Binding of intronic miRNAs to the mRNAs of host genes encoding intronic miRNAs and proteins that participate in tumourigenesis

https://doi.org/10.1016/j.compbiomed.2013.07.011Get rights and content

Abstract

In this study, we examined 615 host genes encoding 915 in-miRNAs as possible targets for interactions with all in-miRNAs. Host genes whose proteins are involved in esophageal, gastric, small bowel, colorectal, and breast cancer development were studied. Unique in-miRNA binding sites with a significance of p<0.0005 were found in the 5′UTRs, CDSs, and 3′UTRs of the host genes encoding proteins that are key participants in tumourigenesis. These data shed light on the interactions between miRNAs and mRNAs and on the role of candidate proteins in cancer. Therefore, our findings have potential application in the development of diagnostic and treatment methods.

Introduction

MicroRNAs (miRNAs) are small noncoding RNAs with a length of approximately 22 nucleotides [1]. They are key post-transcriptional regulators of many physiological and pathological processes [2], including apoptosis [3], cell cycle, proliferation, development, etc. [4]. miRNAs are transcribed as primary microRNAs (pri-miRNAs) that vary in length from hundreds to tens of thousands of bases. Many pri-miRNAs contain sequences encoding several miRNAs. pri-miRNAs are shortened to precursor microRNAs (pre-miRNAs) with lengths of approximately 75 nucleotides pre-miRNAs are processed into mature miRNAs and then activated by the RNA-induced silencing complex (RISC) [5]. This action leads to the production of mature miRNAs. All miRNAs can be classified into two types: intergenic miRNAs (ig-miRNAs) and intragenic miRNAs (ing-miRNAs) [6]. ing-miRNAs are encoded within genes, which are referred to as host genes. The majority of ing-miRNAs are intronic miRNAs (in-miRNAs), which are encoded within intronic regions of host protein-coding genes. Some precursors of ing-miRNAs are encoded within the exonic regions (ex-miRNAs) of host non-protein-coding genes [6]. A small proportion of ing-miRNA genes are located in the 5'-untranslated regions (5′UTRs) and 3′-untranslated regions (3′UTRs). The MiRBase (http://mirbase.org/) database (db) includes a list of well-known transcripts that overlap with miRNAs and describe the overlap type (intron, exon, and UTR) [7]. Previous studies have shown that intragenic miRNAs present unique regulatory possibilities and are often coexpressed with their host genes [8], [9], [10], [11], [12], [13].

There are various types of binding sites between miRNAs and the mRNAs of the target genes (1) the canonical type, where a nucleotide sequence located in the 5' part of the miRNA (5'-seed) forms strict Watson–Crick pairs with the target [14]; (2) the 3'-compensatory type, where a 5'-seed has no complete complementary pairing and is compensated by high hybridization in the 3' part of the miRNA [15]; and (3) the complementary type, where all nucleotides of the miRNA and the target site of mRNA are perfectly complementary [16].

Previously, miRNA binding sites were predicted only in the 3′UTR of mRNA targets [17], [18], [19]. However, some investigators have reported on miRNAs that bind to the 5′-untranslated regions (5′UTRs) and coding sequences (CDSs) of mRNAs [20], [21], [22], [23], [24], [25]. The Kyoto Encyclopedia of Genes and Genomes (www.genome.jp/kegg/) pathway analysis has demonstrated different metabolic pathways where the mRNAs of host genes had targets associated with intragenic miRNAs [26]. Different miRNAs can have binding sites for a single gene or multiple genes. Any dysregulation of the miRNA–mRNA interactions may be the result of genetic diseases. Defects in miRNA regulation are associated with tumor development [27] in esophageal [28], gastric [29], [30], small bowel [31], [32], colorectal [33], [34], and breast [35], [36] cancer. Some miRNAs regulate apoptosis and cell proliferation and can act as oncogenes or tumor suppressors [36]. For example, miR-205 may act as a tumor suppressor by inhibiting the proliferation and invasion of tumor cells. On the other hand, miR-205 may act as an oncogene that facilitates tumor initiation. The choice of the pathway depends on the specific target genes and the cancer-specific circumstances [37].

Some miRNAs are potential biomarkers of cancer due to their remarkable stability in the blood and specific expression in different diseases. These miRNAs have different expression patterns in the sera of esophageal [38], gastric [39], colorectal [40], and breast cancer [41] patients than in observed for healthy controls. Several hundred miRNAs have been extensively studied over the last 10 years. It is important to study newfound miRNAs and to identify their target mRNAs with a high confidence for further investigation in experimental studies.

Section snippets

Materials and methods

The nucleotide sequences of 2042 miRNA were downloaded from the miRBase db (http://www.mirbase.org/). Of these 915 in-miRNAs were selected according to the “genome context” miRBase db. These miRNAs had lengths ranging from 16 to 27 nucleotides. Only 615 protein-coding host genes of in-miRNAs were selected, and their nucleotide sequences were obtained from GenBank (http://www.ncbi.nlm.nih.gov). The precursors were mRNAs shortened into the mature mRNA sequences by Lextractor_002_0020E3 script (//sites.google.com/site/malaheenee/software

Results

The presence of 915 in-miRNA binding sites was investigated within the 5′UTRs, CDSs, and 3′UTRs of 615 human host mRNAs (Supplementary Table 1). Supplementary Tables 1–4 are available on the following site: https://sites.google.com/site/malaheenee/articles. Of the 915 in-miRNAs, 322 generated 1751 binding sites located in 478 mRNAs (i.e., 260 sites in the 5′UTRs, 871 sites in the CDSs, and 620 sites in the 3′UTRs), while 137 mRNAs did not have any binding sites with a ΔG/ΔGm value greater than

Discussion

The role of host genes and their in-miRNAs in cancer in comparison with other genes and their proteins have not been thoroughly studied. Previous studies have not investigated the interactions between host genes. The specificity of interactions was studied between intragenic miRNAs and 54 mRNAs whose proteins play a role in carcinogenesis [42]. The interactions between 686 in-miRNAs and the mRNAs of 51 oncogenes encoding in-miRNAs were studied in comparison with exonic and intergenic miRNAs [43]

Conclusion

Possible marker in-miRNAs were revealed in silico that have binding sites in several mRNAs of protein-coding host genes that are key participants in esophageal, gastric, small bowel, colorectal, and breast cancer. These miRNA binding sites (p<0.0005) are located in the 5′UTRs, CDSs, and 3′UTRs of the target mRNAs. The self-regulation system inherent to host genes was demonstrated. The described in-miRNA binding sites should be confirmed experimentally. This study can be used to advance the

Conflict of interest statement

The authors have declared that no conflict of interests exist.

Acknowledgments

We thank V. Khailenko for the Lextractor_002_0020E3, E-RNAhybrid 2.1, and Net_builder_015-1 scripts. This study was supported by a Grant from the Ministry of Education and Science, Kazakhstan Republic.

Olga A. Berillo was born in Almaty, Kazakhstan (18.09.1987). Education 2011 – present: doctorate Ph.D. of al-Farabi Kazakh National University, specialty “Biotechnology”, Almaty, Kazakhstan. 2009–2011: Master of al-Farabi Kazakh National University, specialty “Biotechnology”, Almaty, Kazakhstan. 2005–2009: Bachelor of al-Farabi Kazakh National University, specialty “Biotechnology”, Almaty, Kazakhstan. Work experience, 2013 – present: junior researcher of National Nanotechnology Laboratory,

References (49)

  • L. Farhana et al.

    Upregulation of miR-150⁎ and miR-630 induces apoptosis in pancreatic cancer cells by targeting IGF-1R

    PLoS One

    (2013)
  • P.C. Sanchez-Diaz et al.

    De-regulated microRNAs in pediatric cancer stem cells target pathways involved in cell proliferation, cell cycle and development

    PLoS One

    (2013)
  • A. Rodriguez et al.

    Identification of mammalian microRNA host genes and transcription units

    Genome Res.

    (2004)
  • S. Griffiths-Jones et al.

    miRBase: tools for microRNA genomics

    Nucleic Acid Res.

    (2008)
  • C. He et al.

    Young intragenic miRNAs are less coexpressed with host genes than old ones: implications of miRNA-host gene coevolution

    Nucleic Acids Res.

    (2012)
  • N. Gromak

    in-microRNAs: a crossroad in gene regulation

    Biochem. Soc. Trans.

    (2012)
  • D. Ronchetti et al.

    An integrative genomic approach reveals coordinated expression of in-miR-335, miR-342, and miR-561 with deregulated host genes in multiple myeloma

    BMC Med. Genomics

    (2008)
  • S.Y. Ying et al.

    The microRNA (miRNA): overview of the RNA genes that modulate gene function

    Mol. Biotechnol.

    (2008)
  • S. Barik

    An in-microRNA silences genes that are functionally antagonistic to its host gene

    Nucleic Acids Res.

    (2008)
  • M. Morlando et al.

    Primary microRNA transcripts are processed co-transcriptionally

    Nat. Struct. Mol. Biol.

    (2008)
  • O.A. Berillo et al.

    Intragenic MicroRNAs binding sites in mRNAs of genes involved in carcinogenesis

    World Acad. Sci. Eng. Technol.

    (2013)
  • C. Delay et al.

    Alzheimer-specific variants in the 3′UTR of amyloid precursor protein affect microRNA function

    Mol. Neurodegener.

    (2011)
  • M.V. Iorio et al.

    MicroRNAs in cancer: small molecules with a huge impact

    J. Clin. Oncol.

    (2009)
  • J. Satoh et al.

    Comprehensive analysis of human microRNA target networks

    BioData Mining

    (2011)
  • Cited by (20)

    • Polymorphisms of miR-196a2 (rs11614913) and miR-605 (rs2043556) confer susceptibility to gastric cancer

      2017, Gene Reports
      Citation Excerpt :

      The miRNAs can be classified in intergenic miRNAs and intragenic miRNAs (Rodriguez et al., 2004), which are encoded within genes denominated as host genes. The majority of intragenic miRNAs are intronic miRNAs, being encoded within intronic regions of host protein-coding genes and presenting unique regulatory possibilities frequently coexpressed with their host genes (Berillo et al., 2013). miR-SNPs can influence the transcription of the target gene, alter miRNA expression, pri-miRNA and pre-miRNA processing or affect miRNA-mRNA interactions (Hu et al., 2014b).

    • A proteomic signature of ovarian cancer tumor fluid identified by highthroughput and verified by targeted proteomics

      2016, Journal of Proteomics
      Citation Excerpt :

      The prediction for the 49 more abundant proteins in malignant pool, we found correlation with eight different microRNAs. Among these, 4 appears described in different studies to be involved with cancer, such as miR-873-5p in lung cancer, and miR-6515-3p in tumorigenesis [37–40]. Interestingly, the other four microRNAs - miR103a-2-5p, miR-2053, miR-3160-5p and miR-6515-3p - were not related to any other diseases or biological processes.

    • Identifying Drug Resistant miRNAs Using Entropy Based Ranking

      2021, IEEE/ACM Transactions on Computational Biology and Bioinformatics
    View all citing articles on Scopus

    Olga A. Berillo was born in Almaty, Kazakhstan (18.09.1987). Education 2011 – present: doctorate Ph.D. of al-Farabi Kazakh National University, specialty “Biotechnology”, Almaty, Kazakhstan. 2009–2011: Master of al-Farabi Kazakh National University, specialty “Biotechnology”, Almaty, Kazakhstan. 2005–2009: Bachelor of al-Farabi Kazakh National University, specialty “Biotechnology”, Almaty, Kazakhstan. Work experience, 2013 – present: junior researcher of National Nanotechnology Laboratory, al-Farabi Kazakh National University. January–February 2013: traineeship in INRIA/LIX team AMIB 1 rue Honoré d′Estienne d′Orves 91120 Palaiseau, France. 2012–2013: junior researcher of National Nanotechnology Laboratory, al-Farabi Kazakh National University. 2010–2011: engineer of Institute of Biology′s and Biotechnology′s Problems. May–September 2009: laboratory assistant in Laboratory of protein and nucleic acids, Institute of biology′s and biotechnology′s problems.

    View full text