Salk Institute for Biological Studies


Katherine A. Jones

Katherine A. Jones

Regulatory Biology Laboratory



Transcription Mechanisms in Human Disease

Our laboratory is interested in the transcriptional mechanisms responsible for rapid induction of mammalian genes. We are currently focused on the control of RNAPII elongation at the HIV-1 promoter by the HIV-1 Tat protein, which acts through an RNA element to recruit the host cell P-TEFb (CycT1:CDK9) elongation factor. We recently found that an alternative splicing factor, SKIP, also regulates RNAPII transcription elongation. SKIP associates with P-TEFb and is required for Tat activation, and current studies are seeking to identify how SKIP and associated factors control transcription elongation at HIV-1 and cellular genes. We are also examining how non-coding regulatory RNAs control transcription elongation and P-TEFb activity, and how transcription elongation is coupled to specific chromatin modifications, including H3K4 methylation and H3K36 methylation in vivo. These studies should help us better understand the intricate links between transcription elongation, nucleosome methylation, and RNA processing and export in human cells.

Another area of interest is the mechanisms that regulate Wnt and Notch signaling in human colon cancers. We recently showed that the Wnt co-activator, beta-catenin, interacts with factors required for H3K4 methylation of target genes, and that the APC tumor suppressor functions to down-regulate beta-catenin transcription at target genes. APC represses transcription through recruiting the CtBP co-repressor, and also promotes the degradation and turnover of beta-catenin at target genes. Interestingly, mutant APC proteins, which are found in human colon cancers, are unable to bind CtBP and unable to repress Wnt target genes, such as c-Myc, in vivo. Beta-catenin and other co-regulators appear in a cyclic fashion at Wnt genes in vivo, in a manner that requires APC-mediated turnover of the complex. We are interested in assessing whether the cyclic recruitment of Wnt coregulators directs cyclic transcription, and how cycling of Wnt transcription may affect Notch target genes. We recently found that the Notch co-activator Mastermind, co-ordinates transcriptional activation with turnover of the Notch intracellular domain activator. This is controlled by binding of Mastermind to the CDK8, a kinase that phosphorylates the C-terminal PEST regulatory domain of Notch. Recent studies indicate that Notch transcription is strongly regulated at the level of transcription elongation through P-TEFb and SKIP, and are studying how these factors are recruited and function in response to Notch signaling.

"The search for unified theories is not limited to those who study physics or the cosmos. A 'unified theory' of gene expression is required to explain how transcription—the complex, multistep process that generates messenger RNA copies from protein-encoding genes—is coordinated within the cell."

If stretched out, the DNA of a single human cell would form a thin thread about six feet in length. To fit inside the cell nucleus, the DNA is threaded around histone proteins and coiled up in a condensed structure called chromatin. When genes are actively transcribed, the tightly folded chromatin must open up just enough to give the transcriptional complex access to the DNA.

Recently, Jones and her team discovered that Spt6, a histone "chaperone" protein that functions to move nucleosomal histones out of the path of the oncoming transcription complex, interacts directly with RNA polymerase II (RNAPII), the central catalytic enzyme responsible for copying genes to RNA. Surprisingly, the complex assembled by Spt6 on RNAPII does not include factors required for transcription, but instead includes enzymes that work with Spt6 to modify the histones during transcription, as well as other proteins that transfer onto the newly made RNA to negotiate its export from the nucleus. They are currently identifying new proteins in this complex that integrate transcription with chromatin organization and downstream steps in gene expression.

The lab has also discovered that transcription elongation and histone methylation of highly induced genes is controlled by RNAbinding proteins that mediate alternative splicing of RNAs. Interestingly, these positive elongation factors become inactivated in cells that are subjected to various kinds of stress, resulting in the rapid shut-off of many cellular genes. However, within the HIV-1 genome and at a handful of cellular genes, transcription is induced by environmental or genotoxic stress, suggesting that stress might also destroy negative regulators of transcription.

Jones' lab recently discovered that a central human RNA-binding protein plays a hitherto unsuspected role in the repression of stressregulated genes. This transcriptional inhibitor protein is removed from the nucleus upon stress, releasing transcription at HIV-1 and other responsive genes. Transcription elongation requires either the inactivation of this negative elongation factor by stress or, in normal cells, its release from the promoter via positive-acting elongation factors. Therefore under stress, transcription elongation may be uncoupled from the Spt6-RNAPII complex.

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