Jj Miranda, PhD

Assistant Investigator, Gladstone
Assistant Professor
Department of Cellular and Molecular Pharmacology
+1 415 502-2783
Research Overview: 

Genes in a cell are organized like clothes in a closet. Similar kinds are grouped together; types that are used often are separated from those not currently needed. This organization even changes in response to external stimuli. In the summer, shorts and T-shirts are in an accessible drawer while hats and scarves are tucked in a box in the back. Indeed, our cells use different genes in response to temperature, aging, and illness. Our lab is interested in understanding the molecular basis of genome organization: How are drawers formed in a cell? What proteins act as boxes for DNA?

Ubiquitous long-range interactions fold genomes into defined conformations. The CCCTC-binding factor (CTCF) has repeatedly emerged as a necessary component for the formation of loops that bridge distal DNA elements on the same and even different chromosomes to regulate transcription. ~10,000 binding sites localize mostly to intergenic regions, but also to introns, promoters, and exons. This dynamic and regulated genome organization is one of the large-scale cellular phenomena now becoming amenable to atomic resolution mechanistic understanding through the concerted efforts of genetics, biochemistry, and structural biology.

Our laboratory studies the genome organization of human viruses associated with cancer. Our long-term goal is to understand the structure-function mechanisms that couple genome organization and transcriptional regulation. We have chosen to examine viruses as our systems of interest not only because of relevance to human disease, but also because viral genomes, unlike human chromosomes, are genetically tractable and well annotated.

Primary Thematic Area: 
Virology & Microbial Pathogenesis
Secondary Thematic Area: 
Cancer Biology & Cell Signaling
Research Summary: 
Spatial organization of viral genomes in the three-dimensional space of the nucleus. Chromatin regulation of viral transcription during cancer.


Featured Publications: 

Epstein-Barr virus latency type and spontaneous reactivation predict lytic induction levels.

Biochemical and biophysical research communications

Phan AT, Fernandez SG, Somberg JJ, Keck KM, Miranda JL

Bendamustine reactivates latent Epstein-Barr virus.

Leukemia & lymphoma

Fernandez SG, Miranda JL

Occupancy of chromatin organizers in the Epstein-Barr virus genome.


Holdorf MM, Cooper SB, Yamamoto KR, Miranda JJ

Molecular architecture of CTCFL.

Biochemical and biophysical research communications

Campbell AE, Martinez SR, Miranda JJ

CTCF terminal segments are unstructured.

Protein science : a publication of the Protein Society

Martinez SR, Miranda JL

The yeast DASH complex forms closed rings on microtubules.

Nature structural & molecular biology

Miranda JJ, De Wulf P, Sorger PK, Harrison SC