Biochemistry and Molecular Biology
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Ross Hardison

Ross Hardison

Main Content

  • T. Ming Chu Professor of Biochemistry and Molecular Biology
304 Wartik Laboratory
University Park, PA 16802
Email: rch8@psu.edu
Phone: (814) 863-0113

Research Interests

Genomics and gene regulation

Research Summary

Genomics of Gene Regulation in Mammals

Hardison lab

 Cells in a particular lineage are derived from multipotential progenitor cells by the processes of commitment, differentiation and maturation. These processes are mediated via induction of lineage-specific genes and repression of other genes that are not part of the lineage. Hence understanding the mechanisms of gene regulation are key to understanding the most fundamental events in biology. Furthermore, aberrant or variant gene expression is not only a cause of overt disease (such as inherited anemias) but it also determines much of the inherited susceptibility to a wide variety of diseases. 

Despite its critical importance, in complex organisms we do not even have a rudimentary idea of a “regulatory code”, i.e. we have not deciphered how information in DNA determines the expression of particular genes at the correct time and place and at the appropriate amount. Of course, we know that regulation of gene expression involves occupancy of cis-regulatory modules (CRMs) by transcription factors – often by recognition of specific binding site motifs, recruitment of co-activators and co-repressors and modifications of the chromatin structure. However, a full picture of these epigenetic features and how they result in induction and repression of specific genes is not yet available.   

We explore these questions in several systems, one of which is a mouse cell line model of erythroid differentiation (collaboration with Drs. Mitch Weiss and Gerd Blobel, Childrens Hospital of Philadelphia). G1E cells are derived from mouse ES cells with a knockout of the gene Gata1, which encodes a transcription factor required for erythroid differentiation. We restore GATA1 in an estradiol-inducible manner by expressing a GATA1-ER hybrid protein in the G1E-ER4 subline. After activation of GATA1-ER, the cells differentiate from proliferating progenitor cells into erythroblasts, making abundant hemoglobin and changing morphology dramatically. We are measuring many aspects of both gene expression and relevant epigenetic features throughout the mouse genome during differentiation, using high through-put methods such as massively parallel sequencing of highly enriched DNA (Illumina and SOLiD platforms) and hybridization to high-density tiling arrays (Affymetrix and NimbleGen). In particular, we measure comprehensively changes in gene expression during this GATA1-dependent differentiation (Affymetrix arrays and RNA-seq). We also measure genome-wide occupancy by the transcription factors GATA1, GATA2,TAL1, and CTCF, as well as chromatin accessibility (DNase hypersensitive sites) and histone modifications in the chromatin (activating marks H3K4me1 and H3K4me3 and the repressing Polycomb mark H3K27me3).    

With this wealth of information, one can see that the interplay of chromatin structure and occupancy by transcription factors helps determine the level of gene expression. While a different story can be deciphered for each gene, some general trends are emerging. Most genes are not expressed even in the proliferating progenitors, and many of these are packaged into chromatin that lacks histone modifications (“dead zones”, perhaps constitutive heterochromatin). Levels of gene expression vary over many orders of magnitude, and within this cohort of expressed genes, we find thousands that change their expression level at least two-fold, with more genes repressed than induced. The major differences in chromatin structure distinguish the “off” genes from the expressed genes; this chromatin structure is established by the time of commitment to erythroid differentiation. In contrast, the induction and repression of genes is not associated with large-scale changes in chromatin structure, although in some cases the induced genes show increased amounts of H3K4me3. Rather, induction and repression appear to be determined by the interplay of transcription factors within the already established chromatin landscape. In particular, occupancy of CRMs by both GATA1 and TAL1 is almost invariably associated with induction. CRMs in the neighborhoods of many repressed genes are bound by GATA1 but TAL1 is removed. Perhaps these are hallmarks of protein complexes that recruit co-activators to induced genes and co-repressors to repressed genes.    

This work on epigenetic features and gene expression is complemented by a project using interspecies sequence alignments (comparative genomics) to find functional regions within noncoding DNA sequences. This long-standing collaboration with Drs. Webb Miller, Francesca Chiaromonte and others has led to the development of software for whole-genome alignments (Miller), use of machine-learning to predict regulatory regions from their patterns in multi-species sequence alignments (Chiaromonte and James Taylor), and the testing of these predictions for function as enhancers and promoters by gene transfer into mammalian erythroid cell lines. We also collaborate with large consortia analyzing genome sequences of various vertebrates (mouse, rat, chicken, rhesus macaque, and platypus). We are active in the ENCODE project, which seeks to identify all functional elements in the human genome using high throughput biochemical and genetic methods. We have a long-standing interest in relating human genotype to phenotype, including maintaining a database of human mutations that lead to changes in hemoglobins or thalassemias (inherited anemias). Recently, we were part of a group headed by Drs. Stephan Schuster, Vanessa Hayes and Webb Miller, who determined the genome sequences of Bushmen and a representative of the south African Bantu, Archbishop Desmond Tutu. All these projects are part of our interwoven efforts to understand regulatory regions and how they evolved, and how changes in them lead to medically and physiologically important phenotypes.

 

Hardison figure 1

Figure legend, Hardison lab

Figure Legend: Dynamics of the epigenetic landscape during erythroid induction. The figure shows82.5 kb around Zfpm1, a gene that is induced immediately after restoration of GATA1. The purple rectangles on the top line mark known CRMs identified in Wang et al. (2007). Underneath the gene structures are indicators of induction (red). This is followed by tracks showing the normalized number of mapped reads for each of the epigenetic features in both differentiating G1E-ER4 cells (with GATA1-ER activated) and progenitor G1E cells (no GATA1). Peaks for GATA1 binding are also marked, by red rectangles. At the bottom is a diagram interpreting the dynamic changes in transcription factor binding at the several CRMs in and around Zfpm1.

Selected Publications

In PubMed, search “hardison r not hardison rm”

  • Hardison, Ross C. (2010) Variable evolutionary signatures at the heart of enhancers. News and Views, Nature Genetics 42: in press, September issue.
  • Schuster SC, Miller W, Ratan A, Tomsho LP, Giardine B, Kasson LR, Harris RS, Petersen DC, Zhao F, Qi J, Alkan C, Kidd JM, Sun Y, Drautz DI, Bouffard P, Muzny  DM, Reid JG, Nazareth LV, Wang Q, Burhans R, Riemer C, Wittekindt NE, Moorjani P, Tindall EA, Danko CG, Teo WS, Buboltz AM, Zhang Z, Ma Q, Oosthuysen A, Steenkamp  AW, Oostuisen H, Venter P, Gajewski J, Zhang Y, Pugh BF, Makova KD, Nekrutenko A, Mardis ER, Patterson N, Pringle TH, Chiaromonte F, Mullikin JC, Eichler EE, Hardison RC, Gibbs RA, Harkins TT, Hayes VM. (2010) Complete Khoisan and Bantu genomes from southern Africa. Nature 463:943-947.
  • Chih-Hao Hsu, Yu Zhang, Ross C. Hardison, NISC Comparative Sequencing Program, Eric Green, and Webb Miller (2010) An Effective Method for Detecting Gene Conversion Events in Whole Genomes, J. Computational Biology, accepted.
  • Yu M, Riva L, Xie H, Schindler Y, Moran TB, Cheng Y, Yu D, Hardison R, Weiss MJ, Orkin SH, Bernstein BE, Fraenkel E, Cantor AB. (2009) Insights into GATA-1-mediated gene activation versus repression via genome-wide chromatin occupancy analysis. Molecular Cell 36:682-695.
  • Cheng Y, Wu W, Kumar SA, Yu D, Deng W, Tripic T, King DC, Chen KB, Zhang Y, Drautz D, Giardine B, Schuster SC, Miller W, Chiaromonte F, Zhang Y, Blobel GA, Weiss MJ, Hardison RC. (2009) Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression. Genome Res. 19:2172-2184. Epub 2009 Nov 3.
  • Hardison, Ross C. (2010) Comparative Genomics, Chapter 19 in the textbook Human Genetics - Principles and Approaches - 4th Edition, Editors: Friedrich Vogel, Arno Motulsky, Stylianos Antonarakis, and Michael Speicher, Springer Publishing, pp. 557-588 (981 pages total).
  • Zhang Y, Wu W, Cheng Y, King DC, Harris RS, Taylor J, Chiaromonte F, Hardison RC. (2009) Primary sequence and epigenetic determinants of in vivo occupancy of genomic DNA by GATA1. Nucleic Acids Res. 37:7024-7038. Epub ahead of print, Sept. 18.
  • Tripic T, Deng W, Cheng Y, Zhang Y, Vakoc CR, Gregory GD, Hardison RC, and Blobel GA. (2009) SCL and associated proteins distinguish active from repressive GATA transcription factor complexes. BLOOD. 113:2191-2201. Epub 2008 Nov 14.
  • Hardison, Ross C. (2009) It takes (LMO) two to tango (An Inside Blood commentary). BLOOD 113: 5693.
  • Chou ST, Khandros E, Bailey LC, Nichols KE, Vakoc C, Yao Y, Huang Z, Crispino JD, Hardison RC, Blobel GA, Weiss MJ. (2009) Graded repression of PU.1/Sfpi1 gene transcription by GATA factors regulates hematopoietic cell fate. BLOOD 114: 983-994. [Epub ahead of print Jun 2., 2009].
  • Forget, Bernard G. and Hardison, Ross C. (2009) The Normal Structure and Regulation of Human Globin Gene Clusters, Chapter 3 in the book Disorders of Hemoglobins: Genetics, Pathophysiology, and Clinical Management - 2nd Edition, Editors M.H. Steinberg, B.G. Forget, D.R. Higgs, D.J. Weatherall (Cambridge University Press, Cambridge, UK), pp. 46-61.
  • den Dunnen JT, Sijmons RH, Andersen PS, Vihinen M, Beckmann JS, Rossetti S,Talbot CC Jr, Hardison RC, Povey S, Cotton RG. (2009) Sharing data between LSDBs andcentral repositories. Hum Mutat. 30:493-495.
  • Kaput J, Cotton RG, Hardman L, Watson M, Al Aqeel AI, Al-Aama JY, Al-Mulla F, Alonso S, Aretz S, Auerbach AD, Bapat B, Bernstein IT, Bhak J, Bleoo SL, Blöcker H, Brenner SE, Burn J, Bustamante M, Calzone R, Cambon-Thomsen A, Cargill M,Carrera P, Cavedon L, Cho YS, Chung YJ, Claustres M, Cutting G, Dalgleish R, den Dunnen JT, Díaz C, Dobrowolski S, dos Santos MR, Ekong R, Flanagan SB, Flicek P, Furukawa Y, Genuardi M, Ghang H, Golubenko MV, Greenblatt MS, Hamosh A, HancockJM, Hardison R, Harrison TM, Hoffmann R, Horaitis R, Howard HJ, Barash CI,Izagirre N, Jung J, Kojima T, Laradi S, Lee YS, Lee JY, Gil-da-Silva-Lopes VL,Macrae FA, Maglott D, Marafie MJ, Marsh SG, Matsubara Y, Messiaen LM, Möslein G, Netea MG, Norton ML, Oefner PJ, Oetting WS, O'Leary JC, de Ramirez AM, PaalmanMH, Parboosingh J, Patrinos GP, Perozzi G, Phillips IR, Povey S, Prasad S, Qi M, Quin DJ, Ramesar RS, Richards CS, Savige J, Scheible DG, Scott RJ, Seminara D,Shephard EA, Sijmons RH, Smith TD, Sobrido MJ, Tanaka T, Tavtigian SV, Taylor GR,Teague J, Töpel T, Ullman-Cullere M, Utsunomiya J, van Kranen HJ, Vihinen M, Webb E, Weber TK, Yeager M, Yeom YI, Yim SH, Yoo HS; Contributors to the Human VariomeProject Planning Meeting. (2009) Planning the human variome project: the Spain report. Hum Mutat. 30:496-510.
  • Cheng Y, King DC, Dore LC, Zhang X, Zhou Y, Zhang Y, Dorman C, Abebe D, Kumar S, Chiaromonte F, Miller W, Green RD, Weiss MJ, Hardison RC (2008) Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif. Genome Res. 18: 1896-1905.
  • Louis C. Dore, Julio D. Amigo, Camila O. dos Santos, Zhe Zhang, Xiaowu Gai, John W. Tobias, Duonan Yu, Christine Dorman, Weisheng Wu, Ross C. Hardison, Barry H. Paw and Mitchell J. Weiss (2008) A GATA-1-regulated microRNA locus essential for erythropoiesis. Proc. Natl. Acad. Sci., USA, 105:3333-3338. [Epub 2008 Feb 26]
  • Wesley C. Warren, LaDeana W. Hillier, Jennifer A. Marshall Graves, Ewan Birney, Chris P. Ponting, Frank Grützner, Katherine Belov, Webb Miller, and many authors in the Platypus Genome Sequence Project, including from Penn State Robert S. Harris and Ross Hardison; last authors Elaine R. Mardis and Richard K. Wilson (2008) Genome analysis of the platypus reveals unique signatures of evolution. Nature 453: 175-183. Dr. Miller was the lead author and organizer on the section on Genome Landscape, and Drs. Hardison and Harris (with James Taylor from NYU) analyzed the implications of the very high G+C content of platypus on gene regulation.
  • Chen, Zhiyi, Luo, Hong-yuan, Basran, R.V., Rosenfield, C.V., Patrinos, G.P., Hardison, Ross C., Steinberg, M.H., Chui, David H.K. (2008) A T>G transversion at nucleotide -567 upstream of the G-gamma-globin gene in a GATA-1 binding motif is associated with elevated HbF. Mol. Cell. Biology 28: 4386-4393.
  • Svitlana Tyekucheva, Kateryna D. Makova, John E. Karro, Ross C. Hardison, Webb Miller and Francesca Chiaromonte (2008) Human-macaque comparisons illuminate variation in neutral substitution rates. Genome Biology 9: R76/
  • John E. Karro, Martin Peifer, R.C. Hardison, M. Kollmann and Hans Hennig von Grünberg (2008) Exponential decay of GC-content detected by variation in local strand symmetric substitution rates affects the isochore structure of mammalian genomes. Mol. Biol. and Evol. 25: 362-374. [Epub 2007 Nov 27]
  • Camila O. dos Santos, Louis C. Dore, Eric Valentine, Suresh Shelat, Ross C. Hardison, Manik Ghosh, Wei Wang, Richard S. Eisenstein, Fernando F. Costa, Mitchell J. Weiss (2008) An iron reponsive element-like stem-loop regulates alpha hemoglobin stabilizing protein mRNA. J. Biol. Chem., 283: 26956-26964.
  • Hardison, Ross C. (2008) Globin genes on the move. Minireview for Journal of Biology (BioMed Central) 7: 35.
  • Kasturi, Jyotsna, Acharya, Raj, and Hardison, Ross (2008) Identifying Conserved Discriminative Motifs, in Pattern Recognition in Bioinformatics, eds. Madhu Chetty, Aligoune Ngom and Shandar Ahmad, Third International Association for Pattern Recognition, International Conference PRIB 2008, in the series Lecture Notes in Computer Science, eds. S. Istrail, P. Pevzner and M. Waterman (Volume 5265/2008), Publisher Springer Berlin / Heidelberg, pp. 334-348. [One of 39 technical papers selected from 121 submissions.]
  • Griffith OL, Montgomery SB, Bernier B, Chu B, Aerts S, Sleumer MC, Bilenky M, Haeussler M, Griffith M, Gallo SM, Giardine B, Mahony S, Hooghe B, Van Loo P, Blanco E, Ticoll A, Lithwick S, Portales-Casamar E, Donaldson IJ, Robertson G, Wadelius C, De Bleser P, Vlieghe D, Halfon MS, Wasserman W, Hardison R, Bergman CM, Jones SJM; The Open Regulatory Annotation Consortium. (2008) ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Research, 36 (Database issue): D107-113. [Epub 2007 Nov 15].
  • Birney, E. and many authors from the ENCODE Project Consortium (2007) The ENCODE pilot project: identification and analysis of functional elements in 1% of the human genome. Nature 447:799-816. Authors from Penn State were James Taylor, Ross C. Hardison, David C. King, Minmei Hou, Joel D. Martin, and Webb Miller. They contributed to the sections on “Regulation of transcription” (pp. 804-807) and “Evolutionary constraint and population variability” (pp. 809-812).
  • Webb Miller, Kate Rosenbloom, Ross C. Hardison, Minmei Hou, James Taylor, Brian Raney, Richard Burhans, David C. King, Robert Baertsch, Daniel Blankenberg, Sergei L. Kosakovsky Pond, Anton Nekrutenko, Belinda Giardine, Svitlana Tyekucheva, Mark Diekhans, Thomas H. Pringle, William J. Murphy, Arthur Lesk, George M. Weinstock, Kerstin Lindblad-Toh, Richard A. Gibbs, Eric S. Lander, Adam Siepel, David Haussler, W. James Kent (2007) 28-way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Res. 17: 1797-1808.
  • King, David C., James Taylor, Ying Zhang, Yong Cheng, Heather A. Lawson, Joel Martin, ENCODE groups for Transcriptional Regulation and Multispecies Alignment, Francesca Chiaromonte, Webb Miller, and Ross C. Hardison (2007) Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data. Genome Res. 17:775-786.
  • Margulies, Elliott H., Gregory M. Cooper, George Asimenos, Daryl J. Thomas, and many authors from the ENCODE Multispecies Sequence Analysis Consortium, including from Penn State Minmei Hou, James Taylor, Ross Hardison and Webb Miller (2007) Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res. 17:760-774. The Penn State group provided one of the three major sets of alignments and helped analyze the patterns of conservation and constraint in the several functional classes.
  • Blankenberg, Daniel, James Taylor, Ian Schenck, Jianbin He, Yi Zhang, Matthew Ghent, Narayanan Veeraraghavan, Istvan Albert, Webb Miller, Kateryna Makova, Ross C. Hardison, and Anton Nekrutenko (2007) A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly. Genome Res. 17:960-964.
  • Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, Mardis ER, Remington KA, Strausberg RL, Venter JC, Wilson RK, and many authors in the Rhesus Macaque Genome Sequencing and Analysis Consortium, including from Penn State Hardison RC, Makova KD, Miller W, Burhans R, Karro JE, Ma J, Addo-Quaye C, Schenck I, Giardine B, and Lesk A. (2007) Evolutionary and biomedical insights from the rhesus macaque genome. Science 316: 222-234. Drs. Miller, Makova and Hardison were three of the 13 analysis leaders; the Penn State group made major contributions to the sections on “Determining ancestral genome structure”, “Gene family expansions”, “Orthologous genes”, “Sex chromosome evolution” and “Human disease orthologs in macaque” pp. 224-233.
  • Giardine B, van Baal S, Kaimakis P, Riemer C, Miller W, Samara M, Kollia P, Anagnou NP, Chui DH, Wajcman H, Hardison RC, Patrinos GP. (2007) HbVar database of human hemoglobin variants and thalassemia mutations: 2007 update. Hum Mutat. 28: 206.
  • Giardine, Belinda, Cathy Riemer, Tim Hefferon, Daryl Thomas, Fan Hsu, Julian Zielenski, Yunhua Sang, Laura Elnitski, Garry Cutting, Heather Trumbower, Andy Kern, Robert Kuhn, George P. Patrinos, Jim Hughes, Doug Higgs, David Chui, Charles Scriver, Manyphong Phommarinh , Santosh K. Patnaik, Olga Blumenfeld, Bruce Gottlieb, Jim Kent, Webb Miller, Ross C. Hardison (2007) PhenCode: Connecting ENCODE data with mutations and phenotype, Human Mutat. 28: 554-562.
  • Wang, Hao, Ying Zhang, Yong Cheng, Yuepin Zhou, David C. King, James Taylor, Francesca Chiaromonte, Jyotsna Kasturi, Hanna Petrykowska, Bryan Gibb, Christine Dorman, Webb Miller, Louis C. Dore, John Welch, Mitchell J. Weiss, Ross C. Hardison (2006) Experimental Validation of Predicted Mammalian Erythroid Cis-Regulatory Modules. Genome Res. 16:1480-1492.
  • Taylor, James, Svitlana Tyekucheva, David C. King, Ross C. Hardison, Webb Miller and Francesca Chiaromonte (2006) ESPERR: Learning Strong and Weak Signals in Genomic Sequence Alignments to Identify Functional Elements. Genome Res. 16:1585-1595.