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Related Concept Videos

What is Gene Expression?01:42

What is Gene Expression?

Overview
Gene expression is the process in which DNA directs the synthesis of functional products, that is, proteins. Cells can regulate gene expression at various stages. It allows organisms to generate different cell types and enables cells to adapt to internal and external factors.
Genetic Information Flows from DNA to RNA to Protein
A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is made up of nucleotides and proteins consist of amino...
Transcription Factors02:16

Transcription Factors

Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
Regulation of Expression Occurs at Multiple Steps02:24

Regulation of Expression Occurs at Multiple Steps

Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...
What is Gene Expression?01:36

What is Gene Expression?

A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is comprised  of nucleotides and proteins are comprised of amino acids, a mediator is required to convert the information encoded in DNA into proteins. This mediator is the messenger RNA (mRNA). mRNA copies the blueprint from DNA by a process called transcription. In eukaryotes, transcription occurs in the nucleus by complementary base-pairing with the DNA template. The mRNA is then processed and...
General Transcription Factors01:30

General Transcription Factors

Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
Regulation of Expression at Multiple Steps01:23

Regulation of Expression at Multiple Steps

The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the addition of a...

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An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations
10:17

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Published on: November 3, 2010

Tissue effect on genetic control of transcript isoform variation.

Tony Kwan1, Elin Grundberg, Vonda Koka

  • 1Department of Human Genetics, McGill University, Montréal, Canada. tony.kwan@mcgill.ca

Plos Genetics
|August 15, 2009
PubMed
Summary

Genome-wide association studies (GWAS) can use cell lines to find disease relevance. This study in human osteoblasts (HObs) identified genetic variants controlling transcript isoform expression, revealing cell-specific variants important for GWAS follow-up.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Genome-wide association studies (GWAS) increasingly utilize primary cell lines for biological relevance.
  • Human osteoblasts (HObs) and lymphoblastoid cell lines (LCLs) exhibit distinct transcriptomic profiles reflecting tissue-specific pathways.

Purpose of the Study:

  • To perform a transcriptomic survey in human osteoblasts (HObs).
  • To identify genetic variations influencing transcript isoform expression in HObs.
  • To investigate the role of cis-regulatory variants in differential isoform expression.

Main Methods:

  • Transcriptomic survey of human osteoblasts (HObs).
  • Cis-association analysis using SNP genotypes to identify genetic control of transcript isoforms.
  • RT-PCR validation of identified associations.
  • Examination of top SNPs from bone mineral density GWAS for overlap with probeset associations.

Main Results:

  • Differential expression of transcript isoforms in HObs is partly controlled by cis-regulatory genetic variants.
  • Genetic variants regulate isoforms in both tissue-specific and tissue-independent manners.
  • Multiple transcript isoforms are present, with genetic control affecting relative expression levels.
  • Overlap was observed between top SNPs from bone mineral density GWAS and probeset associations in HObs.
  • A novel transcript isoform variant of the FAM118A gene was identified.

Conclusions:

  • Examining transcriptome variation across multiple cell types aids in identifying common and cell-specific genetic variations.
  • Cell-specific transcript isoform variants are functionally relevant for follow-up studies in GWAS.
  • This approach enhances the biological interpretation of genetic signals identified through GWAS.