miRNA-mRNA network involved in folliculogenesis interactome: systems biology approach

被引:17
作者
Bahrami, Abolfazl [1 ]
Miraie-Ashtiani, Seyed Reza [1 ]
Sadeghi, Mostafa [1 ]
Najafi, Ali [2 ]
机构
[1] Univ Tehran, Univ Coll Agr & Nat Resources, Dept Anim Sci, Karaj, Iran
[2] Baqiyatallah Univ Med Sci, Mol Biol Res Ctr, Tehran, Iran
关键词
BOVINE GRANULOSA-CELLS; GENE-EXPRESSION; FOLLICLE DEVELOPMENT; DOMINANT FOLLICLE; OVARIAN-FOLLICLES; MICRORNA; GROWTH; DIFFERENTIATION; INHIBITION; SELECTION;
D O I
10.1530/REP-17-0049
中图分类号
Q [生物科学];
学科分类号
07 ; 0710 ; 09 ;
摘要
At later phases of folliculogenesis, the mammalian ovarian follicle contains layers of granulosa cells surrounding an antral cavity. To better understand the molecular basis of follicular growth and granulosa cell maturation, we study transcriptome profiling of granulosa cells from small (<5 mm) and large(>10 mm) bovine follicles using simultaneous method of Affymetrix microarrays (24,128 probe sets) and RNA-Seq data sets. This study proposes a computational method to discover the functional miRNA-mRNA regulatory modules, that is, groups of miRNAs and their target mRNAs that are believed to take part cooperatively in posttranscriptional gene regulation under specific conditions. The reconstructed network was named Integrated miRNA-mRNA Bipartite Network. 277 genes and 6 key modules were disclosed through clustering for mRNA master list. The 66 genes are among the genes that belong to at least two modules. All these genes, being involved in at least one of the phenomena, namely cell survival, proliferation, metastasis and apoptosis, have an overexpression pattern (P <0.01). For miRNA master list, a total of 172 sequences were differentially expressed (P < 0.01) between dominant (large) and each of subordinate (small) follicles. Within the follicle, these miRNAs were predominantly expressed in mural granulosa cells. Finally, predicted and validated targets of these miRNAs enriched in dominant (large) follicles were identified, which are mapped to signaling pathways involved in follicular cell proliferation, steroidogenesis, PI3K/AKT/mTOR and Ras/Raf/MEK/ERK. The identification of miRNAs and their target mRNAs and the construction of their regulatory networks may give new insights into biological procedures.
引用
收藏
页码:51 / 65
页数:15
相关论文
共 64 条
[1]   Relationships of hormonal patterns and fertility to occurrence of two or three waves of ovarian follicles, before and after breeding, in beef cows and heifers [J].
Ahmad, N ;
Townsend, EC ;
Dailey, RA ;
Inskeep, EK .
ANIMAL REPRODUCTION SCIENCE, 1997, 49 (01) :13-28
[2]   Pathguide: a Pathway Resource List [J].
Bader, Gary D. ;
Cary, Michael P. ;
Sander, Chris .
NUCLEIC ACIDS RESEARCH, 2006, 34 :D504-D506
[3]   An automated method for finding molecular complexes in large protein interaction networks [J].
Bader, GD ;
Hogue, CW .
BMC BIOINFORMATICS, 2003, 4 (1)
[4]  
Bader GD, 2003, NUCLEIC ACIDS RES, V31, P248, DOI 10.1093/nar/gkg056
[5]   Altered Th17 Cytokine Expression in Helicobacter pylori Patients with TLR4 (D299G) Polymorphism [J].
Bagheri, Nader ;
Azadegan-Dehkordi, Fatemeh ;
Rahimian, Ghorbanali ;
Hashemzadeh-Chaleshtori, Morteza ;
Rafieian-Kopaei, Mahmoud ;
Kheiri, Soleyman ;
Gholipour, Abolfazl ;
Shirzad, Hedayatollah .
IMMUNOLOGICAL INVESTIGATIONS, 2016, 45 (02) :161-171
[6]  
Bao B, 1998, J ANIM SCI, V76, P1903
[7]   NCBI GEO: archive for functional genomics data sets-update [J].
Barrett, Tanya ;
Wilhite, Stephen E. ;
Ledoux, Pierre ;
Evangelista, Carlos ;
Kim, Irene F. ;
Tomashevsky, Maxim ;
Marshall, Kimberly A. ;
Phillippy, Katherine H. ;
Sherman, Patti M. ;
Holko, Michelle ;
Yefanov, Andrey ;
Lee, Hyeseung ;
Zhang, Naigong ;
Robertson, Cynthia L. ;
Serova, Nadezhda ;
Davis, Sean ;
Soboleva, Alexandra .
NUCLEIC ACIDS RESEARCH, 2013, 41 (D1) :D991-D995
[8]   MicroRNAs: Genomics, biogenesis, mechanism, and function (Reprinted from Cell, vol 116, pg 281-297, 2004) [J].
Bartel, David P. .
CELL, 2007, 131 (04) :11-29
[9]   Integrin beta-3 genetic variants and risk of venous thromboembolism in colorectal cancer patients [J].
Bianconi, Daniela ;
Schuler, Alexandra ;
Pausz, Clemens ;
Geroldinger, Angelika ;
Kaider, Alexandra ;
Lenz, Heinz-Josef ;
Kornek, Gabriela ;
Scheithauer, Werner ;
Zielinski, Christoph C. ;
Pabinger, Ingrid ;
Ay, Cihan ;
Prager, Gerald W. .
THROMBOSIS RESEARCH, 2015, 136 (05) :865-869
[10]   Trimmomatic: a flexible trimmer for Illumina sequence data [J].
Bolger, Anthony M. ;
Lohse, Marc ;
Usadel, Bjoern .
BIOINFORMATICS, 2014, 30 (15) :2114-2120