Transcriptomics The Study Of RNA E-Book

Hussan Ahmad Ks

• Herausgeber: Hussan Ahmad Ks
• Kategorie: Bildung
• Sprache: Englisch

Veröffentlichungsjahr: 2020

Beschreibung

Book By Hussan Ahmad Ks
Transcriptomics, the study of RNA in any of its forms.
The transcriptome is the complete set of transcripts in a cell and their quantity, for a specific developmental stage or physiological condition.
The transcriptome is the set of all RNA molecules, including mRNA, rRNA, tRNA, and other non-coding RNA produced in one or a population of cells.
TRANSCRIPTOMICS AIMS
To catalogue all species of transcripts, including mRNAs, noncoding RNAs and small RNAs.
To determine the transcriptional structure of genes, in terms of their start sites, 5' and 3' ends, splicing patterns and other post-transcriptional modifications.
To quantify the changing expression levels of each transcript during development and under different conditions.

Leseprobe

TRANSCRIPTOMICS, PROTEOMICS,

STRUCTURAL AND FUNCTIONAL

PROTEOMICS, METHODS OF

STUDYING PROTEOMICS

TRANSCRIPTOMICS

• Transcriptomics, the study of RNA in any of its forms.

• The transcriptome is the complete set of transcripts in a cell and their quantity, for a specific developmental stage or physiological condition.

• The transcriptome is the set of all RNA molecules, including mRNA, rRNA, tRNA, and other non-coding RNA produced in one or a population of cells.

TRANSCRIPTOMICS AIMS

• To catalogue all species of transcripts, including mRNAs, noncoding RNAs and small RNAs.

• To determine the transcriptional structure of genes, in terms of their start sites, 5′ and 3′ ends, splicing patterns and other post-transcriptional modifications.

• To quantify the changing expression levels of each transcript during development and under different conditions.

TECHNOLOGIES

• Hybridization-based approaches

• fluorescently labelled cDNA with custom-made microarrays

• commercial high-density oligo microarrays

• Sequence-based approaches

• Sanger sequencing of cDNA or EST libraries

• serial analysis of gene expression (SAGE)

• cap analysis of gene expression (CAGE)

• massively parallel signature sequencing (MPSS)

APPLICATIONS IN PLANT BREEDING

• Transcriptome assembly and profiling

• The widespread use of transcriptome sampling strategies is a complementary approach to genome sequencing, and results in a large collection of expressed sequence tags (ESTs) for almost all the important plant species.

• Small RNA characterization

• Small RNAs (sRNA) are non-protein-coding small RNA molecules ranging from 20 to 30 nt that have a role in development, genome maintenance and plant responses to environmental stresses.

INTRODUCTION OF PROTEOMICS

• Proteomics aims to identify all the proteins in a cell or organism including any post translationally modified forms, as well as their cellular localization, functions, and interactions

• Understanding the proteome allows for:

• Characterization of proteins

• Understanding protein interactions

• Identification of disease biomarkers

BIOMARKER

• Biomarkers are biological indicators of a disease.

• They are useful both for diagnosis, prognosis and response to therapy.

TYPES OF PROTEOMICS

• Expression proteomics

• Structural proteomics

• Functional proteomics

• Interaction proteomics

EXPRESSION PROTEOMICS

• Expression proteomics is used to study the qualitative and quantitative expression of total proteins under two different conditions.

• Normal and diseased state.

• E.g : tumor or normal cell.

• It studied that protein is over expressed or under expressed.

• 2-D electrophoresis.

STRUCTURAL PROTEOMICS

• Structural proteomics helps to understand three dimensional shape and structural complexities of functional proteins.

• It determine either by amino acid sequence in protein or from a gene this process is known as homology modeling.

• It identify all the protein present in complex system or protein-protein interaction.

• Mass spectroscopy is used for structure determination.

FUNCTIONAL PROTEOMICS

• Functional proteomics explains understanding the protein functions as well as unrevealing molecular mechanisms within the cell that depend on the identification of the interacting protein partners.

• So that detailed description of the cellular signaling pathways might greatly benefit from the elucidation of protein- protein interactions

INTERACTION PROTEOMICS

• Proteins are not discrete and independent molecules they need other proteins or cofactors for their activity.

• Such interactions are necessary for signal transduction, trafficking, cell cycle and gene regulation.

WHY PROTEOMICS?

• Many types of information cannot be obtained from the study of genes alone. For example, proteins, not genes, are responsible for the phenotypes of cells. It is impossible to elucidate mechanisms of disease, aging, and effects of the environment solely by studying the genome.

TECHNIQUES IN PROTEOMIC STUDY

• 2-D electrophoresis

• MALDI

• Mass spectrometry

• PMF(peptide mass fingerprinting)

2-D ELECTROPHORESIS

• Electrophoresis is the migration of charged molecules, particles or ion in a liquid or solid medium under the influence of an electric field.

• 1969 - introduction of denaturing agents especially SDS separation of protein subunit ( Weber and Osborn ).

• This technique combines the technique IEF (first dimension), which separates proteins in a mixture according to charge, with the size separation technique of SDS-PAGE (second dimension).

• The combination of these two technique to give 2-D PAGE provides a highly sophisticated analytical method for analyzing protein mixtures.

2-DE

• Several forms of PAGE exist and can provide different types of information about the protein(s).

• SDS-PAGE (sodium dodecyl sulphate-polyacrylamide gel electrophoresis), the most widely used electrophoresis technique, separates proteins primarily by mass.

• Non denaturing PAGE, also called native PAGE, separates proteins according to their mass: charge ratio.

• Two-dimensional PAGE (2D-PAGE) separates proteins by isoelectric point in the first dimension and by mass in the second dimension.

MASS SPECTROMETRY

• MS/MS plays important role in protein identification (fast and sensitive).

• Derivation of peptide sequence an important task in proteomics.

• Derivation without help from a protein database, especially important in identification of unknown protein.

MAJOR PARTS

• Sours ionized the sample

• Analyzer separate the ions on m/z ratio

• Detector sees the ions and analyzed the result