Muhammad Younas Khan Barozai

Identification and characterization of the microRNAs and their targets in Salmo salar.

MicroRNAs (miRNAs) are small, non-coding and regulatory RNAs about 18 to 26 nucleotides long. Their conserved nature among the various organisms makes them a good source of new miRNAs discovery by comparative genomics approach. The study resulted in novel 75 precursor miRNAs containing 102 mature sequences belonging to 46 families in an important aquatic environmental monitoring fish (Salmo salar). All the miRNA families (let-7, mir-1, 7, 9, 21, 22, 92, 96, 122, 126, 128, 129, 132, 133, 142, 144, 147, 148, 196, 202, 212, 223, 375, 429, 430, 449, 451, 457, 466, 682, 700, 1388, 1594, 1600, 1607, 1616, 1642, 1681, 1701, 1720, 1772, 1782, 1787, 1814, 2189 and 3540) are found for the first time in S. salar. All 75 miRNA precursors form stable minimum free energy stem loop and the mature miRNAs reside in the stem portion of the stem loop structure. Their target proteins are involved in transcription factors (28%), metabolism (23%), signaling (18%), transportation (9%), immunity (8%), stress related activity (5%), cancer and tumor related activity (5%), growth and development (3%), and cell division (1%).

The novel 172 sheep (Ovis aries) microRNAs and their targets.

MicroRNAs (miRNAs) are small, non-coding and regulatory RNAs about ≈22 nucleotides in length. The comparative genomics approach due to their conserved nature is a good source for the novel miRNAs discovery. In this study, total 172 novel miRNAs from 140 precursor sequences belonging to 114 families were identified in sheep (Ovis aries), the most important livestock animal. All the miRNA families (oar-mir-95, 129, 130, 186, 214, 219, 223, 324, 339, 423, 450, 499, 544, 562, 568, 584, 669, 671, 763, 935, 1281, 1282, 1306, 1552, 1584, 1587, 1603, 1607, 1706, 1711, 1718, 1732, 1738, 1761, 1771, 1777, 1778, 1780, 1807, 1843, 1895, 1930, 2127, 2139, 2182, 2284, 2287, 2295, 2296, 2310, 2311, 2314, 2315, 2316, 2320, 2359, 2378, 2381, 2382, 2395, 2400, 2404, 2410, 2412, 2423, 2426, 2435, 2470, 2477, 2482, 2487, 2881, 2883, 2885, 2888, 2889, 2896, 2901, 2904, 2917, 2964, 3063, 3064, 3074, 3080, 3432, 3529, 3533, 3613, 3649, 3654, 3658, 3661, 3662, 3940, 3960, 4273, 4426, 4447, 4459, 4468, 4493, 4507, 4647, 4680, 4785, 4788, 4800, 5102, 5105, 5109, 5115, 5125 and 5132) are found for the first time in Sheep. All 140 miRNA precursors form stable minimum free energy stem loop and the mature miRNAs reside in the stem portion of the stem loop structure. Their putative targets are involved in transcription factors (26%), signaling (19%), metabolism (18%), transportation (10%), immunity (9%), cancer and tumor related (5%), growth and development (5%), stress related (4%), and structural proteins (3%).

Profiling microRNAs and their targets in an important fleshy fruit: Tomato (Solanum lycopersicum)

Tomato (Solanum lycopersicum) is an important and the most useful plant based diet. It is widely used for its antioxidant property. Presently, only two digits, tomato microRNAs (miRNAs) are reported in miRBase: a miRNA database. This study is aimed to profile and characterize more miRNAs and their targets in tomato. A comprehensive comparative genomic approach is applied and a total of 109 new miRNAs belonging to 106 families are identified and characterized from the tomato expressed sequence tags (ESTs). All these potential miRNAs are profiled for the first time in tomato. The profiled miRNAs are also observed with stable stem-loop structures (Precursor-miRNAs), whose length ranges from 45 to 329 nucleotides (nt) with an average of 125 nt. The mature miRNAs are found in the stem of pre-miRNAs and their length ranges from 19 to 24 nt with an average of 21 nt. Furthermore, twelve miRNAs are randomly selected and experimentally validated through RT-PCR. A total of 406 putative targets are also predicted for the newly 109 tomato miRNAs. These targets are involved in structural protein, metabolism, transcription factor, growth & development, stress related, signaling pathways, storage proteins and other vital processes. Some important proteins like; 9-cisepoxycarotenoid dioxygenase (NCED), transcription factor MYB, ATP-binding cassette transporters, terpen synthase, 14-3-3 and TIR-NBS proteins are also predicted as putative targets for tomato miRNAs. These findings improve a baseline data of miRNAs and their targets in tomato. This baseline data can be utilized to fine tune this important fleshy fruit for nutritional & antioxidant properties and also under biotic & abiotic stresses.

Structural and functional based identification of the bean (Phaseolus) microRNAs and their targets from expressed sequence tags

MicroRNAs (miRNAs) are small, 18–26 nucleotides long, non-coding RNAs that play role in post-transcriptional gene regulation. Many of these are evolutionarily conserved. This suggests a powerful approach to predict new miRNAs in other species. In this research, structural and functional approaches were combined to make computational prediction of potential miRNAs and their targets in Bean (Phaseolus). Total 55 novel miRNAs were detected from 38 miRNAs families in Bean (Phaseolus). These families are; miR156, 160, 164, 168, 170, 171, 172, 319, 393, 396, 397, 398, 408, 414, 438, 444, 535, 1310, 1424, 1426, 1848, 1860, 1863, 2055, 2091, 2093, 2094, 2102, 2103, 2105, 2864, 2866, 2925, 2926, 4221, 4245, 4246 and 4250. In the 55 putative miRNAs; 28 miRNAs belong to Phaseolus acutifolius, 23 to Phaseolus vulgaris, 4 to Phaseolus coccineus. All the mature miRNAs reside in the stem portion of the hairpin structures. Total 146 potential protein targets were predicted for these miRNAs.

Profiling and characterization of eggplant (Solanum melongena L.) microRNAs and their targets

MicroRNAs (miRNAs) are small, non-protein coding and functional RNAs. They play negative regulatory role in gene regulation. They are endogenous in nature and are ~21 nucleotides in length. They are reported in many plant species, but still missing and need to be identified in other important plants like; eggplant. The comparative genomic methodology due to their conserved nature is a reasonable approach for the novel miRNAs discovery. In this research, total 76 novel miRNAs from 67 families were identified in the important vegetable eggplant (Solanum melongena L.). All precursor miRNAs form stable minimum free energy secondary structures and the mature miRNAs reside in the stem regions. Furthermore, eight miRNAs were randomly selected and experimentally validated through RT-PCR. A total of 345 putative targets were also identified for the novel 76 eggplant miRNAs. Their targets are involved in regulation, metabolism, transcription factors, growth and development and other physiological processes. These findings provide a baseline to unravel the miRNAs role in eggplant and utilize them for the improvement of the plant biology.

Initial screening of plant most conserved MicroRNAs targeting infectious viruses: HBV and HCV

MicroRNAs (miRNAs) belong to small RNA world are involve in posttranslational gene regulation. They are small in size (18–26 nt), non-coding and endogenously produced by cell. Recently, some evidence showing cross gene regulation of plants miRNAs targeting animal genes is attracting the researchers to do research in this interesting area of regulatory RNAs. This research is aimed to initially screen the role of plant most conserved miRNAs against the hepatitis B and C viruses causing an infectious diseases that affect the human liver. Combinations of various bioinformatics tools were applied to predict the cross-kingdom interactions of plant miRNAs targeting HBV and HCV. For this purpose six most conserved plant miRNAs miR156/157, 166, 169, 172 390 and 399 were subjected to find targets in the reported nucleic acid sequences of HBV and HCV in GenBank. This initial screening is resulted a total of 12 HBC and HCV genes as potential targets by plant conserved miRNAs. These findings provide a baseline data of plant based miRNAs and their targets in HBV and HCV. This initial baseline data would be helpful to elucidate in detail the link between plant miRNAs against animal and human infectious viruses such as; HBV and HCV.

In-silico identification and characterization of organic and inorganic chemical stress responding genes in yeast (Saccharomyces cerevisiae)

To study the life processes of all eukaryotes, yeast (Saccharomyces cerevisiae) is a significant model organism. It is also one of the best models to study the responses of genes at transcriptional level. In a living organism, gene expression is changed by chemical stresses. The genes that give response to chemical stresses will provide good source for the strategies in engineering and formulating mechanisms which are chemical stress resistant in the eukaryotic organisms. The data available through microarray under the chemical stresses like lithium chloride, lactic acid, weak organic acids and tomatidine were studied by using computational tools. Out of 9335 yeast genes, 388 chemical stress responding genes were identified and characterized under different chemical stresses. Some of these are: Enolases 1 and 2, heat shock protein-82, Yeast Elongation Factor 3, Beta Glucanase Protein, Histone H2A1 and Histone H2A2 Proteins, Benign Prostatic Hyperplasia, ras GTPase activating protein, Establishes Silent Chromatin protein, Mei5 Protein, Nondisjunction Protein and Specific Mitogen Activated Protein Kinase. Characterization of these genes was also made on the basis of their molecular functions, biological processes and cellular components.