We study the principles of Chromatin Regulation and Dynamics

using Genomics and Biochemistry

Welcome to Brahma Lab

Our laboratory investigates the fundamental mechanisms governing the organization of DNA inside a cell’s nucleus into chromatin. These processes play a crucial role in regulating normal cellular functions, as well as the development of diseases, including cancer. To achieve our research objective, we adopt an interdisciplinary approach utilizing cutting-edge structural and functional epigenomics, biochemistry, bioinformatics, and microscopy techniques. Our ultimate goal is to unravel how various cell types in the human body package DNA and use the information encoded in DNA in distinct ways to perform specific functions. This comprehensive exploration will enable us to gain valuable insights into disease mechanisms and, ultimately, devise interventions to alter the outcomes of such diseases.

At the Brahma Lab, we are committed to fostering an inclusive, diverse, supportive, and safe environment that promotes discovery and the development of the next generation of scientists at the forefront of chromatin biology and epigenetics research.

We are part of the Department of Genetics, Cell Biology & Anatomy at the University of Nebraska Medical Center College of Medicine.

Current Projects

Projects undertaken in the lab are united by a broad inquiry into how chromatin factors dynamically regulate the landscape of genomic nucleosomes and genome access in normal cellular development and cancer. A major emphasis is on understanding the interplay between chromatin regulators, including ATP-dependent nucleosome remodelers and transcription factors, and their roles in regulating chromatin structure and gene expression. Current efforts are aimed towards:

  • Solving the chromatin structure of genes at distinct stages of transcription.

  • Determining how ATP-dependent nucleosome remodeling modifies chromatin structure and modulates the interaction of transcription factors with chromatin, at high spatial and temporal resolution.

  • Identifying how defective chromatin remodelers drive disease gene expression patterns.

Research Highlights

How does the mammalian SWI/SNF family ATP-dependent nucleosome remodeler BAF (BRG1/Brahma Associated Factor) target specific genomic regions? BAF is a crucial regulator of chromatin accessibility and transcription, and it is recurrently mutated in >20% of human cancers. Our chemical genetic approach coupled with time-resolved CUT&Tag, CUT&RUN, and CUT&RUN.ChIP chromatin profiling in embryonic stem cells revealed a dynamic synergy between BAF, RNA Polymerase II promoter-proximal pausing, and DNA-sequence-specific transcription factors for locus-specific chromatin remodeling. Our study shows the mechanistic basis of chromatin accessibility and how BAF functions may be hijacked in cancers!

Brahma & Henikoff, 2023, Nature Genetics