Welcome to the Rohs Lab

The main focus of our Computational Structural Biology research group is the integration of two fields of research: genomics and structural biology. Our primary goal is to reveal yet unknown molecular mechanisms underlying gene regulation using bioinformatics analyses of high-throughput sequencing and DNA methylation data of whole genomes.

Professor Rohs can accept graduate students from the following Ph.D. Programs as primary thesis adviser: Computational Biology and Bioinformatics, Molecular Biology, Chemistry, Physics, and Computer Science.

Selected Publications

Chiu et al. GBshape: a genome browser database for DNA shape annotations.
Nucleic Acids Res. 43, D103-109 (2015)

GBshape GBshape provides DNA shape annotations of entire genomes. The database currently contains annotations for minor groove width, roll, propeller twist, helix twist and hydroxyl radical cleavage for 94 different organisms. Additional genomes can easily be added in the provided framework. GBshape contains two major tools, a genome browser and a table browser. The genome browser (Figure) provides a graphical representation of DNA shape annotations along standard genome browser annotations. 

Dantas Machado et al. Evolving insights on how cytosine methylation affects protein–DNA binding.
Brief. Funct. Genomics 14(1), 61-73 (2014)

Many anecdotal observations exist of a regulatory effect of DNA methylation on gene expression. However, the underlying mechanisms of this effect are poorly understood. In this review, we summarize what is currently known about how this important epigenetic mark impacts cellular function. DNA methylation can abrogate or enhance interactions with DNA-binding proteins, or it may have no effect, depending on the context. The presence of cytosine methyl groups (Figure) can affect direct interactions between the protein and its DNA binding site, cause an indirect effect on DNA structure, and alter nucleosome stability.

Feature Review
Slattery et al. Absence of a simple code: how transcription factors read the genome.
Trends Biochem. Sci. 39(9), 381-399 (2014)

Transcription factors (TFs) play a key role in the central dogma of molecular biology by interpreting the language of DNA to control transcription. However, it has become clear that the “code” they read does not comprise DNA sequence alone. We discuss in this Feature Review the recent work that has used structural, computational, in vitro and in vivo approaches to move toward understanding the transcription factor code. We highlight the many variables that influence TF-DNA binding, including cofactors, cooperativity, and chromatin. The cover shows the IFN-β enhanceosome (Figure), an example of cooperativity through TF-TF interactions.

NAR Breakthrough Article
RECOMB/ISCB Top-10 Paper in Regulatory and Systems Genomics in 2013/14
Yang et al. TFBSshape: a motif database for DNA shape features of transcription factor binding sites.
Nucleic Acids Res. 42, D148-155 (2014)

TFBSshape Our new TFBSshape database disentangles the complex relationships between DNA sequence, its 3D structure, and protein-DNA binding specificity. This task is like solving a Rubik's cube (Figure; top face: DNA sequences with transcription factor binding sites (TFBS); left face: 3D structure of a protein-DNA complex; front face: heat map representing minor groove width patterns selected by a transcription factor (TF) in a high-throughput experiment). The TFBSshape database augments nucleotide sequence motifs with heat maps and quantitative predictions of DNA shape features for 739 TF datasets from 23 different species.

Dror et al. Covariation between homeodomain transcription factors and the shape of their DNA binding sites.
Nucleic Acids Res. 42, 430-441 (2014)

Using our new method for high-throughput prediction of DNA shape, we analyzed DNA binding sites of 168 mouse and 84 Drosophila homeodomains to determine a general DNA shape recognition code (Figure) for this family of transcription factors. We predicted DNA shape features for almost 25,000 DNA targets derived from protein binding microarray (PBM) and bacterial-one hybrid (B1H) experiments and found distinct homeodomain regions that were more correlated with either the nucleotide sequence or the DNA shape of their preferred binding sites.

Zhou et al. DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale.
Nucleic Acids Res. 41, W56-62 (2013)

We developed a new method for predicting DNA shape in a high-throughput manner on a genome-wide scale. This approach predicts structural features (several helical parameters and minor groove width) for the entire yeast genome in less than one minute on a regular laptop. The prediction can be visualized as genome browser tracks and compared to other properties of the genome such as sequence conservation.

RECOMB/ISCB Top-10 Paper in Regulatory and Systems Genomics in 2012/13
Gordân et al. Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape.
Cell Rep. 3, 1093-1104 (2013)

How transcription factors (TFs) with highly similar DNA binding-site motifs recognize distinct targets in vivo is poorly understood. In this study, we show in collaboration with Martha Bulyk's lab that the paralogous Saccharomyces cerevisiae TFs Cbf1 and Tye7 exhibit different DNA binding preferences both in vitro and in vivo, depending on the genomic context of the sites. Results of computational analyses suggest that nucleotides outside of their core binding sites contribute to specificity by influencing the three-dimensional structure of the DNA targets.

RECOMB/ISCB Top-10 Paper in Regulatory and Systems Genomics in 2012/13
Lazarovici et al. Probing DNA shape and methylation state on a genomic scale with DNase I.
Proc. Natl. Acad. Sci. USA 110, 6376-6381 (2013)

To address the relationship between DNase I cleavage rate and minor groove geometry, we predicted DNA shape parameters for sequences covering the entire range from highly to poorly cleavable. The variation in these shape parameters turned out to be highly predictive of the variation in cleavage rate. Other insights obtained from this project in collaboration with Harmen Bussemaker's and John Stamatoyannopoulos' labs were related to DNA methylation. We found that even though cytosine methylation happens in the major groove, one of its key effects is to narrow the minor groove. Thus, varying the base sequence of genomic DNA is not the only way in which the cell can modulate the landscape of minor groove shape along its genome.

Chang et al. Mechanism of origin DNA recognition and assembly of an initiator-helicase complex by SV40 large tumor antigen.
Cell Rep. 3, 1117-1127 (2013)

The first essential step in activating genomic DNA replication is the site-specific assembly of initiator proteins on origin (ori) DNA, a process that is not well characterized. In collaboration with Xiaojiang Chen's lab, we report a major step toward understanding this process by determining the long-sought cocrystal structure of the SV40 initiator/helicase, large tumor antigen (LTag), in complex with its ori DNA. The structure shows that multidomain LTag assembles on ori DNA differently from what one would expect from previous studies. The structure also reveals an intrinsic DNA shape readout mechanism using histidines.

RECOMB/ISCB Top-10 Paper in Regulatory and Systems Genomics in 2011
Slattery et al. Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins
Cell 147, 1270-1282 (2011)

In vivo transcription factor-DNA recognition is much more specific than in vitro binding. The eight Drosophila Hox proteins bind to very similar target sites but execute distinct in vivo functions. The figure illustrates that the cofactor Exd (yellow) unlocks a wide range in specificity of Hox proteins (cyan) for recognizing DNA target sites (metallic). Based on SELEX-seq experiments, we present specificity fingerprints of Hox proteins and reveal that DNA shape is a determining factor in achieving specificity. This is the first study, for which a preliminary version of our new approach for high-throughput DNA shape prediction has been applied to thousands of sequences, showing that anterior and posterior Hox proteins recognize different DNA shape. Moreover, DNA shape indicates how Hox genes have differentiated in evolution.

Bishop et al. A map of minor groove shape and electrostatic potential from hydroxyl radical cleavage patterns of DNA
ACS Chem. Biol. 6(12), 1314-1320 (2011)

The figure shows a nucleosome, the fundamental repeating unit of chromatin, bound to a compatible site in a vast sea of genomic DNA. We used the hydroxyl radial as a chemical probe to map the electrostatic potential along the DNA minor groove, and show how DNA shape underlies nucleosome formation. The nucleotide sequences in the background are occupied by nucleosomes in yeast.

Rohs et al. The role of DNA shape in protein-DNA recognition
Nature 461, 1248-1253 (2009)

nucleosome The figure illustrates the molecular shape of nucleosomal DNA when wrapped around the histone core. The narrow minor groove is color-coded in dark grey. The red mesh shows an isopotential surface with negative electrostatic potential. The shape of narrow minor groove regions induces an enhanced negative electrostatic potential, which attracts histone arginines. Such interactions between the protein and DNA contribute to the stabilization of the nucleosome core particle.

Rohs et al. Origin of specificity in protein-DNA recognition
Annu. Rev. Biochem. 79, 233-269 (2010)

In order to carry out their unique biological functions, proteins need to recognize their DNA binding sites in a highly specific manner. Specificity in protein-DNA binding is achieved through the recognition of both linear sequence and three-dimensional structure. Therefore, the nucleotide sequence of a binding site is only one part of the story, and the three-dimensional structures of both the DNA and the protein must be taken into account to fully understand recognition on a molecular basis. DNA shape is specifically recognized by a variety of protein families, and we have identified different ways of modulating DNA shape. The figure shows the shape of the molecular surface (top) of ideal A-DNA (left), B-DNA (center), and Z-DNA, and the resulting specific variations in electrostatic potential (bottom).

November 13, 2014
Two of our recent papers, Yang et al. NAR and Barozzi et al. Mol. Cell, received RECOMB/ISCB Top-10 Paper Awards in the field of Regulatory and Systems Genomics.

October 17, 2014
Paper on genome browser database for DNA shape annotation published in NAR. Congratulations, Tsu-Pei!

October 14, 2014
Review article on DNA methylation and its effect on protein-DNA binding published in Brief Funct. Genomics.

September 26, 2014
Tianyin successfully defends his Ph.D thesis. Congratulations and good luck at Google!

September 4, 2014
Remo was awarded an NSF grant for studies of human paralogous TFs.

August 14, 2014
Feature Review on how TFs read the genome published in Trends Biochem. Sci. as a cover article.

May 8, 2014
Paper with Natoli group on co-binding of TFs and nucleosomes published in Molecular Cell with Lin as a co-author.

May 7, 2014
Tianyin receives the university-wide Ph.D. Achievement Award. Congratulations, Tianyin, for this exceptional honor!

April 30, 2014
Carolina is awarded a WiSE Merit Fellowship for Ph.D. students who demonstrate exceptional work. Congratulations, Carolina!

April 22, 2014
Tianyin receives the Harrison Kurtz Award for the most outstanding Ph.D. student in the biological sciences. Congratulations, Tianyin!

January 28, 2014
NIGMS awards Remo an NIH R01 grant for studies of the genome by integrating DNA sequence and shape.

January 1, 2014
NAR Breakthrough Article on TFBSshape database published as NAR cover story.

January 1, 2014
Two collaborative articles on p53 highlighted on year-round NAR cover for 2014.

Recent news

November 9-14, 2014
RECOMB/ISCB Conference on Regulatory & Systems Genomics, San Diego, CA

November 17, 2014
Center for Genomic and Computational Biology, Duke University, Durham, NC

December 5-9, 2014
4th Zing Nucleic Acids Conference, Cancun, Mexico

February 9, 2015
Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany

BISC 481 syllabus
Strctural Bioinformatics from Atoms to Cells