Genome-wide identification and characterization of circular RNA m6A modification in pancreatic cancer

Abstract Background N 6-methyladenosine (m6A) is the most abundant modification of RNA in eukaryotic cells and play critical roles in cancer. While most related studies focus on m6A modifications in linear RNA, transcriptome-wide profiling and exploration of m6A modification in circular RNAs in canc...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Ying Ye, Weiyi Feng, Jialiang Zhang, Kaiyu Zhu, Xudong Huang, Ling Pan, Jiachun Su, Yanfen Zheng, Rui Li, Shuang Deng, Ruihong Bai, Lisha Zhuang, Lusheng Wei, Junge Deng, Mei Li, Rufu Chen, Dongxin Lin, Zhixiang Zuo, Jian Zheng
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	m6A modification Circular RNA m6A-seq Pancreatic cancer Medicine R Genetics QH426-470
Acceso en línea:	https://doaj.org/article/e3222aaaf0e645849a02605f06969dc8
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:e3222aaaf0e645849a02605f06969dc8
record_format	dspace
spelling	oai:doaj.org-article:e3222aaaf0e645849a02605f06969dc82021-11-21T12:27:13ZGenome-wide identification and characterization of circular RNA m6A modification in pancreatic cancer10.1186/s13073-021-01002-w1756-994Xhttps://doaj.org/article/e3222aaaf0e645849a02605f06969dc82021-11-01T00:00:00Zhttps://doi.org/10.1186/s13073-021-01002-whttps://doaj.org/toc/1756-994XAbstract Background N 6-methyladenosine (m6A) is the most abundant modification of RNA in eukaryotic cells and play critical roles in cancer. While most related studies focus on m6A modifications in linear RNA, transcriptome-wide profiling and exploration of m6A modification in circular RNAs in cancer is still lacking. Methods For the detection of m6A modification in circRNAs, we developed a new bioinformatics tools called Circm6A and applied it to the m6A-seq data of 77 tissue samples from 58 individuals with pancreatic ductal adenocarcinoma (PDAC). Results Circm6A performs better than the existing circRNA identification tools, which achieved highest F1 score among these tools in the detection of circRNAs with m6A modifications. By using Circm6A, we identified a total of 8807 m6A-circRNAs from our m6A-seq data. The m6A-circRNAs tend to be hypermethylated in PDAC tumor tissues compared with normal tissues. The hypermethylated m6A-circRNAs were associated with a significant gain of circRNA-mRNA coexpression network, leading to the dysregulation of many important cancer-related pathways. Moreover, we found the cues that hypermethylated m6A-circRNAs may promote the circularization and translation of circRNAs. Conclusions These comprehensive findings further bridged the knowledge gaps between m6A modification and circRNAs fields by depicting the m6A-circRNAs genomic landscape of PDAC patients and revealed the emerging roles played by m6A-circRNAs in pancreatic cancer. Circm6A is available at https://github.com/canceromics/circm6a .Ying YeWeiyi FengJialiang ZhangKaiyu ZhuXudong HuangLing PanJiachun SuYanfen ZhengRui LiShuang DengRuihong BaiLisha ZhuangLusheng WeiJunge DengMei LiRufu ChenDongxin LinZhixiang ZuoJian ZhengBMCarticlem6A modificationCircular RNAm6A-seqPancreatic cancerMedicineRGeneticsQH426-470ENGenome Medicine, Vol 13, Iss 1, Pp 1-19 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	m6A modification Circular RNA m6A-seq Pancreatic cancer Medicine R Genetics QH426-470
spellingShingle	m6A modification Circular RNA m6A-seq Pancreatic cancer Medicine R Genetics QH426-470 Ying Ye Weiyi Feng Jialiang Zhang Kaiyu Zhu Xudong Huang Ling Pan Jiachun Su Yanfen Zheng Rui Li Shuang Deng Ruihong Bai Lisha Zhuang Lusheng Wei Junge Deng Mei Li Rufu Chen Dongxin Lin Zhixiang Zuo Jian Zheng Genome-wide identification and characterization of circular RNA m6A modification in pancreatic cancer
description	Abstract Background N 6-methyladenosine (m6A) is the most abundant modification of RNA in eukaryotic cells and play critical roles in cancer. While most related studies focus on m6A modifications in linear RNA, transcriptome-wide profiling and exploration of m6A modification in circular RNAs in cancer is still lacking. Methods For the detection of m6A modification in circRNAs, we developed a new bioinformatics tools called Circm6A and applied it to the m6A-seq data of 77 tissue samples from 58 individuals with pancreatic ductal adenocarcinoma (PDAC). Results Circm6A performs better than the existing circRNA identification tools, which achieved highest F1 score among these tools in the detection of circRNAs with m6A modifications. By using Circm6A, we identified a total of 8807 m6A-circRNAs from our m6A-seq data. The m6A-circRNAs tend to be hypermethylated in PDAC tumor tissues compared with normal tissues. The hypermethylated m6A-circRNAs were associated with a significant gain of circRNA-mRNA coexpression network, leading to the dysregulation of many important cancer-related pathways. Moreover, we found the cues that hypermethylated m6A-circRNAs may promote the circularization and translation of circRNAs. Conclusions These comprehensive findings further bridged the knowledge gaps between m6A modification and circRNAs fields by depicting the m6A-circRNAs genomic landscape of PDAC patients and revealed the emerging roles played by m6A-circRNAs in pancreatic cancer. Circm6A is available at https://github.com/canceromics/circm6a .
format	article
author	Ying Ye Weiyi Feng Jialiang Zhang Kaiyu Zhu Xudong Huang Ling Pan Jiachun Su Yanfen Zheng Rui Li Shuang Deng Ruihong Bai Lisha Zhuang Lusheng Wei Junge Deng Mei Li Rufu Chen Dongxin Lin Zhixiang Zuo Jian Zheng
author_facet	Ying Ye Weiyi Feng Jialiang Zhang Kaiyu Zhu Xudong Huang Ling Pan Jiachun Su Yanfen Zheng Rui Li Shuang Deng Ruihong Bai Lisha Zhuang Lusheng Wei Junge Deng Mei Li Rufu Chen Dongxin Lin Zhixiang Zuo Jian Zheng
author_sort	Ying Ye
title	Genome-wide identification and characterization of circular RNA m6A modification in pancreatic cancer
title_short	Genome-wide identification and characterization of circular RNA m6A modification in pancreatic cancer
title_full	Genome-wide identification and characterization of circular RNA m6A modification in pancreatic cancer
title_fullStr	Genome-wide identification and characterization of circular RNA m6A modification in pancreatic cancer
title_full_unstemmed	Genome-wide identification and characterization of circular RNA m6A modification in pancreatic cancer
title_sort	genome-wide identification and characterization of circular rna m6a modification in pancreatic cancer
publisher	BMC
publishDate	2021
url	https://doaj.org/article/e3222aaaf0e645849a02605f06969dc8
work_keys_str_mv	AT yingye genomewideidentificationandcharacterizationofcircularrnam6amodificationinpancreaticcancer AT weiyifeng genomewideidentificationandcharacterizationofcircularrnam6amodificationinpancreaticcancer AT jialiangzhang genomewideidentificationandcharacterizationofcircularrnam6amodificationinpancreaticcancer AT kaiyuzhu genomewideidentificationandcharacterizationofcircularrnam6amodificationinpancreaticcancer AT xudonghuang genomewideidentificationandcharacterizationofcircularrnam6amodificationinpancreaticcancer AT lingpan genomewideidentificationandcharacterizationofcircularrnam6amodificationinpancreaticcancer AT jiachunsu genomewideidentificationandcharacterizationofcircularrnam6amodificationinpancreaticcancer AT yanfenzheng genomewideidentificationandcharacterizationofcircularrnam6amodificationinpancreaticcancer AT ruili genomewideidentificationandcharacterizationofcircularrnam6amodificationinpancreaticcancer AT shuangdeng genomewideidentificationandcharacterizationofcircularrnam6amodificationinpancreaticcancer AT ruihongbai genomewideidentificationandcharacterizationofcircularrnam6amodificationinpancreaticcancer AT lishazhuang genomewideidentificationandcharacterizationofcircularrnam6amodificationinpancreaticcancer AT lushengwei genomewideidentificationandcharacterizationofcircularrnam6amodificationinpancreaticcancer AT jungedeng genomewideidentificationandcharacterizationofcircularrnam6amodificationinpancreaticcancer AT meili genomewideidentificationandcharacterizationofcircularrnam6amodificationinpancreaticcancer AT rufuchen genomewideidentificationandcharacterizationofcircularrnam6amodificationinpancreaticcancer AT dongxinlin genomewideidentificationandcharacterizationofcircularrnam6amodificationinpancreaticcancer AT zhixiangzuo genomewideidentificationandcharacterizationofcircularrnam6amodificationinpancreaticcancer AT jianzheng genomewideidentificationandcharacterizationofcircularrnam6amodificationinpancreaticcancer
_version_	1718419037362323456

Genome-wide identification and characterization of circular RNA m6A modification in pancreatic cancer

Ejemplares similares