Faculty of Biological Sciences

Prof Ian Hope

BA, Oxford; PhD 1984, Edinburgh.
Professor of Invertebrate Developmental Genetics
School of Biology

Background: I studied for my PhD in the Department of Molecular Biology, The University of Edinburgh for research on the human malaria parasite, Plasmodium falciparum. I then worked on the regulation of gene expression in the yeast Saccharomyces cerevisiae, as a postdoctoral research associate in Harvard Medical School. I returned to the UK to begin studying animal development in Caenorhabditis elegans as a junior staff scientist at the Medical Research Council's Laboratory of Molecular Biology, Cambridge and in 1991 moved to Leeds as a lecturer.

Contact:  Manton 9.22a, +44(0) 113 34 32889 (office) / 32888 (lab), email address for  

You can read more about Prof Hope's interests here:
http://bgypc059.leeds.ac.uk/~web/


Research Interests

Animal Development, Gene Expression and Locomotion In The Nematode, Caenorhabditis elegans

Expression of a Reporter Gene Fusion in a C. elegans embryo. The reporter gene GFP (green fluorescent protein) was fused to the C. elegans gene, F52F12.6, which encodes a homologue of human myelin transcription factor 1.

Animal development is the process by which a single cell, the fertilised egg, becomes a mature and highly complex adult organism. Differential gene expression from cell to cell is a major factor in the generation of the cellular diversity generated during development. Nerve cells and muscle cells function to drive an animal's interaction with the environment to achieve purposeful locomotion. The nematode worm Caenorhabditis elegans (C. elegans) has many characteristics which make this species a particularly powerful model system for study of various aspects of biology, including development, genetics and behaviour. (See WormClassroom for more background information.) C. elegans is the subject of the research pursued in this laboratory.

Through the years we have used a series of approaches, with progressive improvements in efficiency and quality, for determination of the developmental expression patterns for genes across the C. elegans genome. In each approach regulatory regions of C. elegans genes have been fused to a reporter gene and transgenic C. elegans lines, transformed with these constructions, were examined to reveal gene expression patterns in situ. The strategies used most recently have involved MultiSite Gateway Recombination and Recombineering. MultiSite Gateway Recombination was applied in a collaboration led by Marc Vidal (CCSB, DFCI, Harvard), and including Marian Walhout (UMass Med School). Transgenic C. elegans lines containing these reporter gene fusions were made by microprojectile bombardment rather than the microinjection procedures used previously (Reece-Hoyes, J.S. et al. ('07) BMC Genomics, 8, 27Dupuy, D., et al. ('07) Nature Biotechnology, 25, 663-8.). Currently, however, we use recombineering of fosmids to introduce reporter genes seamlessly into precise positions within genes within large genomic DNA fragments to maximize the likelihood that all regulatory elements acting on the target gene have been retained (Dolphin, C.T. and Hope, I.A. ('06) Nucleic Acids Research, 34, e72.) in a collaboration with Colin Dolphin (King's College, London). Recombineering has been used specifically to examine the operon based expression of the C. elegans sirtuin gene sir-2.1 (Bamps, S. et al. ('09) Mech. Aging Development, 130, 762-70.) and the regulation of transcription factor genes expressed in the nervous system (Bamps, S. et al. ('11) Mol. Genetics Genomics, 286, 95-107, Feng, H. et al. ('12) Gene, 494, 73-84, Feng, H. and Hope, I.A. ('13) Genesis; Journal of Genetics & Development, 51, 163-78.). We have also examined the significance of alternative transcripts for C. elegans transcription factor genes (Craig, H. et al ('13) BMC Genomics, 14, 249.) Results of these studies are contributing to our understanding of how gene expression is orchestrated, genome wide, through development.

Recently, collaborations with Elwyn Isaac (also in School of Biology, Leeds) and Netta Cohen (School of Computing, Leeds) have led into Systems Biology and Computer Modelling concerning the C. elegans nervous system and locomotory behaviour. For example, the differential turnover of proteins integral to muscle contraction has been documented (Ghosh, S. and Hope, I.A. ('10) Eur. J. Cell Biol. 89, 437-48.) and mathematical representations of C. elegans movement across an agar surface and in liquid of varying viscosities have been derived (Berri, S. et al. ('09) HFSP J., 3, 186-93, Boyle, J. et al. ('11) Frontiers in Behavioral Neuroscience, 5, 10.). Another collaboration, this time with Steve Sait (also in School of Biology, Leeds), has led in an ecological direction. The genetics behind the link between cold tolerance and longevity in C. elegans has been characterized (Savory, F. et al. ('11) PLoS One, 6, e24550.).

All the expression pattern data we have generated are available in our database. Our data may also be found in the C. elegans database WormBase, where it is integrated with the genetic and sequence data for this organism.

Faculty research groupings from which our research benefits include Ecology & Evolution and Neuroscience.
 

Faculty Research and Innovation



Studentship information

Postgraduate studentship areas:

  • Molecular Genetics of Caenorhabditis elegans.

See also:

Modules managed

BLGY2262 - Animal Developmental Biology
BLGY3251 - Animal Developmental Biology

Modules taught

BLGY1304 - Research Experience and Skills Level 1
BLGY2262 - Animal Developmental Biology
BLGY2301 - Research Experience and Skills Level 2
BLGY2321 - Marine Zoology Field Course
BLGY3251 - Animal Developmental Biology
BLGY3291 - Comparative Genomics
BLGY3340 - Biology Research Projects
BLGY3395 - Advanced Research Skills and Experience
BLGY3396 - Research Literature Review
BLGY5380M - Extended Research Project
FOBS1135/BLGY1115 - The Basis of Life/Introduction to Cell Biology: from Molecules to Cells and Tissues

Committees

Member of Graduate School Committee (Faculty representative on Graduate Board Group on Higher Doctorates)

Group Leader Prof Ian Hope  (Professor of Invertebrate Developmental Genetics)

Animal Development, Gene Expression and Locomotion In The Nematode, Caenorhabditis elegans 

Mr William Porter  (Technician)

Postgraduates

Brittany Graham (Primary supervisor) 75% FTE
Christopher Brittin (Co-supervisor) 50% FTE
Rosamund Clifford (Co-supervisor) 10% FTE
Elpiniki Kalogeropoulou (Co-supervisor) 40% FTE
Ali Taylor (Co-supervisor) 10% FTE
Laura Warwick (Co-supervisor) 33% FTE

Baines KN, Ferreira C, Hopkins PM, Shaw MA, Hope IA Aging effects of caenorhabditis elegans ryanodine receptor variants corresponding to human myopathic mutations G3: Genes, Genomes, Genetics 7 1451-1461, 2017
DOI:10.1534/g3.117.040535
View abstract

Savory FR, Benton TG, Varma V, Hope IA, Sait SM Stressful environments can indirectly select for increased longevity. Ecol Evol 4 1176-1185, 2014
DOI:10.1002/ece3.1013
View abstract

Feng H, Hope IA The Caenorhabditis elegans homeobox gene ceh-19 is required for MC motorneuron function. Genesis 51 163-178, 2013
DOI:10.1002/dvg.22365
View abstract

Hirani N, Westenberg M, Gami MS, Davis P, Hope IA, Dolphin CT A simplified counter-selection recombineering protocol for creating fluorescent protein reporter constructs directly from C. elegans fosmid genomic clones BMC Biotechnology 13 -, 2013
DOI:10.1186/1472-6750-13-1
View abstract

Craig HL, Wirtz J, Bamps S, Dolphin CT, Hope IA The significance of alternative transcripts for Caenorhabditis elegans transcription factor genes, based on expression pattern analysis BMC Genomics 14 249-, 2013
DOI:10.1186/1471-2164-14-249
View abstract

Feng H, Reece-Hoyes JS, Walhout AJM, Hope IA A regulatory cascade of three transcription factors in a single specific neuron, DVC, in Caenorhabditis elegans. Gene 494 73-84, 2012
DOI:10.1016/j.gene.2011.11.042
View abstract

Feng H, Craig HL, Hope IA Expression pattern analysis of regulatory transcription factors in Caenorhabditis elegans. Methods Mol Biol 786 21-50, 2012
DOI:10.1007/978-1-61779-292-2_2
View abstract

Bamps S, Wirtz J, Hope IA Distinct mechanisms for delimiting expression of four Caenorhabditis elegans transcription factor genes encoding activators or repressors. Mol Genet Genomics 286 95-107, 2011
DOI:10.1007/s00438-011-0630-3
View abstract

Savory FR, Sait SM, Hope IA DAF-16 andΔ9 desaturase genes promote cold tolerance in long-lived Caenorhabditis elegans age-1 mutants. PLoS One 6 e24550-, 2011
DOI:10.1371/journal.pone.0024550
View abstract

Boyle JH, Berri S, Tassieri M, Hope IA, Cohen N Gait Modulation in C. Elegans: It's Not a Choice, It's a Reflex! Front Behav Neurosci 5 10-, 2011
DOI:10.3389/fnbeh.2011.00010

Bamps S, Wirtz J, Hope IA Distinct mechanisms for delimiting expression of four Caenorhabditis elegans transcription factor genes encoding activators or repressors Molecular Genetics and Genomics 1-13, 2011

Schuster E, McElwee JJ, Tullet JMA, Doonan R, Matthijssens F, Reece-Hoyes JS, Hope IA, Vanfleteren JR, Thornton JM, Gems D DamID in C-elegans reveals longevity-associated targets of DAF-16/FoxO MOL SYST BIOL 6 -, 2010
DOI:10.1038/msb.2010.54

Ghosh SR, Hope IA Determination of the mobility of novel and established Caenorhabditis elegans sarcomeric proteins in vivo EUR J CELL BIOL 89 437-448, 2010
DOI:10.1016/j.ejcb.2009.11.027

Westenberg M, Bamps S, Soedling H, Hope IA, Dolphin CT Escherichia coli MW005: lambda Red-mediated recombineering and copy-number induction of oriV-equipped constructs in a single host BMC BIOTECHNOL 10 -, 2010
DOI:10.1186/1472-6750-10-27

Bamps S, Wirtz J, Savory FR, Lake D, Hope IA The Caenorhabditis elegans sirtuin gene, sir-2.1, is widely expressed and induced upon caloric restriction MECH AGEING DEV 130 762-770, 2009
DOI:10.1016/j.mad.2009.10.001

Berri S, Boyle JH, Tassieri M, Hope IA, Cohen N Forward locomotion of the nematode C. elegans is achieved through modulation of a single gait HFSP J 3 186-193, 2009
DOI:10.2976/1.3082260

Berri S, Boyle JH, Cohen N, Tassieri M, Tassieri M, Hope IA, Cohen N Forward locomotion of the nematode C. elegans is achieved through modulation of a single gait HFSP Journal 3 1-9, 2009
DOI:10.2976/1.3082260
View abstract

Bamps S, Hope IA Large-scale gene expression pattern analysis, in situ, in Caenorhabditis elegans. Brief Funct Genomic Proteomic 7 175-183, 2008
DOI:10.1093/bfgp/eln013
View abstract

Dupuy D, Bertin N, Hidalgo CA, Venkatesan K, Tu D, Lee D, Rosenberg J, Svrzikapa N, Blanc A, Carnec A, Carvunis AR, Pulak R, Shingles J, Reece-Hoyes J, Hunt-Newbury R, Viveiros R, Mohler WA, Tasan M, Roth FP, Le Peuch C, Hope IA, Johnsen R, Moerman DG, Barabasi AL, Baillie D, Vidal M Genome-scale analysis of in vivo spatiotemporal promoter activity in Caenorhabditis elegans NAT BIOTECHNOL 25 663-668, 2007
DOI:10.1038/nbt1305

Reece-Hoyes JS, Shingles J, Dupuy D, Grove CA, Walhout AJM, Vidal M, Hope IA Insight into transcription factor gene duplication from Caenorhabditis elegans promoterome-driven expression patterns BMC GENOMICS 8 -, 2007
DOI:10.1186/1471-2168-8-27

Deplancke B, Mukhopadhyay A, Ao WY, Elewa AM, Grove CA, Martinez NJ, Sequerra R, Doucette-Stamm L, Reece-Hoyes JS, Hope IA, Tissenbaum HA, Mango SE, Walhout AJM A gene-centered C. elegans protein-DNA interaction network CELL 125 1193-1205, 2006
DOI:10.1016/j.cell.2006.04.038

Dolphin CT, Hope IA Caenorhabditis elegans reporter fusion genes generated by seamless modification of large genomic DNA clones NUCLEIC ACIDS RES 34 -, 2006
DOI:10.1093/nar/gkl352

Reece-Hoyes JS, Deplancke B, Shingles J, Grove CA, Hope IA, Walhout AJM A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks GENOME BIOLOGY 6 -, 2005
DOI:10.1186/gb-2005-6-13-r110

Hope IA, Stevens J, Garner A, Hayes J, Cheo DL, Brasch MA, Vidal M Feasibility of genome-scale construction of promoter::reporter gene fusions for expression in Caenorhabditis elegans using a multisite gateway recombination system. Genome Res 14 2070-2075, 2004
DOI:10.1101/gr.2463804
View abstract

Dupuy D, Li QR, Deplancke B, Boxem M, Hao T, Lamesch P, Sequerra R, Bosak S, Doucette-Stamm L, Hope IA, Hill DE, Walhout AJM, Vidal M A first version of the Caenorhabditis elegans promoterone Genome Research 14 2169-2175, 2004
DOI:10.1101/gr.2497604
View abstract

Appleford PJ, Griffiths M, Yao SYM, Ng AML, Chomey EG, Isaac RE, Coates D, Hope IA, Cass CE, Young JD, Baldwin SA Functional redundancy of two nucleoside transporters of the ENT family (CeENT1, CeENT2) required for development of Caenorhabditis elegans. Mol Membr Biol 21 247-259, 2004
DOI:10.1080/09687680410001712550
View abstract

Hope IA, Mounsey A, Bauer P, Aslam S The forkhead gene family of Caenorhabditis elegans GENE 304 43-55, 2003
DOI:10.1016/S0378-1119(02)01175-7

Mounsey A, Bauer P, Hope IA Evidence suggesting that a fifth of annotated Caenorhabditis elegans genes may be pseudogenes. Genome Res 12 770-775, 2002
View abstract

Hope IA Broadcast interference - functional genomics. Trends Genet 17 297-299, 2001
View abstract

Hope IA RNAi surges on: application to cultured mammalian cells Trends in Genetics 17 pp.440-, 2001
DOI:10.1016/S0168-9525(01)02385-X

Blaxter M, Hope IA, Barstead R, Kim S Caenorhabditis elegans Yeast 17 37-42, 2000

Molin L, Mounsey A, Aslam S, Bauer PK, Young J, James M, Sharma Oates A, Hope IA Evolutionary conservation of redundancy between a diverged pair of forkhead transcription factor homologues Development (Cambridge) 127 4825-4835, 2000

Hope IA C.elegans: A practical approach, 1999

Hope IA C.elegans database, 1999

Hope IA C elegans: A Practical Approach In C. elegans: A Practical Approach , 1999

Molin L, Schnabel H, Kaletta T, Feichtinger R, Hope IA, Schnabel R Complexity of developmental control: Analysis of embryonic cell lineage specification in C.elegans using pes-1 as an early marker Genetics 151 131-141, 1999
View abstract

Hope IA, Arnold JM, Mccarroll D, Jun G, Krupa AP, Herbert R Promoter trapping identifies real genes in C-elegans Molecular and General Genetics 260 300-308, 1998
View abstract

Hope IA PCR based sex test for the platyfish xiphophorus maculatus Journal of Fish Biology 54 218-222, 1998

Coates D, Briggs DA, MacGregor D, Lynch AS, Kolakowski LF, Hope IA, Isaac RE Characterisation of ZK643-3: a putative 7TM neuropeptide receptor. Biochem Soc Trans 25 440S-, 1997

Hope IA, Albertson DG, Martinelli SD, Lynch AS, Sonnhammer E, Durbin R The C.elegans expression pattern database: A beginning Trends in Genetics 12 370-371, 1996
View abstract

Hope IA A screen of developmental expression patterns for genes predicted in the C. elegans genome project. Nature Genetics 11 309-313., 1995

Hope IA PES1 is expressed during early C. elegans embryogenesis and has homology to the fork head family of transcription factors. Development 120 505-14., 1994

Hope IA Caenorhabditis elegans, the nematode worm. In Embryos, Colour atlas of development , 1994

Hope IA Molecular markers of differentiation in Caenorhabditis elegans obtained by promoter trapping. Developmental Dynamics 196 124-132, 1993

Hope IA 'Promoter trapping' in Caenorhabditis elegans. Development 113 399-408, 1991
View abstract

Hope IA, Mahadevan S, Struhl K Structural and functional characterization of the short acidic transcriptional activation region of yeast GCN4 protein. Nature 333 635-640, 1988
DOI:10.1038/333635a0
View abstract

Struhl K, Brandl CJ, Chen W, Harbury PA, Hope IA, Mahadevan S Transcriptional activation by yeast GCN4, a functional homolog to the jun oncoprotein. Cold Spring Harb Symp Quant Biol 53 Pt 2 701-709, 1988

Hope IA, Struhl K GCN4, a eukaryotic transcriptional activator protein, binds as a dimer to target DNA. EMBO J 6 2781-2784, 1987
View abstract

HILL DE, HOPE IA, MACKE JP, STRUHL K SATURATION MUTAGENESIS OF THE YEAST HIS3 REGULATORY SITE - REQUIREMENTS FOR TRANSCRIPTIONAL INDUCTION AND FOR BINDING BY GCN4 ACTIVATOR PROTEIN SCIENCE 234 451-457, 1986

HOPE IA, STRUHL K FUNCTIONAL DISSECTION OF A EUKARYOTIC TRANSCRIPTIONAL ACTIVATOR PROTEIN, GCN4 OF YEAST CELL 46 885-894, 1986

SCAIFE J, BONE N, GOMAN M, HALL R, HOPE IA, HYDE JE, LANGSLEY G, MACKAY M, OQUENDO P, SIMMONS D ANTIGENS OF PLASMODIUM-FALCIPARUM BLOOD STAGES WITH CLINICAL INTEREST CLONED AND EXPRESSED IN ESCHERICHIA-COLI PARASITOLOGY 92 S119-S137, 1986

HOPE IA, STRUHL K GCN4 PROTEIN, SYNTHESIZED INVITRO, BINDS HIS3 REGULATORY SEQUENCES - IMPLICATIONS FOR GENERAL CONTROL OF AMINO-ACID BIOSYNTHETIC GENES IN YEAST CELL 43 177-188, 1985

HOPE IA, MACKAY M, HYDE JE, GOMAN M, SCAIFE J THE GENE FOR AN EXPORTED ANTIGEN OF THE MALARIA PARASITE PLASMODIUM-FALCIPARUM CLONED AND EXPRESSED IN ESCHERICHIA-COLI NUCLEIC ACIDS RES 13 369-379, 1985

STRUHL K, CHEN W, HILL DE, HOPE IA, OETTINGER MA CONSTITUTIVE AND COORDINATELY REGULATED TRANSCRIPTION OF YEAST GENES - PROMOTER ELEMENTS, POSITIVE AND NEGATIVE REGULATORY SITES, AND DNA-BINDING PROTEINS COLD SPRING HARB SYM 50 489-503, 1985

HALL R, HYDE JE, GOMAN M, SIMMONS DL, HOPE IA, MACKAY M, SCAIFE J, MERKLI B, RICHLE R, STOCKER J MAJOR SURFACE-ANTIGEN GENE OF A HUMAN MALARIA PARASITE CLONED AND EXPRESSED IN BACTERIA NATURE 311 379-382, 1984

HALL R, OSLAND A, HYDE JE, SIMMONS DL, HOPE IA, SCAIFE JG PROCESSING, POLYMORPHISM, AND BIOLOGICAL SIGNIFICANCE OF P190, A MAJOR SURFACE-ANTIGEN OF THE ERYTHROCYTIC FORMS OF PLASMODIUM-FALCIPARUM MOL BIOCHEM PARASIT 11 61-80, 1984

HYDE JE, GOMAN M, HALL R, OSLAND A, HOPE IA, LANGSLEY G, ZOLG JW, SCAIFE JG CHARACTERIZATION AND TRANSLATION STUDIES OF MESSENGER-RNA FROM THE HUMAN MALARIA PARASITE PLASMODIUM-FALCIPARUM AND CONSTRUCTION OF A CDNA LIBRARY MOL BIOCHEM PARASIT 10 269-285, 1984

HOPE IA, HALL R, SIMMONS DL, HYDE JE, SCAIFE JG EVIDENCE FOR IMMUNOLOGICAL CROSS-REACTION BETWEEN SPOROZOITES AND BLOOD STAGES OF A HUMAN MALARIA PARASITE NATURE 308 191-194, 1984

Hall R, Osland A, Hyde JE, Simmons DL, Hope IA, Scaife JG Processing, polymorphism, and biological significance of P190, a major surface antigen of the erythrocytic forms of Plasmodium falciparum Molecular and Biochemical Parasitology 11 61-80, 1984
DOI:10.1016/0166-6851(84)90055-0
View abstract