Transcriptome Analyses of β-Thalassemia -28(A>G) Mutation Using Isogenic Cell Models Generated by CRISPR/Cas9 and Asymmetric Single-Stranded Oligodeoxynucleotides (assODNs)

Frontiers in Genetics
Jing LiYing Gu

Abstract

β-thalassemia, caused by mutations in the human hemoglobin β (HBB) gene, is one of the most common genetic diseases in the world. The HBB -28(A>G) mutation is one of the five most common mutations in Chinese patients with β-thalassemia. However, few studies have been conducted to understand how this mutation affects the expression of pathogenesis-related genes, including globin genes, due to limited homozygote clinical materials. Therefore, we developed an efficient technique using CRISPR/Cas9 combined with asymmetric single-stranded oligodeoxynucleotides (assODNs) to generate a K562 cell model with HBB -28(A>G) named K562-28(A>G). Then, we systematically analyzed the differences between K562-28(A>G) and K562 at the transcriptome level by high-throughput RNA-seq before and after erythroid differentiation. We found that the HBB -28(A>G) mutation not only disturbed the transcription of HBB, but also decreased the expression of HBG, which may further aggravate the thalassemia phenotype and partially explain the more severe clinical outcome of β-thalassemia patients with the HBB -28(A>G) mutation. Moreover, we found that the K562-28(A>G) cell line is more sensitive to hypoxia and shows a defective erythrogenic program compared with...Continue Reading

References

Jul 25, 1983·Nucleic Acids Research·S H OrkinH H Kazazian
Sep 1, 1983·Proceedings of the National Academy of Sciences of the United States of America·A DeanA N Schechter
Dec 11, 1999·Nucleic Acids Research·M Kanehisa, S Goto
Dec 6, 2002·The American Journal of Pathology·Connie MyersNancy Boudreau
Jul 15, 2003·Proceedings of the National Academy of Sciences of the United States of America·Jeffrey A GrassEmery H Bresnick
Feb 26, 2005·Experimental Hematology·George Stamatoyannopoulos
Feb 20, 2008·Advances in Genetics·Robert-Jan PalstraFrank Grosveld
Jan 21, 2009·Blood Cells, Molecules & Diseases·Zhiyi ChenDavid H K Chui
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Jan 26, 2010·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Antonio Cao, Renzo Galanello
Jan 30, 2010·Bioinformatics·Aaron R Quinlan, Ira M Hall
Mar 6, 2010·British Journal of Haematology·Vijay G SankaranStuart H Orkin
Mar 12, 2010·Leukemia & Lymphoma·Hana Bruchova-VotavovaJosef T Prchal
May 25, 2010·Orphanet Journal of Rare Diseases·Renzo Galanello, Raffaella Origa
Aug 3, 2010·Nature Genetics·Dewang ZhouTim M Townes
Nov 16, 2010·Hematology/oncology Clinics of North America·D J WeatherallA O'Donnell
Jan 12, 2011·Nature Biotechnology·James T RobinsonJill P Mesirov
May 7, 2011·Bioinformatics·Arthur LiberzonJill P Mesirov
Mar 30, 2012·Omics : a Journal of Integrative Biology·Guangchuang YuQing-Yu He
Jun 8, 2013·Molecular and Cellular Biochemistry·Yan-Ni MaJun-Wu Zhang
Oct 26, 2013·Nature Protocols·F Ann RanFeng Zhang
Jul 25, 2014·PLoS Computational Biology·Rekin's JankyStein Aerts
Feb 19, 2015·Nature Biotechnology·Mihaela PerteaSteven L Salzberg
Mar 10, 2015·Nature Methods·Daehwan KimSteven L Salzberg
Mar 30, 2016·Human Gene Therapy·Jorge Mansilla-SotoMichel Sadelain
Apr 15, 2016·Biotechnology Letters·Laleh ShariatiMohammad Hossein Modarressi
Apr 24, 2016·Biomedical Journal·Edouard de DreuzyEmmanuel Payen
Jun 4, 2016·Molecular Therapy. Methods & Clinical Development·Sandeep Rp KumarRoland W Herzog
Oct 14, 2016·Science Translational Medicine·Mark A DeWittJacob E Corn
Nov 5, 2016·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Raffaella Origa
May 24, 2017·Science China. Life Sciences·Xiaohui ZhangDali Li
May 24, 2017·Science China. Life Sciences·Ke MenYuquan Wei
Aug 5, 2017·Lancet·Ali T TaherMaria Domenica Cappellini
Sep 25, 2017·Protein & Cell·Puping LiangJunjiu Huang
Jan 24, 2018·Proceedings of the National Academy of Sciences of the United States of America·Arnab GhoshDennis J Stuehr

❮ Previous
Next ❯

Methods Mentioned

BETA
RNA-seq
ELISA
Transfection
flow cytometry
PCR
Profiler

Software Mentioned

StringTie
Bed Tools
Biotek
DAVID
Cytoscape
UCSC
SOAPnuke
cluster Profiler R package
Samtools
EdgeR Bioconductor

Related Concepts

Related Feeds

CRISPR (general)

Clustered regularly interspaced short palindromic repeats (CRISPR) are DNA sequences in the genome that are recognized and cleaved by CRISPR-associated proteins (Cas). CRISPR-Cas system enables the editing of genes to create or correct mutations. Discover the latest research on CRISPR here.

CRISPR for Genome Editing

Genome editing technologies enable the editing of genes to create or correct mutations. Clustered regularly interspaced short palindromic repeats (CRISPR) are DNA sequences in the genome that are recognized and cleaved by CRISPR-associated proteins (Cas). Here is the latest research on the use of CRISPR-Cas system in gene editing.