Research in the Paralkar Lab spans the spectrum from human patient sample studies and mouse models to cutting-edge molecular biology tools, high-throughput sequencing approaches, and novel computational algorithms, all with the goal of gaining insight into how the transcription of coding genes and noncoding ribosomal DNA genes is regulated in hematopoietic stem cells, myeloid progenitors, and in leukemia.

rRNA Transcription in Hematopoiesis and Leukemia

Ribosomal RNA (rRNA) forms the majority of cellular RNA, and its transcription in the nucleolus by RNA Polymerase I from ribosomal DNA (rDNA) repeats accounts for the bulk of all transcription. rRNA transcription rates vary dramatically between different normal cell types in the hematopoietic tree, and leukemic cells have characteristic prominent nucleoli, indicating robust ribosome synthesis.

The rate of ribosome production has far-reaching influence on the fate of the cell, and dictates its size, proliferation, and ability to translate global or specific mRNAs. Little is known however about how rRNA transcription is regulated and fine-tuned across normal and malignant tissues, and whether this regulation can be targeted for leukemia treatment.

The Paralkar Lab has identified that key hematopoietic and leukemic transcription factors bind to rDNA and regulate rRNA transcription, and we are interested in understanding how the binding of cell-type-specific transcription factors regulates the activity of Polymerase I and the transcription of rRNA in normal hematopoiesis, and how this regulation is co-opted in leukemia to drive abundant ribosome biogenesis.

Stemness and Differentiation in Hematopoiesis and Leukemia

Normal hematopoiesis requires an intricate balance in the bone marrow between the ability of stem cells to maintain themselves for decades of life while producing billions of mature blood cells every day. This balance is maintained by the combinatorial activity of transcription factors and chromatin proteins that dictate the transcription of coding gene networks instructing fate choice decisions. Several of the critical factors involved in these decisions are mutated in acute and chronic leukemias, and their mutations tip the equilibrium in the bone marrow towards accumulation of aberrant progenitor populations.

The Paralkar Lab is interested in gaining a detailed mechanistic understanding of how chromatin proteins regulate the stemness-differentiation balance, and how mutations in them produce malignancy.

Bioinformatic Pipelines for Genetics and Epigenetics

Current bioinformatic pipelines for high-throughput studies like whole genome sequencing, RNA-seq, ChIP-seq, and single cell RNA-seq are limited in their ability to map repetitive elements of the genome like ribosomal DNA. Such loci therefore tend to be ignored in genome wide analyses. Given that rRNA accounts for the bulk of the transcriptional output of the cell, the inability to map datasets to rDNA has historically been a major limitation, and has created a significant knowledge gap in our understanding of the most abundant RNA in the cell.

The Paralkar Lab has developed customized genomes and computational pipelines to map datasets to rDNA, and we are interested in developing advanced tools to map and interpret the genetic and epigenetic profiles of rDNA in normal and malignant cells.

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