Elucidation of the Molecular Interaction between miRNAs and the Gene, Involved in Acute Myeloid Leukemia, by the Assistance of Argonaute Protein through a Computational Approach
Acute myeloid leukemia is a well characterized blood cancer in which the unnatural growth of immature white blood cell takes place, where several genes transcription is regulated by the micro RNAs (miRNAs). Argonaute (AGO) protein is a protein family that binds to the miRNAs and mRNA complex where a...
Saved in:
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BioMed Central
2015-06-01
|
| Series: | Genomics & Informatics |
| Subjects: | |
| Online Access: | http://genominfo.org/upload/pdf/gni-13-45.pdf |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1832572870418497536 |
|---|---|
| author | Rohit Pritam Das V. Badireenath Konkimalla Surya Narayan Rath Jagadish Hansa Manaswini Jagdeb |
| author_facet | Rohit Pritam Das V. Badireenath Konkimalla Surya Narayan Rath Jagadish Hansa Manaswini Jagdeb |
| author_sort | Rohit Pritam Das |
| collection | DOAJ |
| description | Acute myeloid leukemia is a well characterized blood cancer in which the unnatural growth of immature white blood cell takes place, where several genes transcription is regulated by the micro RNAs (miRNAs). Argonaute (AGO) protein is a protein family that binds to the miRNAs and mRNA complex where a strong binding affinity is crucial for its RNA silencing function. By understanding pattern recognition between the miRNAs-mRNA complex and its binding affinity with AGO protein, one can decipher the regulation of a particular gene and develop suitable siRNA for the same in disease condition. In the current work, HOXA9 gene has been selected from literature, whose deregulation is well-established in acute myeloid leukemia. Four miRNAs (mir-145, mir-126, let-7a, and mir-196b) have been selected to target mRNA of HOXA9 (NCBI accession No. NM_152739.3). The binding interaction between mRNAs and mRNA of HOXA9 gene was studied computationally. From result, it was observed mir-145 has highest affinity for HOXA9 gene. Furthermore, the interaction between miRNAs-mRNA duplex of all chosen miRNAs are docked with AGO protein (PDB ID: 3F73, chain A) to study their interaction at molecular level through an in silico approach. The residual interaction and hydrogen bonding are inspected in Discovery Studio 3.5 suites. The current investigation throws light on understanding of AGO-assisted miRNA based gene silencing mechanism in HOXA9 gene associated in acute myeloid leukemia computationally. |
| format | Article |
| id | doaj-art-3fde047c14184f59af1e6a0282e9f3e4 |
| institution | Kabale University |
| issn | 1598-866X 2234-0742 |
| language | English |
| publishDate | 2015-06-01 |
| publisher | BioMed Central |
| record_format | Article |
| series | Genomics & Informatics |
| spelling | doaj-art-3fde047c14184f59af1e6a0282e9f3e42025-02-02T06:43:42ZengBioMed CentralGenomics & Informatics1598-866X2234-07422015-06-01132455210.5808/GI.2015.13.2.45150Elucidation of the Molecular Interaction between miRNAs and the Gene, Involved in Acute Myeloid Leukemia, by the Assistance of Argonaute Protein through a Computational ApproachRohit Pritam Das0V. Badireenath Konkimalla1Surya Narayan Rath2Jagadish Hansa3Manaswini Jagdeb4BIF Centre, Department of Bioinformatics, Orissa University of Agriculture & Technology, Bhubaneswar 751003, India.School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar 751005, India.BIF Centre, Department of Bioinformatics, Orissa University of Agriculture & Technology, Bhubaneswar 751003, India.Department of Surgical Oncology, IMS and SUM Hospital, SOA University, Bhubaneswar 751003, India.BIF Centre, Department of Bioinformatics, Orissa University of Agriculture & Technology, Bhubaneswar 751003, India.Acute myeloid leukemia is a well characterized blood cancer in which the unnatural growth of immature white blood cell takes place, where several genes transcription is regulated by the micro RNAs (miRNAs). Argonaute (AGO) protein is a protein family that binds to the miRNAs and mRNA complex where a strong binding affinity is crucial for its RNA silencing function. By understanding pattern recognition between the miRNAs-mRNA complex and its binding affinity with AGO protein, one can decipher the regulation of a particular gene and develop suitable siRNA for the same in disease condition. In the current work, HOXA9 gene has been selected from literature, whose deregulation is well-established in acute myeloid leukemia. Four miRNAs (mir-145, mir-126, let-7a, and mir-196b) have been selected to target mRNA of HOXA9 (NCBI accession No. NM_152739.3). The binding interaction between mRNAs and mRNA of HOXA9 gene was studied computationally. From result, it was observed mir-145 has highest affinity for HOXA9 gene. Furthermore, the interaction between miRNAs-mRNA duplex of all chosen miRNAs are docked with AGO protein (PDB ID: 3F73, chain A) to study their interaction at molecular level through an in silico approach. The residual interaction and hydrogen bonding are inspected in Discovery Studio 3.5 suites. The current investigation throws light on understanding of AGO-assisted miRNA based gene silencing mechanism in HOXA9 gene associated in acute myeloid leukemia computationally.http://genominfo.org/upload/pdf/gni-13-45.pdfacute myeloid leukemiaArgonautemicroRNAsmRNA |
| spellingShingle | Rohit Pritam Das V. Badireenath Konkimalla Surya Narayan Rath Jagadish Hansa Manaswini Jagdeb Elucidation of the Molecular Interaction between miRNAs and the Gene, Involved in Acute Myeloid Leukemia, by the Assistance of Argonaute Protein through a Computational Approach Genomics & Informatics acute myeloid leukemia Argonaute microRNAs mRNA |
| title | Elucidation of the Molecular Interaction between miRNAs and the Gene, Involved in Acute Myeloid Leukemia, by the Assistance of Argonaute Protein through a Computational Approach |
| title_full | Elucidation of the Molecular Interaction between miRNAs and the Gene, Involved in Acute Myeloid Leukemia, by the Assistance of Argonaute Protein through a Computational Approach |
| title_fullStr | Elucidation of the Molecular Interaction between miRNAs and the Gene, Involved in Acute Myeloid Leukemia, by the Assistance of Argonaute Protein through a Computational Approach |
| title_full_unstemmed | Elucidation of the Molecular Interaction between miRNAs and the Gene, Involved in Acute Myeloid Leukemia, by the Assistance of Argonaute Protein through a Computational Approach |
| title_short | Elucidation of the Molecular Interaction between miRNAs and the Gene, Involved in Acute Myeloid Leukemia, by the Assistance of Argonaute Protein through a Computational Approach |
| title_sort | elucidation of the molecular interaction between mirnas and the gene involved in acute myeloid leukemia by the assistance of argonaute protein through a computational approach |
| topic | acute myeloid leukemia Argonaute microRNAs mRNA |
| url | http://genominfo.org/upload/pdf/gni-13-45.pdf |
| work_keys_str_mv | AT rohitpritamdas elucidationofthemolecularinteractionbetweenmirnasandthegeneinvolvedinacutemyeloidleukemiabytheassistanceofargonauteproteinthroughacomputationalapproach AT vbadireenathkonkimalla elucidationofthemolecularinteractionbetweenmirnasandthegeneinvolvedinacutemyeloidleukemiabytheassistanceofargonauteproteinthroughacomputationalapproach AT suryanarayanrath elucidationofthemolecularinteractionbetweenmirnasandthegeneinvolvedinacutemyeloidleukemiabytheassistanceofargonauteproteinthroughacomputationalapproach AT jagadishhansa elucidationofthemolecularinteractionbetweenmirnasandthegeneinvolvedinacutemyeloidleukemiabytheassistanceofargonauteproteinthroughacomputationalapproach AT manaswinijagdeb elucidationofthemolecularinteractionbetweenmirnasandthegeneinvolvedinacutemyeloidleukemiabytheassistanceofargonauteproteinthroughacomputationalapproach |