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Giant chromosomes and deep sequences: what the frog egg tells us about RNA transcription

Wednesday, February 26, 2014


Joseph G. Gall, Ph.D.
Staff Member
Adjunct Professor, Johns Hopkins University
Professor, American Cancer Society
Carnegie Institution for Science

Dr. Gall’s long-term research interests have been in the structure and function of the cell, particularly the nucleus. In recent years the focus of his research has been on the organization of transcription in the nucleus. His lab has concentrated on several nuclear organelles that contain small nuclear RNAs (snRNAs), including the nucleolus, Cajal bodies, histone locus body, and the nuclear speckles. His most recent studies involve deep sequencing of cytoplasmic and nuclear RNA from the amphibian oocyte. These studies have identified a new class of stable intronic sequence RNA (sisRNA) in the nucleus derived from the introns of transcribed genes. In 2006, Dr. Gall received the Lasker Award for Special Achievement in Medical Science in recognition of his distinguished 57-year career—as a founder of modern cell biology and the field of chromosome structure and function; bold experimentalist; inventor of in situ hybridization; and early champion of women in science.


The eggs of frogs and salamanders contain exceptionally large chromosomes, known since the 19th century as “lampbrush” chromosomes because of their unusual fuzzy appearance under the microscope. The many “bristles” on these chromosomes are actually loops composed of one or a few actively transcribing genes. These genes synthesize RNA at rates much higher than in typical somatic cells, making it possible to study RNA synthesis in exquisite detail by immunofluorescent staining and in situ hybridization. The giant lampbrush chromosomes are contained in an equally giant nucleus, known as the germinal vesicle (GV). Because the GV has a diameter of up to a millimeter in some species, it can be removed manually from the egg under a dissecting microscope. In this way one can prepare absolutely pure nuclear and cytoplasmic fractions of the egg for molecular analysis. Deep sequencing of nuclear and cytoplasmic RNA confirms that the cytoplasm contains many species of messenger RNA, as expected. However, much of the nuclear RNA consists of sequences derived from the non-coding introns of genes. Some of these introns persist into the developing embryo and could be involved in gene regulatory processes.

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