Molecular Recognition in Biological Systems and Bioinformatics

Organization and function of the cell nucleus; DNA replication; Transcription; 3-D microscopy and computer image analysis.

Multidimensional image analysis of genomic organization and function in the interphase nucleus of mammalian cells.
We are investigating the 3-D organization and dynamics of chromosome territories, subchromosomal domains and individual genes in the interphase cell nucleus in relationship to replication, transcription and splicing factor domains. Recent results indicate that a small subclass of nuclear matrix associated proteins mediate the organization of the chromatin into discrete territories and subchromosomal domains.

Molecular cloning of nuclear matrix proteins and genomic function.
Multidisciplinary studies spanning the fields of molecular and cell biology are in progress on nuclear matrix proteins. These include the genomic organization and regulation of nuclear matrin 3 and the analysis, nuclear assembly, cell cycle regulation, and functional properties of a recently discovered cyclophilin-type nuclear matrix protein, termed matrin cyp (cyclophilin), which co-localizes in three-dimensions with splicing component domains inside the cell nucleus.

• Fluorescence microscopes and associated software for 3-D analysis in fixed and living cells
• Automated microinjection system
• Temperature controlled chamber for live cell microscopy

A suite of in-house developed programs for analysis of microscopic images at the 2-D and 3-D levels.

Human and mouse cell lines

• Nuclear proteins involved in nuclear organization (matrin 3, SAF A, chromatin remodeling factors) or function (PNCA, pol II)
• Type I interferon gene cluster
• MHC gene locus
• Dystrophin gene
• Genes that replicate in early S-phase

Cancer

• 3-D microscopy and computer image analysis in fixed and living cells
• Microinjection into living cells
• GFP-constructs and cell lines
• FISH
• Chromosome painting

• Human chromosome paints
• A variety of BAC and cosmid probes to human genes used for FISH analysis

• HeLa
• MC63
• WI-38

http://www.biology.buffalo.edu/dept/faculty/berezney/berezney.html