Related Experiment Video
Updated: May 30, 2025
07:17
Generation of Chimeric Axolotls with Mutant Haploid Limbs Through Embryonic Grafting
Published on: January 29, 2020
7.2K
Chromosome-scale genome assembly reveals how repeat elements shape non-coding RNA landscapes active during newt limb
Thomas Brown1, Ketan Mishra2, Ahmed Elewa3
1DRESDEN-concept Genome Center (DcGC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, 01307 Dresden, Germany; Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.
Cell Genomics
|January 28, 2025
Summary
Giant newt genomes, rich in repeat elements, are key to their regeneration. This study presents a high-quality genome assembly, revealing how repeat elements influence non-coding RNAs and drive the unique regenerative capabilities in newts.
Area of Science:
- Genomics
- Developmental Biology
- Regenerative Medicine
Background:
- Newts possess exceptionally large genomes with abundant repetitive elements, yet their role in genome structure and regeneration is poorly understood.
- Understanding the genomic basis of newt regeneration is crucial for advancing regenerative medicine and evolutionary biology.
Purpose of the Study:
- To generate a chromosome-scale genome assembly for the Iberian ribbed newt (Pleurodeles waltl).
- To investigate the role of repeat elements in shaping the newt genome and their connection to regenerative abilities.
- To characterize non-coding RNAs, including microRNAs and circular RNAs, in the context of regeneration.
Main Methods:
- Chromosome-scale genome assembly of Pleurodeles waltl.
- Comparative genomics to identify synteny and rearrangements.
- Analysis of intronic repeat elements and their role in circular RNA biogenesis.
- Annotation and chromosomal mapping of microRNAs.
Main Results:
- A highly contiguous and complete 20.3 Gb genome assembly of Pleurodeles waltl was achieved.
- Conserved synteny and genetic rearrangements were identified, including within the major histocompatibility complex.
- Intronic repeat elements were found to drive newt-specific circular RNA biogenesis with regeneration-specific expression.
- A distinct regulatory pattern of microRNAs was observed in regenerating limbs, alongside genomic expansion profiles.
Conclusions:
- Repeat elements play a significant role in newt-specific circular RNA biogenesis and are linked to adult regeneration.
- Non-coding RNAs, particularly microRNAs, exhibit unique genomic organization and regulatory patterns associated with limb regeneration.
- This genome assembly provides a foundational resource for studying the genetic and molecular mechanisms underlying newt regeneration, development, and evolution.
Related Concept Videos
01:33Whole Body Regeneration
3.3K
Regeneration is the process of restoring injured or lost tissues, organs, or body parts. While simpler organisms generally show greater ability to regenerate their whole body, few complex animals show similarly exceptional regeneration. For example, planarian flatworms have a unique regenerative potential making them a popular study organism among biologists to understand the mechanisms of whole body regeneration. Other organisms, such as hydra, also show extreme regeneration potential;...
3.3K
02:39lncRNA - Long Non-coding RNAs
8.5K
In humans, more than 80% of the genome gets transcribed. However, only around 2% of the genome codes for proteins. The remaining part produces non-coding RNAs which includes ribosomal RNAs, transfer RNAs, telomerase RNAs, and regulatory RNAs, among other types. A large number of regulatory non-coding RNAs have been classified into two groups depending upon their length – small non-coding RNAs, such as microRNA, which are less than 200 nucleotides in length, and long non-coding RNA...
8.5K
02:02Cis-regulatory Sequences
9.7K
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
9.7K
03:18Non-LTR Retrotransposons
11.4K
As the name suggests, non-LTR retrotransposons lack the long terminal repeats characteristic of the LTR retrotransposons. Additionally, both LTR and non-LTR retrotransposons use distinct mechanisms of mobilization. Non-LTR retrotransposons are further divided into two classes - Long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs), both of which occur abundantly in most mammals, including humans. Some of the active non-LTR retrotransposons in humans are L1...
11.4K
01:24Methods of Nuclear Reprogramming
1.8K
Nuclear reprogramming is a process of transforming one cell type into an unrelated cell type by epigenetic changes that alter the cell’s original gene expression pattern. Such epigenetic changes force cells to express a different set of genes, which play a significant role in inducing transformation into other cell types. Nuclear reprogramming offers applications in reproductive cloning for livestock propagation and regenerative medicine — developing patient-specific cells for...
1.8K
02:18Alternative RNA Splicing
20.9K
Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...
20.9K