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New Insights on DNA Transcription: Start Region Shown to Be Directional

2015-02-19 / To bind enzymes that read a gene at the right place, the DNA contains so-called promoters, recognition sequences that are located near the transcription start sites of the genes. Since the advent of high-throughput sequencing technology, which enables the precise investigation of gene expression patterns, scientists had shown that a large percentage of promoters is not unidirectional and that the DNA is read on both opposing strands. Now, in the present study, Professor Uwe Ohler of the Max DelbrĂĽck Center for Molecular Medicine (MDC) and Professor James T. Kadonaga of the University of California in San Diego (USA) have shown in human cells that a central part of promoters, the core promoter, is intrinsically unidirectional. Thus, transcripts of the opposing DNA strand arise from their own core promoters (Molecular Cell, doi:10.1016/j.molcel.2014.12.029)*.

Our genetic material, the DNA, is double-stranded and packaged in a highly compacted state so that it can fit into the tiny space of the cell nucleus. It is tightly wound into so-called nucleosomes, which are connected by free DNA segments. In this it resembles a pearl necklace. On the DNA fragments between the individual "pearls" are recognition sequences, so-called promoters. Here, enzymes that read the DNA can bind and make a copy of the blueprint for the production of proteins. This copying process is called transcription.

A promoter is divided into several parts that regulate, for example, in which cells the subsequent gene is to be read. The part that lies immediately before the gene to be read is called the core promoter and is of special significance for the initiation of transcription. Professor Ohler and his colleagues have now shown in human cells that this core promoter is intrinsically unidirectional. The transcription machinery runs from there only in the direction of the gene and does not also read the opposing DNA strand.

If the second strand is copied as well, this arises from a separate core promoter. This core promoter is located in the same region as the first, which is why researchers previously assumed that the direction of the gene is not encoded in the promoter.

Over half of the promoters only enable unidirectional transcripts

By means of high-throughput experiments and quantitative analysis, Professor Ohler and his colleagues determined that in fact about 40 percent of the genes have two opposite core promoters at variable distances. Through the copy of the opposing strand a long non-coding RNA arises (lncRNA), i.e. a transcript, which is not translated into a protein and whose function has not yet been elucidated. More than half of the promoters, however, only show the recognition sequence for one direction, namely the direction in which the gene lies. Here a reverse-directed core promoter and other recognition sequences for the counterpart are lacking.

Influence on gene regulation?

A comparison of the different promoter types showed that the structure of the “string of pearls” around them differs. In the nucleosomes the DNA is wrapped around histone proteins. Depending on whether the promoter allows transcription in one or in both directions, and whether a gene is located on the opposite side or not, different histones can be found in the adjacent nucleosomes.

Since reverse-directed core promoters are common but not universal, the researchers suggest that these help to regulate the transcription of the gene. For example, it is conceivable that they increase the local concentration of transcription factors. An indication of this is that genes whose promoters have recognition sequences for both directions are read more often.

*Human Promoters Are Intrinsically Directional

Sascha H.C. Duttke1,8, Scott A. Lacadie5,8, Mahmoud M. Ibrahim5,6, Christopher K. Glass2,3, David L. Corcoran7, Christopher Benner4, Sven Heinz2,4, James T. Kadonaga1,*, Uwe Ohler5,6,*

1Section of Molecular Biology

2Department of Cellular and Molecular Medicine

3Department of Medicine

 University of California, San Diego, La Jolla, CA 92093, USA

4Salk Institute for Biological Studies, La Jolla, CA 92037, USA

5Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany

6Department of Biology, Humboldt University, 10115 Berlin, Germany

7Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA

8 Co-first Authors

*Correspondence: jkadonaga@ucsd.edu (J.T.K.), uwe.ohler@mdc-berlin.de (U.O.)

Source: MDC

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