Rethinking the Gene New findings Inheritance of traits that lack corresponding genes on genomic DNA Examples in plants and animals Majority of mRNA transcripts do not conform to traditional structure of gene sequence Is it time to rethink the definition of a “gene”? The rise of genomics has caused biologists to rethink many fundamental aspects of biology. Recently, a number of papers have challenged the concept of the gene. One recent animal study provided evidence for the transmission of traits despite the absence of the underlying gene in the genomic DNA. Previous studies had also made similar observations in plants. Another study indicated that the transcription of RNA from DNA in gene sequences is far more complicated than previously understood. Observations such as these have caused many scientists to consider revising the definition of a gene. © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458

Perplexing patterns of inheritance Non-Mendelian inheritance in mouse Conferred maternally and paternally Persists through generations Mediated by small fragments of RNA Reprinted by permission from Macmillan Publishers Ltd: Nature. From Figure 1b in Rassoulzadegan, M. et al. (2006) “RNA-mediated non-mendelian inheritance of an epigenetic change in the mouse” Nature 441: 469-474. In 2006, a group of researchers from France’s Universite de Nice-Sophia Antipolis reported the transmission of a clearly observable trait to offspring that were missing the corresponding gene in their genomic DNA. The Kit gene codes for a tyrosine kinase involved in a variety of developmental processes. Homozygous mice with the Kittm1Alf mutation die soon after birth, but heterozygotes survive and can be identified by their white feet and a white tail tip. An example of such a mouse is shown in the slide. Amazingly, when heterozygotes were crossed with wild-type mice, wild-type offspring (denoted by Kit* in the photograph) had the same phenotype as the heterozygote parent. The transmission of the phenotype occurred regardless of whether the heterozygote parent was male or female. Even more surprising was that the heterozygote phenotype persisted through several generations when Kit* mice were crossed. The transmission of the white feet and tail tip phenotype appears to be mediated by RNA. When the researchers injected RNA transcripts from Kittm1Alf heterozygotes into wild-type fertilized mouse eggs, they found that offspring also had white feet and tail tips. This was also the case when the RNA injected into the mouse eggs consisted of only small fragments of the Kit gene. The study described in the next slide provides evidence for the existence of RNA transcripts of multiple lengths in human cells. © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458

Unconventional transcripts in the human transcriptome Poly A+ and poly A- RNA present in both cytosol and nucleus Overlapping RNA transcripts Transcription from both DNA strands The RNA-mediated inheritance described in the previous slide suggests a new role for RNA transcripts. In 2005, a group led by Thomas R. Gingeras at the Affymetrix Corporation in Santa Clara, California had performed a comprehensive study of RNA transcripts from 10 chromosomes at 5-nucleotide resolution using a set of human cell lines. They discovered that the vast majority of RNA transcripts looked nothing like what classical molecular biology would suggest. Instead, they found overlapping transcripts of varying lengths for previously characterized genes and transcripts from both strands of DNA. Also, while it was commonly understood that polyadenylated (poly A) tails are the hallmark of mature mRNA destined for protein synthesis in the cytosol, Gingeras and his group discovered that, in both the nucleus and the cytosol, the majority of RNA transcripts lacked poly A tails, though they were not able to ascribe a function to them. © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458

A working definition Latest definition according to the Sequence Ontology Consortium “A locatable region of genomic sequence, corresponding to a unit of inheritance, which is associated with regulatory regions, transcribed regions and/or other functional sequence regions.” Studies such as those described in the previous two slides (and others) have caused many biologists to question the standard definition of a gene. The Sequence Ontology Consortium is responsible for determining how to name various sequence landmarks in the genomes of different organisms. The motivation for this is to provide a consistent way to compare similar sequences across genomic databases. The consortium recently decided to construct a new working definition of a gene. After two days of vigorous debate, they proclaimed that a gene is “a locatable region of genomic sequence, corresponding to a unit of inheritance, which is associated with regulatory regions, transcribed regions, and/or other functional sequence regions.” © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458