About

Deborah Wuttke is a Professor in the Department of Biochemistry at the University of Colorado Boulder. She earned her PhD from the California Institute of Technology in 1994 and completed her postdoctoral fellowship at the Scripps Research Institute from 1994 to 1996. Her research spans two main areas: telomere biology and plasticity in molecular recognition. Her work in telomere biology focuses on understanding how telomere-associated proteins protect and maintain telomeres, which are essential for chromosome stability and cellular proliferation. This research is significant for human health, as dysregulation of telomere protection or telomerase activity is linked to many human diseases, including over 90% of human cancers. Her investigations include examining the contributions of telomerase subunits, how the single-strand DNA overhang is shielded from DNA damage responses, and the regulation of telomerase activity. In the area of molecular recognition, her research explores the structural plasticity involved in the specific binding of flexible ligands such as single-stranded DNA, RNA, peptides, and carbohydrates. She aims to understand how the malleability of binding interfaces contributes to recognition specificity and function, particularly focusing on telomere end-binding proteins like Pot1 and Cdc13. Her work employs high-resolution structural determination and in vivo assessments to elucidate these mechanisms.

Research topics

• Biology
• Genetics
• Cell biology
• Chemistry
• Biochemistry
• Crystallography
• Computational biology
• Biophysics

Selected publications

• MECP2 MBD-ID Module: A Unified DNA/RNA Binding Interface Disrupted in Rett Syndrome

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-02-15

  articleOpen accessSenior authorCorresponding

  Rett syndrome neurodevelopmental disorder is caused by mutations in the gene encoding the epigenetic regulator MECP2. While the MECP2 methyl-CpG binding domain (MBD) is well-characterized, the function of the adjacent intervening domain (ID) remains largely understudied. The ID has been described as a distinct RNA-binding region, yet evidence also suggests RNA competitively displaces MECP2 from DNA. Here, we address these conflicting findings by demonstrating the MBD and ID do not function in isolation but as a synergistic functional unit, establishing a new model for MECP2 function. We show the ID significantly enhances affinity of the MBD for methylated DNA by ∼35-fold. Moreover, together these two subdomains form a high-affinity, promiscuous RNA-binding module, with affinity for structured RNAs increased over 1,000-fold compared to the MBD or ID alone. We find binding to RNA precludes binding to DNA, such that the integrated MBD-ID unit explains the competition phenomenon. Analysis of Rett syndrome-associated ID mutations (R167W, K174Q, and R190H) and a therapeutic MiniGene reveals they do not disrupt methyl-DNA binding but instead selectively weaken RNA and non-methylated DNA binding, thereby disrupting the competitive balance between nucleic acid ligands. Our work establishes the MBD-ID module as MECP2's central nucleic acid interaction hub, whose disruption provides a potential molecular etiology of Rett syndrome due to mutations in the intervening domain.

  PublisherOA PDFDOI

• DNA affinity driven chromatin dynamics determine Estrogen Receptor α transcriptional activity independent of RNA binding

  Research Square · 2026-03-10

  preprintOpen access1st authorCorresponding
  PublisherOA PDFDOI

• The canonical RPA complex interacts with Est3 to regulate yeast telomerase activity

  Proceedings of the National Academy of Sciences · 2025-02-06 · 4 citations

  articleOpen access

  In most eukaryotic organisms, cells that rely on continuous cell division employ the enzyme telomerase which replenishes chromosome termini through the addition of telomeric repeats. In budding yeast, the telomerase holoenzyme is composed of a catalytic core associated with two regulatory subunits, Est1 and Est3. The Est1 protein binds a telomere-specific RPA-like complex to recruit telomerase to chromosome ends. However, the regulatory function of the Est3 subunit has remained elusive. We report here that an interaction between Est3 and the canonical RPA complex is required for in vivo telomerase function, as revealed by mutations in RPA2 that confer an Est (Ever shorter telomeres) phenotype, characteristic of a defect in the telomerase pathway. Binding between RPA and telomerase, which is supported by compensatory charge-swap mutations in EST3 and RPA2 , utilizes a surface on Est3 that is structurally analogous to an interface on the human TPP1 protein that is required for telomerase processivity. Mutations in a subset of conserved DNA contact residues in RPA also result in short telomeres and senescence, which we show is due to a requirement for DNA binding after RPA interacts with telomerase. We propose that once RPA forms a complex with telomerase, RPA utilizes a subset of DNA-binding domains to stabilize the interaction between the telomerase active site and telomeric substrates, thereby facilitating enzyme processivity. These results, combined with prior observations, show that yeast telomerase interacts with two different high-affinity ssDNA-binding complexes, indicating that management of single-stranded DNA is integral to effective telomerase function.

  PublisherOA PDFDOI

• A Distinct Mechanism of RNA Recognition by the Transcription Factor GATA1

  Biochemistry · 2025-02-25 · 2 citations

  articleOpen accessSenior authorCorresponding

  Several human transcription factors (TFs) have been reported to directly bind RNA through noncanonical RNA-binding domains; however, most of these TFs remain to be further validated as bona fide RNA-binding proteins (RBPs). Our systematic analysis of RBP discovery data sets reveals a varied set of candidate TF-RBPs that encompass most TF families. These candidate RBPs include members of the GATA family that are essential factors in embryonic development. Investigation of the RNA-binding features of GATA1, a major hematopoietic TF, reveals robust sequence independent binding to RNAs in vitro. Moreover, RNA binding by GATA1 is competitive with DNA binding, which occurs through a shared binding surface spanning the DNA-binding domain and arginine-rich motif (ARM)-like domain. We show that the ARM-like domain contributes substantially to high-affinity DNA binding and electrostatically to plastic RNA recognition, suggesting that the separable RNA-binding domain assigned to the ARM-domain in GATA1 is an oversimplification of a more complex recognition network. These biochemical data demonstrate a unified integration of DNA- and RNA-binding surfaces within GATA1, whereby the ARM-like domain provides an electrostatic surface for RNA binding but does not fully dominate GATA1-RNA interactions, which may also apply to other TF-RBPs. This competitive DNA/RNA binding activity using overlapping nucleic acid binding regions points to the possibility of RNA-mediated regulation of the GATA1 function during hematopoiesis. Our study highlights the multifunctionality of DNA-binding domains in RNA recognition and supports the need for robust characterization of predicted noncanonical RNA-binding domains such as ARM-like domains.

  PublisherOA PDFDOI

• Transcription factors ERα and Sox2 have differing multiphasic DNA and RNA binding mechanisms

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-03-19

  preprintOpen accessCorresponding

  ABSTRACT Many transcription factors (TFs) have been shown to bind RNA, leading to open questions regarding the mechanism(s) of this RNA binding and its role in regulating TF activities. Here we use biophysical assays to interrogate the k on , k off , and K d for DNA and RNA binding of two model human transcription factors, ERα and Sox2. Unexpectedly, we found that both proteins exhibited multiphasic nucleic acid binding kinetics. We propose that Sox2 RNA and DNA multiphasic binding kinetics could be explained by a conventional model for sequential Sox2 monomer association and dissociation. In contrast, ERα nucleic acid binding exhibited biphasic dissociation paired with novel triphasic association behavior, where two apparent binding transitions are separated by a 10-20 min “lag” phase depending on protein concentration. We considered several conventional models for the observed kinetic behavior, none of which adequately explained all the ERα nucleic acid binding data. Instead, simulations with a model incorporating sequential ERα monomer association, ERα nucleic acid complex isomerization, and product “feedback” on isomerization rate recapitulated the general kinetic trends for both ERα DNA and RNA binding. Collectively, our findings reveal that Sox2 and ERα bind RNA and DNA with previously unappreciated multiphasic binding kinetics, and that their reaction mechanisms differ with ERα binding nucleic acids via a novel reaction mechanism.

  PublisherOA PDFDOI

• The RNA-binding selectivity of the RGG/RG motifs of hnRNP U is abolished by elements within the intrinsically disordered region

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-05-11

  preprintOpen accessCorresponding

  The abundant nuclear protein hnRNP U interacts with a broad array of RNAs along with DNA and protein to regulate nuclear chromatin architecture. The RNA-binding activity is achieved via a disordered ~100 residue C-terminal RNA-binding domain (RBD) containing two distinct RGG/RG motifs. Although the RNA-binding capabilities of RGG/RG motifs have been widely reported, less is known about hnRNP U's RNA-binding selectivity. Furthermore, while it is well established that hnRNP U binds numerous nuclear RNAs, it remains unknown whether it selectively recognizes sequence or structural motifs in target RNAs. To address this question, we performed equilibrium binding assays using fluorescence anisotropy (FA) and electrophoretic mobility shift assays (EMSAs) to quantitatively assess the ability of human hnRNP U RBD to interact with segments of cellular RNAs identified from eCLIP data. These RNAs often, but not exclusively, contain poly-uridine or 5'-AGGGAG sequence motifs. Detailed binding analysis of several target RNAs reveal that the hnRNP U RBD binds RNA in a promiscuous manner with high affinity for a broad range of structured RNAs, but with little preference for any distinct sequence motif. In contrast, the isolated RGG/RG of hnRNP U motif exhibits a strong preference for G-quadruplexes, similar to that observed for other RGG motif bearing peptides. These data reveal that the hnRNP U RBD attenuates the RNA binding selectivity of its core RGG motifs to achieve an extensive RNA interactome. We propose that a critical role of RGG/RG motifs in RNA biology is to alter binding affinity or selectivity of adjacent RNA-binding domains.

  PublisherOA PDFDOI

• The RNA-Binding Domain of hnRNP U Extends beyond the RGG/RG Motifs

  Biochemistry · 2024-02-08 · 6 citations

  articleOpen accessCorresponding

  Heterogeneous nuclear ribonucleoprotein U (hnRNP U) is a ubiquitously expressed protein that regulates chromatin architecture through its interactions with numerous DNA, protein, and RNA partners. The RNA-binding domain (RBD) of hnRNP U was previously mapped to an RGG/RG motif within its disordered C-terminal region, but little is understood about its binding mode and potential for selective RNA recognition. Analysis of publicly available hnRNP U enhanced UV cross-linking and immunoprecipitation (eCLIP) data identified high-confidence binding sites within human RNAs. We synthesized a set of diverse RNAs encompassing 11 of these identified cross-link sites for biochemical characterization using a combination of fluorescence anisotropy and electrophoretic mobility shift assays. These in vitro binding experiments with a rationally designed set of RNAs and hnRNP U domains revealed that the RGG/RG motif is a small part of a more expansive RBD that encompasses most of the disordered C-terminal region. This RBD contains a second, previously experimentally uncharacterized RGG/RG motif with RNA-binding properties comparable to those of the canonical RGG/RG motif. These RGG/RG motifs serve redundant functions, with neither serving as the primary RBD. While in isolation, each RGG/RG motif has modest affinity for RNA, together they significantly enhance the association of hnRNP U with RNA, enabling the binding of most of the designed RNA set with low to midnanomolar binding affinities. Identification and characterization of the complete hnRNP U RBD highlight the perils of a reductionist approach to defining biochemical activities in this system and pave the way for a detailed investigation of its RNA-binding specificity.

  PublisherOA PDFDOI

• The RNA-binding Selectivity of the RGG/RG Motifs of hnRNP U is Abolished by Elements Within the C-terminal Intrinsically Disordered Region

  Journal of Molecular Biology · 2024-07-10 · 4 citations

  articleOpen accessCorresponding
  PublisherOA PDFDOI

• Transcription factors ERα and Sox2 have differing multiphasic DNA- and RNA-binding mechanisms

  RNA · 2024-05-17 · 4 citations

  articleOpen access

  Many transcription factors (TFs) have been shown to bind RNA, leading to open questions regarding the mechanism(s) of this RNA binding and its role in regulating TF activities. Here, we use biophysical assays to interrogate the k on , k off , and K d for DNA and RNA binding of two model human TFs, ERα and Sox2. Unexpectedly, we found that both proteins exhibit multiphasic nucleic acid–binding kinetics. We propose that Sox2 RNA and DNA multiphasic binding kinetics can be explained by a conventional model for sequential Sox2 monomer association and dissociation. In contrast, ERα nucleic acid binding exhibited biphasic dissociation paired with novel triphasic association behavior, in which two apparent binding transitions are separated by a 10–20 min “lag” phase depending on protein concentration. We considered several conventional models for the observed kinetic behavior, none of which adequately explained all the ERα nucleic acid–binding data. Instead, simulations with a model incorporating sequential ERα monomer association, ERα nucleic acid complex isomerization, and product “feedback” on isomerization rate recapitulated the general kinetic trends for both ERα DNA and RNA binding. Collectively, our findings reveal that Sox2 and ERα bind RNA and DNA with previously unappreciated multiphasic binding kinetics, and that their reaction mechanisms differ with ERα binding nucleic acids via a novel reaction mechanism.

  PublisherOA PDFDOI

• A distinct mechanism of RNA recognition by the transcription factor GATA1

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-12-02

  preprintOpen accessSenior authorCorresponding

  ABSTRACT Several human transcription factors (TFs) have been reported to directly bind RNA through non-canonical RNA-binding domains; however, most of these TFs remain to be further validated as bona fide RNA-binding proteins (RBPs). Our systematic analysis of RBP discovery datasets reveals a varied set of candidate TF-RBPs that encompass most TF families. These candidate RBPs include members of the GATA family, which are essential factors in embryonic development. Investigation of the RNA-binding features of GATA1, a major hematopoietic TF, reveals robust non-sequence specific binding to RNAs in vitro . Moreover, RNA binding by GATA1 is competitive with DNA binding, which occurs through a shared binding surface spanning the DNA-binding domain and arginine-rich motif (ARM) like domain. We show that the ARM-like domain contributes both substantially to high-affinity DNA binding and electrostatically to plastic RNA recognition, suggesting that the separable RBD assigned to the ARM-domain in GATA1 is an oversimplification of a more complex recognition network. These biochemical data demonstrate a unified integration of DNA- and RNA-binding surfaces within GATA1, whereby the ARM-like domain provides an electrostatic surface for RNA binding but does not fully dominate GATA1-RNA interactions, which may also apply to other TF-RBPs. This competitive DNA/RNA binding activity using overlapping nucleic acid binding regions points to the possibility of RNA-mediated regulation of GATA1 function during hematopoiesis. Our study highlights the multifunctionality of DNA-binding domains in RNA recognition and supports the need for robust characterization of predicted non-canonical RNA-binding domains such as ARM-like domains.

  PublisherOA PDFDOI

Recent grants

• How Cyclophilins both Regulate and are Regulated by RNA

  NSF · $800k · 2017–2022

• NIH Grant R21NS059370

  NIH · $189k · 2009

• RNA Regulation of Transcription Factor Activity

  NIH · $3.2M · 2016–2026

• Single Stranded DNA Recognition in Telomeres

  NIH · $3.9M · 1999–2018

• Plasticity in the Recognition of Flexible Ligands

  NSF · $962k · 2011–2017

Frequent coauthors

• Thomas R. Cech

  University of Colorado Boulder

  19 shared

• Robert Batey

  University of Colorado Boulder

  17 shared

• Victoria Lundblad

  University of California, San Diego

  14 shared

• Karen J. Goodrich

  University of Colorado Boulder

  11 shared

• Douglas L. Theobald

  Brandeis University

  10 shared

• Sarah E. Altschuler

  University of Colorado Boulder

  9 shared

• Arthur J. Zaug

  University of Colorado Boulder

  9 shared

• Harry B. Gray

  California Institute of Technology

  7 shared

Education

• Ph.D.

  California Institute of Technology

  1994

• Other

  Scripps Research Institute

  1996

Awards & honors

• University of Colorado, College of Arts and Sciences Faculty…
• Marinus Smith Award (2017)
• University of Colorado College Scholar Award (2013)
• Innovation Award, University of Colorado (2013)
• University of Colorado College Scholar Award (2012)