RNA World – A Sequencing Approach

Author: Dr. Venu Seenappa,
Assistant Professor,
Centre for Functional Genomics & Bio-informatics

Ribonucleic acid (RNA) molecules are single stranded nucleotides and evolutionarily conserved biological molecule in all species, which decodes genetic information from DNA to proteins. Accumulating evidence revealed the function of RNA is not merely synthesizing proteins but also implicated in the regulatory function via noncoding RNA molecules (miRNA, siRNA, long noncoding RNA). The abundance or expression level of messenger RNA (mRNA) is a crucial factor in the regulation of many cellular events starting from cell differentiation, proliferation, cell cycle to apoptosis. The existence of nucleotide variation at specific loci of a gene may implicate in the synthesis of mRNA either by truncating or by leading to the formation of non-functional protein.

There are many genetic disorders are identified in humans as the result of these premature mRNA. Further, the expression status of a gene varies between populations due to epigenetic modifications and existence of nucleotide variations in the DNA. Subsequently, the abundance of the same gene transcript varies between different parts of the plants, which intern help us in identifying/marking the possible pathways involved in the synthesis of gene specific products in tissue specific manner.

Considering the importance of RNA in many cellular events, it is essential to analyze in depth both at sequence level as well as its expression level to delineate the underlying mechanism of these molecules in the cell physiology. Unraveling complete functional role of RNA may take many decades, but by employing existing knowledge along with the help of advanced technological resources we can definitely reduce the incidence of many genetic disorders and we can also progress towards identifying pathways which synthesis complex secondary metabolites in the plants.

In such technological resource, the recent revolution is happened through next generation sequencing technology (NGS). Worldwide most of the researchers and clinicians apply this technology for their research as well as for the diagnostic purposes. It is getting extensively applied by many scientists because the technology is rapid, accurate, and highly efficient in producing large data sets with some limitations. However, there is a huge lacuna exist in the skills set of many researchers to handle the NGS data and to practically run the system, which makes them one step back in designing their experiments and delivering their research objectives.

In view of these issues, we at TDU conducted 6 days training program on transcriptome sequencing and analysis using NGS approach from April 16-21, 2018 at TDU campus, Bangalore. This training program was designed from the learner perspective considering the contemporary knowledge, relevance to the existing research and industry requisites. We have received an overwhelming response for registration from the participants across India and we restricted to 27-30 participants for the productive transformation of the registered candidates.

During this training program, in addition to in-house lectures, we organized 4 invited lectures from eminent speakers who already working in the area of RNA biology and NGS technology from various reputed institutes. This program content was designed and delivered from total RNA isolation to sequencing to data analysis using different bioinformatics tools. The members from Center for Functional Genomics and Bioinformatics, TDU and Bangalore Genomics Center (BGC) supported the whole event in designing and executing at various levels along with the guidance from Dr. Malali Gowda.

Based on feedback received from the participants, we believe this program met the objective, delivered the designed content and increased the confidence in participants to pursue their research with more clarity on RNA and NGS world. Finally, I am fortunate to be the organizing secretary for this event which made me interact with many scientists, scholars, and students.

For more details on this event, please click here./

Comments ( 2 )
  1. Genome sequencing may not be essential in future, now we can sequence RNA directly !!!!
    Great direct RNA sequencing Demo during the training program, now direct RNA sequencing technology is available at TDU campus!

    https://www.nature.com/articles/nmeth.4577
    Highly parallel direct RNA sequencing on an array of Nanopores
    Nature Methods volume 15, pages 201–206 (2018)
    doi:10.1038/nmeth.4577

    Abstract

    Sequencing the RNA in a biological sample can unlock a wealth of information, including the identity of bacteria and viruses, the nuances of alternative splicing or the transcriptional state of organisms. However, current methods have limitations due to short read lengths and reverse transcription or amplification biases. Here we demonstrate nanopore direct RNA-seq, a highly parallel, real-time, single-molecule method that circumvents reverse transcription or amplification steps. This method yields full-length, strand-specific RNA sequences and enables the direct detection of nucleotide analogs in RNA.

  2. Yes, I agree with you.
    It’s a good information Malali.
    Thank you, for sharing

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