Vaishnavi Kardale, Bioinformatics Centre, Savitribai Phule Pune University
The eyes are developed by the end of the second trimester in a fetus. It includes the cornea, lens, pupil, retina, and iris. Each organ needs some specific environment for its development and growth; all of which are provided for in the womb. The eye also has some special needs for its development. Some major changes in oxygen availability are associated with the formation of the eye lens.
This is how the eye lens is formed:
During embryonic development, the lens receives oxygen from the tunica vasculosa lentis and the anterior pupillary membrane. As mature lens fiber cells are being formed, the cellular organelles start eliminating, barring the nuclei and other proteins required for the functioning of the lens fiber cells gets synthesized. The synthesis of these proteins eradicates the capillary network. This creates a hypoxic (oxygen-deficient) environment leaving vitreous and aqueous humors as the only source of oxygen for the lens. The oxygen here is consumed by the mitochondria containing epithelial cells at the surface of the lens. This further intensifies the hypoxic conditions. Studies have shown that there is a 20-fold decrease in oxygen in the differentiating lens fiber cells as compared to the epithelial cell. This oxygen gradient is vital for the development of the eye and the expression of the crucial genes.
Let’s get into the details
Hypoxia is known to induce the BNIP3L gene. This gene directs the elimination of non-nuclear organelles like mitochondria, endoplasmic reticulum, and Golgi apparatus during lens fiber cell formation. The expression of the BNIP3L gene is regulated by hypoxia-induced transcription factor (HIF1). The transcription factor regulates the gene by binding to its promoter region. The lens fiber cells that lack HIF1 protein degenerate shortly after birth and cause birth defects. This reveals a possibility that the role of HIF1 is vital and might also be involved in the regulation of other genes responsible for development and homeostasis.
The HIF1 protein is a heterodimer made of two subunits HIF1α and HIF1β. From these two HIF1β is expressed constitutively while the synthesis of HIF1α is regulated according to the oxygen levels. Hence a functional map of the HIF1α – DNA complex in the eye lens was revealed through multi-omics analysis to better understand the HIF1α protein’s role in cellular processes. The study was carried out in embryonic chick lens cells. CUT and RUN were used to identify the region on DNA complementary to the HIF1α protein relative to the transcription start site of the nearest neighbor gene. CUT and RUN sequencing is performed to analyze protein DNA interactions. CUT and Run were chosen over Chromatin immunoprecipitation (ChIP) as it is faster and requires much fewer cells. While CUT and Run sequencing technology needs a few thousand cells, ChIP needs millions of cells.
What the study found:
The study showed that both hypoxia and activation of HIF1α are essential for the development of the lens fiber cell through HIF1α- dependent activation of the BNIP3L protein which is responsible for mitophagy. The study also found that the HIF1α acts both as an activator and a repressor of lens gene expression. The protein is involved in many pathways in the lens fiber cell including glycolysis, reactive oxygen species pathway, heme metabolism, apoptotic pathway, mTORC1 signaling pathway, UV response, and epithelial-mesenchymal transition. HIF1α repressed genes are involved in lipid metabolism, Wnt signaling, and homeostasis.
Further, the study found that HIF1α binding to regions within 3kbp of gene TSS is significantly associated with gene activation whereas HIF1α binding to 10kbp of gene TSS is significantly associated with gene repression. In addition to identifying the HIF1α dependent genes, the present study also analyzed 151 novel HIF1α dependent genes. These genes were found to be involved in metabolism, chromatin remodeling, development, and differentiation of multiple tissues and cell types.
Collectively the results support the requirement of HIF1α in lens development, structure, and function. Gene expression in the actual lens is complicated as it is subject to regional differences in gene requirements and hypoxic gradient in the lens itself. Therefore further analysis should be carried out in the future in the whole lens.
Also read: Ultrasound-on-chip: a novel platform for medical imaging
Reference:
- Disatham, J., Brennan, L., Chauss, D. et al. A functional map of genomic HIF1α-DNA complexes in the eye lens revealed through multiomics analysis. BMC Genomics 22, 497 (2021). https://doi.org/10.1186/s12864-021-07795-9
About author:
Vaishnavi Kardale is a master’s student at the Bioinformatics Centre, Savitribai Phule University. She is interested in studying and exploring protein folding mechanisms and wants to study them deeper in the future.
Some of her publications at BioXone are:
- https://bioxone.in/news/worldnews/the-effect-of-stroke-on-muscle-sarcomere/
- https://bioxone.in/news/worldnews/comeback-of-tuberculosis-but-its-drug-resistant-now/
- https://bioxone.in/news/worldnews/a-drug-to-reduce-covid-infection-by-99/
- https://bioxone.in/news/worldnews/artificial-intelligence-ai-for-efficient-covid-testing/
- The Corrosion Prediction from the Corrosion Product Performance
- Nitrogen Resilience in Waterlogged Soybean plants
- Cell Senescence in Type II Diabetes: Therapeutic Potential
- Transgene-Free Canker-Resistant Citrus sinensis with Cas12/RNP
- AI Literacy in Early Childhood Education: Challenges and Opportunities
PhyliCS: A Python library package to quantify Intra-tumor Heterogeneity
Sayak Banerjee, Amity University Kolkata Intra-tumor Heterogeneity ( ITH) Aggregation of a distinct set of somatic mutations leads to the generation of tumors. The set of mutations assembled by the prime tumor is known as clonal and the mutations which take place in pre-existing tumors comprise cancer cell sub-populations is known as subclonal. Consequently, the […]