Related Concept Videos
02:32Exon Recombination
The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes.
Exon shuffling follows “splice frame rules.” Each exon has three reading...
Exon shuffling follows “splice frame rules.” Each exon has three reading...
02:32Position-effect Variegation
In 1928, a German botanist Emil Heitz observed the moss nuclei with a DNA binding dye. He observed that while some chromatin regions decondense and spread out in the interphase nucleus, others do not. He termed them euchromatin and heterochromatin, respectively. He proposed that the heterochromatin regions reflect a functionally inactive state of the genome. It was later confirmed that heterochromatin is transcriptionally repressed, and euchromatin is transcriptionally active chromatin.
03:21Genome Size and the Evolution of New Genes
While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
03:21Genome Size and the Evolution of New Genes
While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
02:35Chromatin Position Affects Gene Expression
Chromatin is the massive complex of DNA and proteins packaged inside the nucleus. The complexity of chromatin folding and how it is packaged inside the nucleus greatly influences access to genetic information. Generally, the nucleus' periphery is considered transcriptionally repressive, while the cell's interior is considered a transcriptionally active area.
Topologically Associated Domains (TADs)
The 3-dimensional positioning of chromatin in the nucleus influences the timing and level of...
Topologically Associated Domains (TADs)
The 3-dimensional positioning of chromatin in the nucleus influences the timing and level of...
02:37Gene Duplication and Divergence
The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
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RNA dust: where are the genes?
1Omics Science Center, RIKEN Yokohama Institute, Kanagawa, Japan. carninci@riken.jp
Summary
Vertebrate genomes contain vast non-coding RNAs (ncRNAs) that vastly outnumber protein-coding messenger RNAs (mRNAs). These ncRNAs likely play crucial regulatory roles in development and function.
Area of Science:
- Genomics
- Molecular Biology
- Transcriptomics
Background:
- Vertebrate genomes show limited protein-coding genes, with most DNA not transcribed into messenger RNAs (mRNAs).
- The transcriptome is highly complex, with non-coding RNAs (ncRNAs) constituting the majority of transcripts, far exceeding mRNAs.
Purpose of the Study:
- To explore the regulatory role of transcriptome complexity in vertebrate development and function.
- To investigate the potential function of ncRNAs in gene regulation and their impact on the protein-coding transcriptome.
Main Methods:
- Analysis of genome sequences.
- Identification and characterization of expressed RNAs.
- Comparative analysis of mRNA and ncRNA transcript abundance.
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Main Results:
- A small fraction of the genome is transcribed into protein-coding mRNAs.
- ncRNAs are diverse and abundant, significantly outnumbering mRNAs in vertebrates.
- Transcriptome complexity suggests a regulatory role for ncRNAs.
Conclusions:
- The vast ncRNA repertoire may be essential for the development and function of complex organisms like vertebrates.
- ncRNAs are hypothesized to finely modulate gene activity, acting as regulatory elements.
- Gene regulation is likely intricately linked with ncRNAs, particularly short RNAs, for fine-tuning the protein-coding transcriptome.