Differential expression of small RNAs in human and chimpanzee and the role of transposable elements
(2021) BINP52 20202Degree Projects in Bioinformatics
- Abstract
- Our closest living relatives are the chimpanzees, with whom we last shared a common ancestor about 5-6 million years ago. 98% of our protein-coding regions are identical. However, despite our close similarities when it comes to the protein-coding regions in our genome, our cognitive abilities and the size of our brains differ considerably. The Non coding regions, which cover 98% of our genome, are believed to be one driver of the differences between the two species. These regions regulate gene expression, are involved in transposon reassembly and the production of non-coding RNAs.
Transposable elements (TEs) are elements contained within the non-coding region, which have the ability to move around the genome and regulate nearby genes.... (More) - Our closest living relatives are the chimpanzees, with whom we last shared a common ancestor about 5-6 million years ago. 98% of our protein-coding regions are identical. However, despite our close similarities when it comes to the protein-coding regions in our genome, our cognitive abilities and the size of our brains differ considerably. The Non coding regions, which cover 98% of our genome, are believed to be one driver of the differences between the two species. These regions regulate gene expression, are involved in transposon reassembly and the production of non-coding RNAs.
Transposable elements (TEs) are elements contained within the non-coding region, which have the ability to move around the genome and regulate nearby genes. They are also responsible for the emergence of non-coding RNAs, including non-coding RNAs smaller than 200 nucleotides, called small RNAs.
In this project, small RNAs from humans and chimpanzees were collected from forebrain progenitor cells. Their differential expression and closeness with TEs were analysed, in an attempt to investigate if their differences have had an evolutionary role in human and chimpanzee brain development.
We identified six different types of small RNAs: miRNA, piRNA, tRNA, snoRNA, snRNA and circRNA. 712 small RNAs were found to be differentially expressed, 423 of which were up regulated and 278 down-regulated in human samples. 18 highly expressed small RNAs were found to intersect with transposable elements (TEs) - mainly downstream on the TEs - indicating that they may be TE-derived small RNAs, and of TEs acting as their promoters. Finally, we analyzed the conservation between primate groups of piRNAs and miRNAs in the UCSC genome browser and found that UCSC conservation tracks indicating human-specific piRNAs.
In this study, we show differences in small RNAs expression in forebrain progenitors between humans and chimpanzees. This takes us one step closer to understanding how small RNA expression may contribute to the emergence of human cognitive abilities and brain development. (Less) - Popular Abstract
- Why are we so different?
Our closest living relative is the chimpanzee; we last shared a common ancestor about 5-6 million years ago. Although our DNA is 98% identical, the human brain is about 3 times larger than the chimpanzee brain. A part of the brain called the cerebral cortex contains twice as many cells in humans than in chimpanzees. The cerebral cortex plays important roles in cognitive abilities such as awareness, memory, language and thought.
About 98% of our genome does not contain the code necessary to make proteins, called the non-coding regions. Contained within these so-called non-coding regions is a type of non-coding molecules called small RNAs which are known to turn gene expressions on and off. Also contained... (More) - Why are we so different?
Our closest living relative is the chimpanzee; we last shared a common ancestor about 5-6 million years ago. Although our DNA is 98% identical, the human brain is about 3 times larger than the chimpanzee brain. A part of the brain called the cerebral cortex contains twice as many cells in humans than in chimpanzees. The cerebral cortex plays important roles in cognitive abilities such as awareness, memory, language and thought.
About 98% of our genome does not contain the code necessary to make proteins, called the non-coding regions. Contained within these so-called non-coding regions is a type of non-coding molecules called small RNAs which are known to turn gene expressions on and off. Also contained within these non-coding regions are transposable elements (TEs) – often called “jumping” genes. These are small sequences that can move around the genome by being “copy and pasted” into different locations. By “jumping” to new locations inside the genome they can provide new materials that can lead to the emergence of small RNAs.
Here we set out to investigate whether small RNAs might have a role in explaining the differences between the human and chimpanzee brain. To do this, small RNA sequencing data was processed from human and chimpanzee forebrain progenitor cells. Subsequently, small RNA expression analysis was performed and the closeness of small RNAs with TEs was analysed.
We identified six different types of small RNAs in our dataset: miRNAs, piRNAs, snRNAs, snoRNAs, tRNAs and circRNAs. Of these, 423 small RNAs were expressed higher and 278 were expressed lower in the human group compared to the chimpanzee group. Interestingly, 18 highly expressed small RNAs were found to intersect or overlap with TEs, which could indicate that these small RNAs are derived from TEs sequences.
Small RNAs that are only found in humans could help explain the emergence of human-specific features. To consider this, we looked at the conservation of highly expressed piRNAs and miRNAs between the human and primate species in the UCSC genome browser. Here, we found an indication of a human-specific piRNAs, that are not present in other primate species.
This study takes us a step closer in understanding how the human and chimpanzee brains differ, and the emergence of human cognitive abilities. It will hopefully lead to more studies of small RNAs, that explore their functions and impact in the evolution of the human brain.
Master’s Degree Project in Bioinformatics 60 credits 2021
Department of Biology, Lund University
Advisor: Diahann Atacho
Laboratory of Molecular Neurogenetics, Faculty of Medicine, Lund University, Lund, Sweden. (Less)
Please use this url to cite or link to this publication:
http://lup.lub.lu.se/student-papers/record/9059736
- author
- Halldórsdóttir, María
- supervisor
- organization
- course
- BINP52 20202
- year
- 2021
- type
- H2 - Master's Degree (Two Years)
- subject
- language
- English
- id
- 9059736
- date added to LUP
- 2021-06-29 14:02:22
- date last changed
- 2021-06-29 14:02:22
@misc{9059736,
abstract = {{Our closest living relatives are the chimpanzees, with whom we last shared a common ancestor about 5-6 million years ago. 98% of our protein-coding regions are identical. However, despite our close similarities when it comes to the protein-coding regions in our genome, our cognitive abilities and the size of our brains differ considerably. The Non coding regions, which cover 98% of our genome, are believed to be one driver of the differences between the two species. These regions regulate gene expression, are involved in transposon reassembly and the production of non-coding RNAs.
Transposable elements (TEs) are elements contained within the non-coding region, which have the ability to move around the genome and regulate nearby genes. They are also responsible for the emergence of non-coding RNAs, including non-coding RNAs smaller than 200 nucleotides, called small RNAs.
In this project, small RNAs from humans and chimpanzees were collected from forebrain progenitor cells. Their differential expression and closeness with TEs were analysed, in an attempt to investigate if their differences have had an evolutionary role in human and chimpanzee brain development.
We identified six different types of small RNAs: miRNA, piRNA, tRNA, snoRNA, snRNA and circRNA. 712 small RNAs were found to be differentially expressed, 423 of which were up regulated and 278 down-regulated in human samples. 18 highly expressed small RNAs were found to intersect with transposable elements (TEs) - mainly downstream on the TEs - indicating that they may be TE-derived small RNAs, and of TEs acting as their promoters. Finally, we analyzed the conservation between primate groups of piRNAs and miRNAs in the UCSC genome browser and found that UCSC conservation tracks indicating human-specific piRNAs.
In this study, we show differences in small RNAs expression in forebrain progenitors between humans and chimpanzees. This takes us one step closer to understanding how small RNA expression may contribute to the emergence of human cognitive abilities and brain development.}},
author = {{Halldórsdóttir, María}},
language = {{eng}},
note = {{Student Paper}},
title = {{Differential expression of small RNAs in human and chimpanzee and the role of transposable elements}},
year = {{2021}},
}