Role of Epigenetic Modifications of DNA in Gene Regulation

Joseph Ecker, Salk Institute for Biological Studies

0000-0001-5799-5895

ACCESS Allocation Request MCB130189

CoPI:	Manoj Hariharan	Salk Institute for Biological Studies
Abstract:	The major focus of our lab is to study the effect of DNA methylation, a heritable epigenetic mark affecting gene regulation in almost all the cells in various organisms. For this purpose, we generate genome-wide maps of DNA methylation at base resolution. We process the large amounts of sequencing data to accurately quantify the levels of methylation at every Cytosine (“C”) residue in a given sample. We then compare these levels across samples and identify regions showing the differences in DNA methylation. Based on these, we get insights into the functions of gene regulatory mechanisms and further lead us to making discoveries of process that are involved in human health and disease, or plant development etc. Recently, we developed novel assays to study the DNA methylation at a much higher resolution – with each single cell. Due to this improvement and technological advances, we can now delve deeper into the complex mechanisms of gene regulation, going beyond the mass of cells to single cells. These also include quantifying the methylation profiles and levels of tens of thousands of transcripts, chromatin conformation, etc., simultaneously within the same individual cell (multi-omic assay). In the application, we outline the major scientific projects based on these assays, their significance, and how the high-performance computational resources provided through ACCESS (at Purdue-Anvil) will be of immense value for successfully implementing these projects.

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Allocations:

2024	Indiana Jetstream2 Large Memory	2,000,000.0 SUs
2024	Indiana Jetstream2 Storage	50,000.0 GB
2024	Purdue Anvil CPU	30,814,398.0 SUs
2024	Purdue Anvil GPU	160,000.0 GPU Hours
The estimated value of these awarded resources is $463,687.90. The allocation of these resources represents a considerable investment by the NSF in advanced computing infrastructure for the U.S. The dollar value of the allocation is estimated from the NSF awards supporting the allocated resources.
2023	Purdue Anvil CPU	12,002,879.0 SUs
2023	Purdue Anvil GPU	2,000.0 GPU Hours
2023	TACC Dell/Intel Knights Landing, Skylake System (Stampede2)	50,000.0 Node Hours
2023	TACC Long-term tape Archival Storage (Ranch)	12,000.0 GB
The estimated value of these awarded resources is $64,861.98. The allocation of these resources represents a considerable investment by the NSF in advanced computing infrastructure for the U.S. The dollar value of the allocation is estimated from the NSF awards supporting the allocated resources.

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