeast and some mammalian nucleoporins sequenced to date. Shift of a strain bearing the temperature-sensitive rat7-1 allele from 23 degrees C to 37 degrees C resulted in rapid (within 15 minutes) cessation of mRNA export, but did not cause concomitant cytoplasmic accumulation of a reporter protein bearing a nuclear localization signal. This suggests that Rat7p may play a direct role in nucleocytoplasmic export of RNA. Immunofluorescence and thin section electron microscopy revealed that in rat7-1 cells grown at 23 degrees C, the majority of nuclear pore complexes (NPCs) were clustered on one side of the nucleus. No ultrastructural abnormalities of the nuclear envelope were seen. Interestingly, shifting rat7-1 cells to 37 degrees C for 1 h caused the NPCs to disperse, restoring near wild-type NPC distribution. After this temperature shift, the mutant Rat7p was no longer detectable by immunofluorescence.

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