Libri Lab
What is a transcription factor? Classical biology tells us that a transcription factor binds to a promoter and activates (or represses) gene expression by promoting (or inhibiting) the initiation of transcription. What about transcription factors that activates gene expression by inhibiting initiation? As in a literary text, a string of characters do not make a story if punctuation marks and conventions do not tell where to start reading and in which direction. In this study we show that Rap1 and other transcription factors called General Regulatory Factors prevent transcription to initiate from inappropriate sites. They function as “guardians” of gene expression fidelity by telling the RNA polymerase where to start transcribing and in which direction.
General Regulatory Factors: guardians of transcription fidelity
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Drawing: Noelle Triaureau
In their absence, spurious initiation occurs frequently generating RNAs that have a different coding potential and that are often degraded by post-transcriptional quality control pathways. Thus these factors promote faithful and robust gene expression not only by regulating the usage of a defined transcription initiation site, but by preventing dispersed initiation at many inappropriate sites.
These findings challenge some of the traditional perspectives on gene expression. For instance, they tell us that the mere fact that a gene is transcribed does not necessarily imply that it is expressed: it depends on the quality of the RNA produced, in this case where it starts from. And perhaps that transcription can start much more frequently than we used to think: as for hyperactive kids, canalizing RNA polymerases activity to the right targets is a major challenge for achieving the best (gene expression) behavior.
Transcription originates in regions of the genome that are generally depleted in nucleosomes and are therefore called Nucleosome Depleted Regions (NDRs). NDRs harbor promoters and contain binding sites for transcriptional activators. In many instances transcription is generated in both directions from NDRs even when only one of the transcription events produces a functional RNA. Bi-directional initiation by many promoters generates transcription events producing non-coding RNAs that have no apparent function but that can interfere with the expression of canonical genes and with other DNA-associated processes (e.g. replication). Cells have adopted strategies for limiting non-functional transcription initiation from bi-directional promoters. However, the underlying mechanisms for this control on initiation are only partially understood. In this study we describe a novel mechanism by which a class of transcription factor inhibit non-functional transcription initiation, thus providing a new paradigm for the control of transcription fidelity.
General Regulatory Factors are a class of transcription factors that are responsible for the robust transcription of many highly expressed genes, such as those encoding ribosomal protein, factors involved in glycolysis and snoRNAs. They bind NDRs, and have important roles in preventing nucleosomes from invading the NDR, which is thought to negatively affect transcription. However, the mechanisms of transcription activation by these essential proteins remains poorly understood, in spite of many studies in the last thirty years.
Often unexpected findings come out from studies directed elsewhere, as when shopping for something and coming back home with something completely different. The authors depleted these factors and generated high resolution transcription maps to study transcription termination. Surprisingly, they found that depletion of these transcription factors, instead of simply preventing the expression of target genes, as would have been expected, led to massive changes in the position where transcription starts. This alters dramatically the quality of the genetic message: pretty much as reading a text with capital letters in the middle of sentences (instead of their beginning) and altered spacing between the characters to generate meaningless words. In many cases, the absence of these proteins caused the appearance of many novel non-coding RNAs, often starting exactly at the site where the factor was previously bound.
When these proteins are present, they “sit” in the NDR and, together with additional factors, sterically prevent transcriptional initiation form occurring at inappropriate positions or in the wrong direction. In so doing they ensure the fidelity of initiation and gene expression and also suppress a large share of non-coding transcription.
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Challal, D., Barucco, M., Kubik, S., Feuerbach, F., Candelli, T., Geoffroy, H., Benaksas, C., Shore, D., and Libri, D. (2018). General Regulatory Factors Control the Fidelity of Transcription by Restricting Non-coding and Ectopic Initiation. Mol. Cell 72, 955-969.e7.