Gene editing and the role of KRAB-zinc finger proteins (ZNFs) in human brain development
(2021) MOBN03 20202Degree Projects in Molecular Biology
- Abstract
- Despite being their closest evolutionary relatives, chimpanzees have a substantially different brain compared to humans: Homo sapiens display larger and more complex forebrains, although the protein-coding genes between the two species are basically unchanged. Therefore, differences in the transcriptome and in regulatory networks must be further investigated to better understand the dissimilarities between the two species. In a previous study performed in Jakobsson’s laboratory (Johansson et al., 2020), three human-specific Krüppel-associated box (KRAB) domain-containing zinc-finger proteins (KRAB-ZNFs), which are part of the largest family of transcriptional regulators in higher vertebrates, were found to be highly expressed in the human... (More)
- Despite being their closest evolutionary relatives, chimpanzees have a substantially different brain compared to humans: Homo sapiens display larger and more complex forebrains, although the protein-coding genes between the two species are basically unchanged. Therefore, differences in the transcriptome and in regulatory networks must be further investigated to better understand the dissimilarities between the two species. In a previous study performed in Jakobsson’s laboratory (Johansson et al., 2020), three human-specific Krüppel-associated box (KRAB) domain-containing zinc-finger proteins (KRAB-ZNFs), which are part of the largest family of transcriptional regulators in higher vertebrates, were found to be highly expressed in the human brain during early development. In this study, the role of these KRAB-ZNFs (ZNF138, ZNF248, ZNF558) during brain development is investigated using CRISPRi experiments, allowing their exploration as transcriptional regulators in human forebrain neural progenitor cells (fbNPCs). By investigating the consequences of the transcriptional inhibition of ZNF138, ZNF248, and ZNF558, we could identify – via RNA-sequencing – any gene that was directly regulated by any one of these proteins. The study on ZNF558 was already initiated, and the gene regulated by this ZNF had been previously identified (Johansson et al., 2020). Thus, to further analyze this regulator’s role in brain development, cerebral organoids were cultured using the available ZNF558 KD cell lines. This investigation showed that the lack of ZNF558 causes differences in growth patterns during early stages of the organoid differentiation. The results obtained in this project shed some light on the role as transcriptional regulators of the candidate KRAB-ZNFs during brain development. However, further investigations, such as their influence on the proteome in the developing brain, are necessary for a deeper understanding of their function. (Less)
- Popular Abstract
- From chimp to human – a trip into our brain
Our brain is known to be considerably big and more complex than that of other apes, even when compared to our closest evolutionary relative, the chimpanzee. However, the most studied part of our DNA (the protein coding genes) show 98% sequence identity between the two species. These limited discrepancies cannot explain all the extensive and relevant differences between the brains of humans and chimps. Instead, we focus on how much of each gene product (expression levels) is present in each species, which might explain some of the species differences.
One family of transcription factors (the KRAB-ZNFs ) has recently raised our interest in the study of brain development and evolution as the... (More) - From chimp to human – a trip into our brain
Our brain is known to be considerably big and more complex than that of other apes, even when compared to our closest evolutionary relative, the chimpanzee. However, the most studied part of our DNA (the protein coding genes) show 98% sequence identity between the two species. These limited discrepancies cannot explain all the extensive and relevant differences between the brains of humans and chimps. Instead, we focus on how much of each gene product (expression levels) is present in each species, which might explain some of the species differences.
One family of transcription factors (the KRAB-ZNFs ) has recently raised our interest in the study of brain development and evolution as the levels of the individual KRAB-ZNFs vary quite significantly between humans and chimpanzees. In this study, we investigate the role of three human-specific KRAB-ZNFs (ZNF138, ZNF248, and ZNF558) in brain development. To do so, the transcription of these target genes was turned-off, allowing us to assess the consequences of their absence in a 2D in vitro model of brain development, neural progenitor cells. Even though usually KRAB-ZNFs regulate the transcription of other genes, we found that ZNF138 does not directly regulate any other gene. This led to the hypothesis that ZNF138 might have a different function compared to most of the other KRAB-ZNFs, making it an interesting candidate for future analyses that might shed more light on the different mechanisms of action of these TFs.
The previously described experiment had already been performed on ZNF558. To further investigate this transcription factor, we therefore cultured cerebral organoids, a 3D in vitro model that partly reproduces a developing human brain. We compared organoids grown from cells that still expressed ZNF558 with those derived from cells where ZNF558 was inhibited. We observed that the organoids with no ZNF558 seem to be more chimp-like in regard to their smaller size early in the culture. These results hint to a relevant function of ZNF558 during human brain development.
Together, our results could open the way to new and exciting studies about the role of KRAB ZNFs in brain development, possibly shading more light on some neurodevelopmental diseases that are not yet fully understood.
Master’s Degree Project in Molecular Biology, Molecular Genetics & Biotechnology. 60 credits Department of Biology, Lund University
Supervisor: Johan Jakobsson Wallenberg Neurocentrum, BMC (Lund University). Molecular Neurogenetics (Less)
Please use this url to cite or link to this publication:
http://lup.lub.lu.se/student-papers/record/9057803
- author
- Adami, Anita
- supervisor
- organization
- course
- MOBN03 20202
- year
- 2021
- type
- H2 - Master's Degree (Two Years)
- subject
- language
- English
- id
- 9057803
- date added to LUP
- 2021-06-22 14:57:43
- date last changed
- 2021-06-22 14:57:43
@misc{9057803,
abstract = {{Despite being their closest evolutionary relatives, chimpanzees have a substantially different brain compared to humans: Homo sapiens display larger and more complex forebrains, although the protein-coding genes between the two species are basically unchanged. Therefore, differences in the transcriptome and in regulatory networks must be further investigated to better understand the dissimilarities between the two species. In a previous study performed in Jakobsson’s laboratory (Johansson et al., 2020), three human-specific Krüppel-associated box (KRAB) domain-containing zinc-finger proteins (KRAB-ZNFs), which are part of the largest family of transcriptional regulators in higher vertebrates, were found to be highly expressed in the human brain during early development. In this study, the role of these KRAB-ZNFs (ZNF138, ZNF248, ZNF558) during brain development is investigated using CRISPRi experiments, allowing their exploration as transcriptional regulators in human forebrain neural progenitor cells (fbNPCs). By investigating the consequences of the transcriptional inhibition of ZNF138, ZNF248, and ZNF558, we could identify – via RNA-sequencing – any gene that was directly regulated by any one of these proteins. The study on ZNF558 was already initiated, and the gene regulated by this ZNF had been previously identified (Johansson et al., 2020). Thus, to further analyze this regulator’s role in brain development, cerebral organoids were cultured using the available ZNF558 KD cell lines. This investigation showed that the lack of ZNF558 causes differences in growth patterns during early stages of the organoid differentiation. The results obtained in this project shed some light on the role as transcriptional regulators of the candidate KRAB-ZNFs during brain development. However, further investigations, such as their influence on the proteome in the developing brain, are necessary for a deeper understanding of their function.}},
author = {{Adami, Anita}},
language = {{eng}},
note = {{Student Paper}},
title = {{Gene editing and the role of KRAB-zinc finger proteins (ZNFs) in human brain development}},
year = {{2021}},
}