1. Role of transcriptomics in gene
expression studies and its relevance
Name: Sarla Yadav
Class: M.Sc.MBT 3rd sem
Roll No.: 1873

2. Introduction
• Transcriptome:
– The transcriptome is the complete set of transcripts in a cell, both in
terms of type and quantity.
• Transcriptomics:
– The global studies of gene expression at the RNA level.
– Comparison of transcriptomes allows the identification of genes that
are differentially expressed in distinct cell population, or in response to
different treatment.

3. Transcriptome: An evolving definition
• (the population of) mRNAs expressed by a genome at any given time(Abbott, 1999)
• The complete collection of transcribed elements of the genome. (Affymetrix, 2004)
 mRNAs
 Non-coding RNAs
 tRNAs
 rRNAs
 snmRNAs (small non-messenger RNAs)
 microRNAs and siRNAs
 snoRNAs (small nucleolar RNAs)
 snRNAs (small nuclear RNAs)
 Pseudogenes

4. Transcriptome
• Transcriptome is much more than just the transcribed portion of the genome..
• A gene may produce many different types of mRNA molecules
• Hence it is highly dynamic and complex.
• Complexity of transcriptome is increased by processes such as
– Alternate splicing
– RNA editing

5. Central dogma of life
“transcripts”

7. Alternative splicing adds to the size
(complexity) of the transcriptome.

8. RNA editing adds to the size
(complexity) of the transcriptome.

9. Methods of observing gene expression
• Focussed Experimental Approaches:
--Northern Blotting Analysis
--Real time PCR (quantitative or semi-quantitative)
• Highthroughput Approaches
– Microarray expression profiling
– Serial analysis of gene expression (SAGE)
– RNA sequencing

10. Northern Blotting Analysis

11. Real time PCR (quantitative or semi-quantitative)

12. Microarray expression profiling

13. SAGE

14. RNA sequencing
Illumina HiSeq2000/2500
Bridge amplification, clonal expansion

15. RNA-sequencing
• Recent advances in sequencing technologies have made possible the comprehensive
and in-depth characterization of transcriptomes via a technique known as RNA-Seq
• Compared to the use of microarrays, RNA-Seq is able to quantify more RNA species,
including non-coding and novel splice variants,

16. Comparison of Methods for Studying the
Transcriptome

17. Role of transcriptomics
• Reveal the process of development
• Determine the role of ncRNAs (miRNA)
• Genetic basis of diseases
• Help in study the response of drug

18. Transcriptomics in diseases diagnosis
• Whole transcriptome sequencing reveals that alzheimer’s patient have different gene
expression splicing pattern in brain regions.
• It affects individuals over the age of 60
• It is characterized by a complex progression of neurodegeneration that results in
– memory impairment
– loss of other cognitive processes as well as the presence of non-cognitive
symptoms including delusions, agitation and changes in mood and personality.

19. Transcriptomics in diseases diagnosis
• A comparative gene expression analysis of normal human brain tissue and tissue
affected by Alzheimer’s disease, using the RNA-Seq technique.
• Along with samples from whole normal and AD brains, mRNA samples from two
different brain regions, namely the frontal and temporal lobes, were analyzed.
• We found significant differences in gene isoform expression levels, alternated use of
promoters and transcription start sites between normal and AD brain tissue

20. Transcriptomics in the analysis of drug
response
• Asthma, a chronic inflammatory respiratory disease that is characterized by variable
airflow limitation and airway hyper responsiveness.
• Glucocorticoids (GCs) are common medications used to treat various inflammatory
diseases, including asthma.
• The mechanism by which glucocorticoids suppress inflammation in ASM remains
poorly understood
• Using RNA-Seq, a high-throughput sequencing method, we characterized
transcriptomic changes in four primary human ASM cell lines that were treated with
dexamethasone—a potent synthetic glucocorticoid (1 mM for 18 hours).

21. One stretch of DNA can encode an mRNA
together with many other types of RNAs.

22. Analysis the role of ncRNAs via
transcriptomics
• Transcriptomics also reveal the regulatory
function of ncRNAs such as miRNA.

23. microRNAs are functional gene products 21
– 22 nucleotides long

24. miRNA functions

25. microRNAs are mis-regulated in human
cancers.
This is important for cancer diagnosis.

26. miRNA responsible for cancer
• Specific miRNA can be upregulated in cancer and global miRNA
downregulation is a common trait of human malignancies
• In human breast cancer high level of miR103/107 are associated to
metastasis
• At cellular level miR103/107 is responsible for the induction of epithelial
to mesenchymal transition (EMT) attained by downregulation miR-200
levels.

27. EMT

28. microRNAs are involved in cancer metastasis

29. miRNAs are involved in cancer metastasis

30. Role in treatment of diseases
• By trancriptome analysis it revealed that hepatocellular
carcinoma cells exhibit reduce expression of miR-26a, a miRNA
that normally expressed at high levels in diverse tissues.

31. microRNAs can be used to treat liver
cancer (in mice).
microRNA miR-26a