Systematic Identification and Characterization of Long Non-Coding RNAs in the Silkworm, Bombyx mori

PloS One
Yuqian WuQingyou Xia

Abstract

Long noncoding RNAs (lncRNAs) are emerging as important regulators in various biological processes. However, to date, no systematic characterization of lncRNAs has been reported in the silkworm Bombyx mori. In the present study, we generated eighteen RNA-seq datasets with relatively high depth. Using an in-house designed lncRNA identification pipeline, 11,810 lncRNAs were identified for 5,556 loci. Among these lncRNAs, 474 transcripts were intronic lncRNAs (ilncRNAs), 6,250 transcripts were intergenic lncRNAs (lincRNAs), and 5,086 were natural antisense lncRNAs (lncNATs). Compared with protein-coding mRNAs, silkworm lncRNAs are shorter in terms of full length but longer in terms of exon and intron length. In addition, lncRNAs exhibit a lower level of sequence conservation, more repeat sequences overlapped and higher tissue specificity than protein-coding mRNAs in the silkworm. We found that 69 lncRNA transcripts from 33 gene loci may function as miRNA precursors, and 104 lncRNA transcripts from 72 gene loci may act as competing endogenous RNAs (ceRNAs). In total, 49.47% of all gene loci (2,749/5,556) for which lncRNAs were identified showed sex-biased expression. Co-expression network analysis resulted in 19 modules, 12 of whic...Continue Reading

References

Feb 22, 2005·PLoS Biology·Julius BrenneckeStephen M Cohen
Dec 17, 2005·Genes & Development·Matthew RonshaugenEric C Lai
Aug 8, 2006·Trends in Biochemical Sciences·Xinxian Deng, Victoria H Meller
Jan 24, 2007·RNA·Xuezhong Cai, Bryan R Cullen
May 19, 2007·Science·Philipp KapranovThomas R Gingeras
Sep 26, 2007·Nature Genetics·Michael KerteszEran Segal
Dec 31, 2008·BMC Bioinformatics·Peter Langfelder, Steve Horvath
Feb 26, 2009·Cell·Chris P PontingWolf Reik
Jul 22, 2009·Developmental Cell·Nicola IovinoUlrike Gaul
Oct 2, 2009·Nucleic Acids Research·Jun DuanQingyou Xia
Feb 6, 2010·Genome Biology·Matthew D YoungAlicia Oshlack
Mar 5, 2010·BMC Genomics·Shiping LiuQingyou Xia
Jul 27, 2010·Molecular Biology and Evolution·Laura C FergusonChris D Jiggins
Nov 17, 2010·Insect Biochemistry and Molecular Biology·Corinne RoyerPierre Couble
Dec 15, 2010·Bioinformatics·Michael E SmootTrey Ideker
Jul 22, 2011·Genetics·Alexey A SoshnevPamela K Geyer
Oct 25, 2011·RNA·Shinpei KawaokaSusumu Katsuma
Nov 24, 2011·Genome Research·Andrea PauliAlexander F Schier
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
Mar 10, 2012·Genome Biology and Evolution·Robert S YoungChris P Ponting
Oct 18, 2012·Nucleic Acids Research·Meixia LiRunsheng Chen

❮ Previous
Next ❯

Citations

Oct 5, 2018·Annual Review of Entomology·Karl M GlastadMichael A D Goodisman
Apr 19, 2017·Journal of the European Academy of Dermatology and Venereology : JEADV·L BaoY Li
Nov 2, 2019·Archives of Insect Biochemistry and Physiology·Ruobing GuanShiheng An
Sep 15, 2016·BMC Bioinformatics·Qiu-Zhong ZhouZe Zhang
Apr 17, 2018·Non-coding RNA·Federico GaitiBernard M Degnan
May 3, 2019·Wiley Interdisciplinary Reviews. RNA·Luis María Vaschetto, Hernán Mario Beccacece
Apr 17, 2018·Non-coding RNA·Valluri SatyavathiSrividya Subramanian
Apr 9, 2019·International Journal of Genomics·Tieshan FengTingcai Cheng
Nov 15, 2019·Cellular and Molecular Life Sciences : CMLS·Jiasheng Song, Shutang Zhou
Nov 13, 2018·Archives of Insect Biochemistry and Physiology·Rui-Ting ChenYun-Gen Miao
Jul 1, 2020·Frontiers in Cell and Developmental Biology·Sufang ZhangZhang Zhen
Jan 31, 2019·Scientific Reports·Yujiao ChenYaozhou Zhang
Apr 5, 2018·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Shenglong LiKazuei Mita
Feb 24, 2021·Archives of Insect Biochemistry and Physiology·Zhendong ZhangXijie Guo
Feb 27, 2021·Scientific Reports·Fatemeh SalabiAyeh Sadat Sadr
Mar 4, 2021·Animals : an Open Access Journal From MDPI·Dongdong BoYuqing Chong
Mar 7, 2021·Insects·Elise J FarleyMichelle M Riehle
May 1, 2021·Animals : an Open Access Journal From MDPI·Chhavi ChoudharyJayendra Nath Shukla

❮ Previous
Next ❯

Datasets Mentioned

BETA
PRJNA284192
DRA001104
PRJNA215013
PRJNA238971

Methods Mentioned

BETA
RNA-seq

Software Mentioned

R package
Cufflinks
DEGseq
miRanda
ENSEMBL
Cuffmerge
StringTie
RNAhybrid
CummeRbund R package
WGCNA

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.