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Related Concept Videos

Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
Ribosomal RNA Synthesis02:53

Ribosomal RNA Synthesis

Ribosome synthesis is a highly complex and coordinated process involving more than 200 assembly factors. The synthesis and processing of ribosomal components occurs not only in the nucleolus but also in the nucleoplasm and the cytoplasm of eukaryotic cells.
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...
Transcription Attenuation in Prokaryotes02:42

Transcription Attenuation in Prokaryotes

Transcriptional attenuation occurs when RNA transcription is prematurely terminated due to the formation of a terminator mRNA hairpin structure.  Bacteria use these hairpins to regulate the transcription process and control the synthesis of several amino acids including histidine, lysine, threonine, and phenylalanine. Transcription attenuation takes place in the non-coding regions of mRNA.
There are several different mechanisms used to attenuate transcription. In ribosome mediated...
Proteins: From Genes to Degradation02:11

Proteins: From Genes to Degradation

Within a biological system, the DNA encodes the RNA, and the nucleotide sequence in the RNA further defines the amino acid sequence in the protein. This is referred to as “The Central Dogma of Molecular Biology” - a term coined by Francis Crick.  Central dogma is a firm principle in biology that defines the flow of genetic information within any life form. The two fundamental steps in central dogma are - transcription and translation.
Transcription is the synthesis of RNA molecules by RNA...
Transfer RNA Synthesis02:36

Transfer RNA Synthesis

One of the unique features of tRNA is the presence of modified bases. In some tRNAs, modified bases account for nearly 20% of the total bases in the molecule. Altogether, these unusual bases protect the tRNA from enzymatic degradation by RNases.
Each of these chemical modifications is carried by a specific enzyme, post-transcription. All of these enzymes have unique base and site-specificity. Methylation, the most common chemical modification, is carried by at least nine different enzymes, with...
Cell Specific Gene Expression01:58

Cell Specific Gene Expression

Multicellular organisms contain a variety of structurally and functionally distinct cell types, but the DNA in all the cells originated from the same parent cells. The differences in the cells can be attributed to the differential gene expression. Liver cells, whose functions include detoxification of blood, production of bile to metabolize fats, and synthesis of proteins essential for metabolism, must express a specific set of genes to perform their functions. Gene expression also varies with...

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Purification of Transcripts and Metabolites from Drosophila Heads
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Published on: March 15, 2013

Transcript profiling of the anoxic rice coleoptile.

Rasika Lasanthi-Kudahettige1, Leonardo Magneschi, Elena Loreti

  • 1Plant and Crop Physiology Laboratory, Scuola Superiore Sant'Anna, 56124 Pisa, Italy.

Plant Physiology
|March 21, 2007
PubMed
Summary

Rice seeds can germinate without oxygen, with coleoptiles elongating more under anoxia. This study reveals key genes and metabolic pathways, including expansins and ethylene response factors, involved in this anaerobic growth.

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Area of Science:

  • Plant Biology
  • Molecular Biology
  • Genomics

Background:

  • Rice seeds exhibit unique germination capabilities, including anoxia tolerance.
  • Coleoptile elongation under anoxia surpasses aerobic conditions, indicating distinct adaptive mechanisms.

Purpose of the Study:

  • To investigate the transcriptomic changes in rice coleoptiles under aerobic versus anaerobic conditions.
  • To identify genes and metabolic pathways crucial for anoxia-induced coleoptile elongation.

Main Methods:

  • Comparative transcriptome analysis of rice coleoptiles grown under aerobic and anaerobic conditions.
  • Gene expression profiling to identify differentially regulated transcripts.

Main Results:

  • Anoxia up-regulates transcripts involved in anaerobic carbohydrate metabolism, particularly pyruvate pathways.
  • Sugars play a signaling role under anoxia, with genes up-regulated by sugar starvation.
  • EXPA7 and EXPB12 expansin genes are implicated in anoxia-driven coleoptile elongation.
  • Anoxia modulates ethylene response factors and heat shock proteins, similar to Arabidopsis.
  • Oxygen-dependent enzymes are down-regulated, suggesting an energy-saving gene regulation strategy.

Conclusions:

  • Anoxia triggers specific transcriptomic reprogramming in rice coleoptiles, optimizing carbohydrate metabolism and growth.
  • Expansins and ethylene response factors are key players in rice coleoptile adaptation to anoxia.
  • Gene expression regulation under anoxia involves energy conservation mechanisms.