Analysis of alternative cleavage and polyadenylation in mature and differentiating neurons using RNA-seq data

Quantitative Biology
Aysegul Guvenek, Bin Tian

Abstract

Most eukaryotic protein-coding genes exhibit alternative cleavage and polyadenylation (APA), resulting in mRNA isoforms with different 3' untranslated regions (3' UTRs). Studies have shown that brain cells tend to express long 3' UTR isoforms using distal cleavage and polyadenylation sites (PASs). Using our recently developed, comprehensive PAS database PolyA_DB, we developed an efficient method to examine APA, named Significance Analysis of Alternative Polyadenylation using RNA-seq (SAAP-RS). We applied this method to study APA in brain cells and neurogenesis. We found that neurons globally express longer 3' UTRs than other cell types in brain, and microglia and endothelial cells express substantially shorter 3' UTRs. We show that the 3' UTR diversity across brain cells can be corroborated with single cell sequencing data. Further analysis of APA regulation of 3' UTRs during differentiation of embryonic stem cells into neurons indicates that a large fraction of the APA events regulated in neurogenesis are similarly modulated in myogenesis, but to a much greater extent. Together, our data delineate APA profiles in different brain cells and indicate that APA regulation in neurogenesis is largely an augmented process taking place...Continue Reading

References

Dec 17, 2005·Genome Biology·Haibo ZhangBin Tian
Nov 4, 2008·Nature·Eric T WangChristopher B Burge
Apr 18, 2009·Proceedings of the National Academy of Sciences of the United States of America·Zhe JiBin Tian
May 14, 2009·Nature Reviews. Molecular Cell Biology·Daniela Rotin, Sharad Kumar
Jul 17, 2009·Genes & Development·Nader ChalhoubSuzanne J Baker
Sep 1, 2009·Trends in Cell Biology·Catia Andreassi, Antonella Riccio
Nov 18, 2009·Molecular Cell·Sheng GaoJoan Massagué
Aug 25, 2010·Proceedings of the National Academy of Sciences of the United States of America·Anthony G LauYue Feng
Oct 29, 2010·Genome Biology·Simon Anders, Wolfgang Huber
Nov 9, 2010·Nature Methods·Yarden KatzChristopher B Burge
Feb 1, 2011·Wiley Interdisciplinary Reviews. RNA·Carol S Lutz, Alexandra Moreira
Feb 19, 2011·Molecular Cell·Takashi NagaikeJames L Manley
Sep 8, 2011·Proceedings of the National Academy of Sciences of the United States of America·Valérie HilgersBenjamin Haley
Sep 29, 2011·Molecular Systems Biology·Zhe JiBin Tian
Oct 1, 2011·Wiley Interdisciplinary Reviews. RNA·Carol S Lutz, Alexandra Moreira
Oct 21, 2011·Wiley Interdisciplinary Reviews. RNA·Bin Tian, Joel H Graber
Dec 20, 2011·Nature Genetics·Vijay K TiwariChristian Beisel
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
Mar 29, 2012·Genome Research·Adnan DertiTomas Babak
Jun 23, 2012·Genome Research·Simon AndersWolfgang Huber
Oct 30, 2012·Bioinformatics·Alexander DobinThomas R Gingeras
Feb 23, 2013·Genes & Development·Kihoon HanHuda Y Zoghbi
Mar 23, 2013·Genome Research·Pedro MiuraEric C Lai
Sep 5, 2014·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Ye ZhangJian Qian Wu
Oct 11, 2014·Nature Communications·Xiaoyu MaHuafeng Zhang
Nov 19, 2014·Molecular Systems Biology·Volker BusskampGeorge M Church
Dec 30, 2014·Molecular Cell·Katarzyna OktabaValérie Hilgers
Apr 23, 2015·Methods : a Companion to Methods in Enzymology·MinHyeok KimJin-Wu Nam
May 3, 2015·Genes & Development·Yongsheng Shi, James L Manley
Nov 26, 2015·Trends in Cell Biology·Christine Mayr

❮ Previous
Next ❯

Citations

Oct 6, 2019·Nucleic Acids Research·Wei HongLeng Han
Sep 29, 2020·Nucleic Acids Research·Weiwei JinJing Gong
May 16, 2020·International Journal of Molecular Sciences·Bongmin Bae, Pedro Miura
May 10, 2020·Computational and Structural Biotechnology Journal·Congting YeQingshun Q Li
Jan 2, 2021·Trends in Molecular Medicine·Kaitlin WeskampRoy Parker
May 15, 2021·Trends in Molecular Medicine·Pia SommerkampAndreas Trumpp
Jun 3, 2021·International Journal of Molecular Sciences·Nitika KandhariTraude H Beilharz
Aug 12, 2021·Journal of Cellular Physiology·Prakash DharmalingamRajarajan A Thandavarayan

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.