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Kimberley Dej

McMaster University, Biology, Faculty Member

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I teach in biology and life sciences. I study regulatory pathways and associated chromosome dynamics vital to proper partitioning of genetic material during cell division. I have undergraduate research opportunities available on this broad theme. In science education I study implicit assumptions and expectations that bias scientific understanding, and whether and how concept inventories can help us identify and measure these factors.

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Nicolae Radu Zabet

University of Essex

Armando Marques-Guedes

UNL - New University of Lisbon

Gwen Robbins Schug

University of North Carolina at Greensboro

Jeffrey Townsend

Yale University

Jean-Jacques Hublin

Max Planck Institute for Evolutionary Anthropology

Jesper Hoffmeyer

University of Copenhagen

Saleh M . Saleh

Arish University

Michael J. Gonzalez

Universidad de Puerto Rico Rio

Richard Cloutier

Université du Québec à Rimouski

Deakin University

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Papers by Kimberley Dej

Mutations in the Drosophila Condensin Subunit dCAP-G Defining the Role of Condensin for Chromosome Condensation in Mitosis and Gene Expression in …

Genetics, Jan 1, 2004

Chromosomes are dynamic structures that are reorganized during the cell cycle to optimize them fo... more Chromosomes are dynamic structures that are reorganized during the cell cycle to optimize them for distinct functions. SMC and non-SMC condensin proteins associate into complexes that have been implicated in the process of chromosome condensation. The roles of the individual non-SMC subunits of the complex are poorly understood, and mutations in the CAP-G subunit have not been described in metazoans. Here we elucidate a role for dCAP-G in chromosome condensation and cohesion in Drosophila. We illustrate the requirement of dCAP-G for condensation during prophase and prometaphase; however, we find that alternate mechanisms ensure that replicated chromosomes are condensed prior to metaphase. In contrast, dCAP-G is essential for chromosome condensation in metaphase of single, unreplicated sister chromatids, suggesting that there is an interplay between replicated chromatids and the condensin complex. In the dcap-g mutants, defects in sister-chromatid separation are also observed. Chromatid arms fail to resolve in prophase and are unable to separate at anaphase, whereas sister centromeres show aberrant separation in metaphase and successfully move to spindle poles at anaphase. We also identified a role for dCAP-G during interphase in regulating heterochromatic gene expression.

Separation anxiety at the centromere

Trends in cell biology, Jan 1, 2000

During mitosis, replicated sister-chromatids must maintain cohesion as they attach to the mitotic... more During mitosis, replicated sister-chromatids must maintain cohesion as they attach to the mitotic spindle. At anaphase, cohesion is lost simultaneously along the entire chromosome, releasing sisters from one another and allowing them to segregate to opposite poles. During meiosis, sisters separate in a two-step process. At anaphase of meiosis I, cohesion is lost along the chromosome arms but is maintained at centromeric regions. Not until meiosis II are sister chromatids able to break the connection at the centromere and separate away from one another. Recent studies suggest that the centromere exhibits dynamics that are very different compared with those of the chromatid arms during both mitosis and meiosis. This review discusses the nature of the specialized chromatid cohesion seen at the centromere.

The endocycle controls nurse cell polytene chromosome structure during Drosophila oogenesis

Development, Jan 1, 1999

Polytene chromosomes exhibit intricate higher order chromatin structure that is easily visualized... more Polytene chromosomes exhibit intricate higher order chromatin structure that is easily visualized due to their precisely aligned component strands. However, it remains unclear if the same factors determine chromatin organization in polyploid and diploid cells. We have analyzed one such factor, the cell cycle, by studying changes in Drosophila nurse cell chromosomes throughout the 10 to 12 endocycles of oogenesis. We find that nurse cells undergo three distinct types of endocycle whose parameters are correlated with chromosome behavior. The first four endocycles support complete DNA replication; poorly banded polytene euchromatin progressively condenses during the late S phases to produce blob-like chromosomes. During the unique fifth endocycle, an incomplete late S phase is followed by a mitosis-like state during which the 64C chromosomes dissociate into 32 chromatid pairs held together by unreplicated regions. All the subsequent endocycles lack any late S phase; during these cycles a new polytene chromosome grows from each 2C chromatid pair to generate 32-ploid polytene nuclei. These observations suggest that euchromatin begins to condense during late S phase and that nurse cell polytene chromosome structure is controlled by regulating whether events characteristic of late S and M phase are incorporated or skipped within a given endocycle.

A hotspot for the Drosophila gypsy retroelement in the ovo locus

Nucleic acids …, Jan 1, 1998

The Drosophila retroelement gypsy has a number of unusual features including an unusual LTR termi... more The Drosophila retroelement gypsy has a number of unusual features including an unusual LTR terminal sequence and an apparent target sequence preference. The ovo locus is a known hotspot for gypsy insertion. We examined the target sequence preference of gypsy within ovo by isolating 26 new insertions and sequencing the gypsy/ovo junctions. Insertions were found at multiple sites within the ovo locus. The insertions clustered within an ∼150 bp region in the non-translated region of the ovoβ transcript, with most insertions falling within the first intron. There were seven sites of insertion within this region and these mostly conform to the consensus sequence YRYRYR (where Y = pyrimidine and R = purine). However, this target sequence is at best necessary but not sufficient to specify a hotspot, as there were several other sequences conforming to this consensus in the ovo locus that were not hit. The results indicate that gypsy may have a higher degree of target specificity than most infectious LTR retroelements.

Mutations in the chromosomal passenger complex and the condensin complex differentially affect synaptonemal complex disassembly and metaphase I configuration …

Genetics, Jan 1, 2009

Production of haploid gametes relies on the specially regulated meiotic cell cycle. Analyses of t... more Production of haploid gametes relies on the specially regulated meiotic cell cycle. Analyses of the role of essential mitotic regulators in meiosis have been hampered by a shortage of appropriate alleles in metazoans. We characterized female-sterile alleles of the condensin complex component dcap-g and used them to define roles for condensin in Drosophila female meiosis. In mitosis, the condensin complex is required for sister-chromatid resolution and contributes to chromosome condensation. In meiosis, we demonstrate a role for dcap-g in disassembly of the synaptonemal complex and for proper retention of the chromosomes in a metaphase I-arrested state. The chromosomal passenger complex also is known to have mitotic roles in chromosome condensation and is required in some systems for localization of the condensin complex. We used the QA26 allele of passenger component incenp to investigate the role of the passenger complex in oocyte meiosis. Strikingly, in incenpQA26 mutants maintenance of the synaptonemal complex is disrupted. In contrast to the dcap-g mutants, the incenp mutation leads to a failure of paired homologous chromosomes to biorient, such that bivalents frequently orient toward only one pole in prometaphase and metaphase I. We show that incenp interacts genetically with ord, suggesting an important functional relationship between them in meiotic chromosome dynamics. The dcap-g and incenp mutations cause maternal effect lethality, with embryos from mutant mothers arrested in the initial mitotic divisions.

Control of centromere localization of the MEI-S332 cohesion protection protein

Current biology: CB, Jan 1, 2004

In mitosis and meiosis, cohesion is maintained at the centromere until sister-chromatid separatio... more In mitosis and meiosis, cohesion is maintained at the centromere until sister-chromatid separation. Drosophila MEI-S332 is essential for centromeric cohesion in meiosis and contributes to, though is not absolutely required for, cohesion in mitosis. It localizes specifically to centromeres in prometaphase and delocalizes at the metaphase-anaphase transition. In mei-S332 mutants, centromeric sister-chromatid cohesion is lost at anaphase I, giving meiosis II missegregation. MEI-S332 is the founding member of a family of proteins important for chromosome segregation. One likely activity of these proteins is to protect the cohesin subunit Rec8 from cleavage at the metaphase I-anaphase I transition. Although the family members do not show high sequence identity, there are two short stretches of homology, and mutations in conserved residues affect protein function. Here we analyze the cis- and trans-acting factors required for MEI-S332 localization. We find a striking correlation between domains necessary for MEI-S332 centromere localization and conserved regions within the protein family. Drosophila MEI-S332 expressed in human cells localizes to mitotic centromeres, further highlighting this functional conservation. MEI-S332 can localize independently of cohesin, assembling even onto unreplicated chromatids. However, the separase pathway that regulates cohesin dissociation is needed for MEI-S332 delocalization at anaphase.

Undergraduate Essay Writing: Online and Face-to-Face Peer Reviews

CELT: Collected Essays on Learning and Teaching, 2012

We implemented two different approaches of using peer review to support undergraduate essay assig... more We implemented two different approaches of using peer review to support undergraduate essay assignments for students taking large second-year courses in life sciences and biology: a web-based online peer review (OPR) approach and a more traditional face-to-face peer review (FPR) approach that was conducted in tutorial settings. The essays consisted of a review of current literature to discuss the molecular involvement of cancer development or stem-cell growth. Following implementation of the peer reviews, we conducted a preliminary analysis of the pros and cons of using the two methods. Student and instructor feedback suggested that the activity of peer review was generally perceived as valuable regardless of which approach was used. OPR was convenient and saved time and resources relative to FPR, but the technical drawbacks using the OPR approach made it challenging for some students to use. A subsequent investigation using alternative OPR programs that offer additional functionality is planned.

The E2F cell cycle regulator is required for Drosophila nurse cell DNA replication and apoptosis

Mechanisms of …, Jan 1, 2002

During Drosophila oogenesis nurse cells become polyploid, enabling them to provide the developing... more During Drosophila oogenesis nurse cells become polyploid, enabling them to provide the developing oocyte with vast amounts of maternal messages and products. The nurse cells then die by apoptosis. In nurse cells, as in many other polyploid or polytene tissues, replication is differentially controlled and the heterochromatin is underreplicated. The nurse cell chromosomes also undergo developmentally induced morphological changes from being polytene, with tightly associated sister chromatids, to polyploid, with dispersed sister chromatids. We used female-sterile dE2F1 and dDP mutants to assess the role of the E2F cell cycle regulator in oogenesis and the relative contributions of transcriptional activation versus repression during nurse cell development. We report here that E2F1 transcriptional activity in nurse cells is essential for the robust synthesis of S-phase transcripts that are deposited into the oocyte. dE2F1 and dDP are needed to limit the replication of heterochromatin in nurse cells. In dE2F1 mutants the nurse cell chromosomes do not properly undergo the transition from polyteny to polyploidy. We also find that dDP and dE2F1 are needed for nurse cell apoptosis, implicating transcriptional activation of E2F target genes in this process.

Characterization and Reconstitution of Drosophila y-Tubulin Ring Complex Subunits

Journal of Cell Biology, Dec 25, 2000

The γ-tubulin ring complex (γTuRC) is important for microtubule nucleation from the centrosome. I... more The γ-tubulin ring complex (γTuRC) is important for microtubule nucleation from the centrosome. In addition to γ-tubulin, the Drosophila γTuRC contains at least six subunits, three of which [Drosophila gamma ring proteins (Dgrips) 75/d75p, 84, and 91] have been characterized previously. Dgrips84 and 91 are present in both the small γ-tubulin complex (γTuSC) and the γTuRC, while the remaining subunits are found only in the γTuRC. To study γTuRC assembly and function, we first reconstituted γTuSC using the baculovirus expression system. Using the reconstituted γTuSC, we showed for the first time that this subcomplex of the γTuRC has microtubule binding and capping activities. Next, we characterized two new γTuRC subunits, Dgrips128 and 163, and showed that they are centrosomal proteins. Sequence comparisons among all known γTuRC subunits revealed two novel sequence motifs, which we named grip motifs 1 and 2. We found that Dgrips128 and 163 can each interact with γTuSC. However, this interaction is insufficient for γTuRC assembly.

Mutations in the Drosophila Condensin Subunit dCAP-G Defining the Role of Condensin for Chromosome Condensation in Mitosis and Gene Expression in …

Genetics, Jan 1, 2004

Chromosomes are dynamic structures that are reorganized during the cell cycle to optimize them fo... more Chromosomes are dynamic structures that are reorganized during the cell cycle to optimize them for distinct functions. SMC and non-SMC condensin proteins associate into complexes that have been implicated in the process of chromosome condensation. The roles of the individual non-SMC subunits of the complex are poorly understood, and mutations in the CAP-G subunit have not been described in metazoans. Here we elucidate a role for dCAP-G in chromosome condensation and cohesion in Drosophila. We illustrate the requirement of dCAP-G for condensation during prophase and prometaphase; however, we find that alternate mechanisms ensure that replicated chromosomes are condensed prior to metaphase. In contrast, dCAP-G is essential for chromosome condensation in metaphase of single, unreplicated sister chromatids, suggesting that there is an interplay between replicated chromatids and the condensin complex. In the dcap-g mutants, defects in sister-chromatid separation are also observed. Chromatid arms fail to resolve in prophase and are unable to separate at anaphase, whereas sister centromeres show aberrant separation in metaphase and successfully move to spindle poles at anaphase. We also identified a role for dCAP-G during interphase in regulating heterochromatic gene expression.

Separation anxiety at the centromere

Trends in cell biology, Jan 1, 2000

During mitosis, replicated sister-chromatids must maintain cohesion as they attach to the mitotic... more During mitosis, replicated sister-chromatids must maintain cohesion as they attach to the mitotic spindle. At anaphase, cohesion is lost simultaneously along the entire chromosome, releasing sisters from one another and allowing them to segregate to opposite poles. During meiosis, sisters separate in a two-step process. At anaphase of meiosis I, cohesion is lost along the chromosome arms but is maintained at centromeric regions. Not until meiosis II are sister chromatids able to break the connection at the centromere and separate away from one another. Recent studies suggest that the centromere exhibits dynamics that are very different compared with those of the chromatid arms during both mitosis and meiosis. This review discusses the nature of the specialized chromatid cohesion seen at the centromere.

The endocycle controls nurse cell polytene chromosome structure during Drosophila oogenesis

Development, Jan 1, 1999

Polytene chromosomes exhibit intricate higher order chromatin structure that is easily visualized... more Polytene chromosomes exhibit intricate higher order chromatin structure that is easily visualized due to their precisely aligned component strands. However, it remains unclear if the same factors determine chromatin organization in polyploid and diploid cells. We have analyzed one such factor, the cell cycle, by studying changes in Drosophila nurse cell chromosomes throughout the 10 to 12 endocycles of oogenesis. We find that nurse cells undergo three distinct types of endocycle whose parameters are correlated with chromosome behavior. The first four endocycles support complete DNA replication; poorly banded polytene euchromatin progressively condenses during the late S phases to produce blob-like chromosomes. During the unique fifth endocycle, an incomplete late S phase is followed by a mitosis-like state during which the 64C chromosomes dissociate into 32 chromatid pairs held together by unreplicated regions. All the subsequent endocycles lack any late S phase; during these cycles a new polytene chromosome grows from each 2C chromatid pair to generate 32-ploid polytene nuclei. These observations suggest that euchromatin begins to condense during late S phase and that nurse cell polytene chromosome structure is controlled by regulating whether events characteristic of late S and M phase are incorporated or skipped within a given endocycle.

A hotspot for the Drosophila gypsy retroelement in the ovo locus

Nucleic acids …, Jan 1, 1998

The Drosophila retroelement gypsy has a number of unusual features including an unusual LTR termi... more The Drosophila retroelement gypsy has a number of unusual features including an unusual LTR terminal sequence and an apparent target sequence preference. The ovo locus is a known hotspot for gypsy insertion. We examined the target sequence preference of gypsy within ovo by isolating 26 new insertions and sequencing the gypsy/ovo junctions. Insertions were found at multiple sites within the ovo locus. The insertions clustered within an ∼150 bp region in the non-translated region of the ovoβ transcript, with most insertions falling within the first intron. There were seven sites of insertion within this region and these mostly conform to the consensus sequence YRYRYR (where Y = pyrimidine and R = purine). However, this target sequence is at best necessary but not sufficient to specify a hotspot, as there were several other sequences conforming to this consensus in the ovo locus that were not hit. The results indicate that gypsy may have a higher degree of target specificity than most infectious LTR retroelements.

Mutations in the chromosomal passenger complex and the condensin complex differentially affect synaptonemal complex disassembly and metaphase I configuration …

Genetics, Jan 1, 2009

Production of haploid gametes relies on the specially regulated meiotic cell cycle. Analyses of t... more Production of haploid gametes relies on the specially regulated meiotic cell cycle. Analyses of the role of essential mitotic regulators in meiosis have been hampered by a shortage of appropriate alleles in metazoans. We characterized female-sterile alleles of the condensin complex component dcap-g and used them to define roles for condensin in Drosophila female meiosis. In mitosis, the condensin complex is required for sister-chromatid resolution and contributes to chromosome condensation. In meiosis, we demonstrate a role for dcap-g in disassembly of the synaptonemal complex and for proper retention of the chromosomes in a metaphase I-arrested state. The chromosomal passenger complex also is known to have mitotic roles in chromosome condensation and is required in some systems for localization of the condensin complex. We used the QA26 allele of passenger component incenp to investigate the role of the passenger complex in oocyte meiosis. Strikingly, in incenpQA26 mutants maintenance of the synaptonemal complex is disrupted. In contrast to the dcap-g mutants, the incenp mutation leads to a failure of paired homologous chromosomes to biorient, such that bivalents frequently orient toward only one pole in prometaphase and metaphase I. We show that incenp interacts genetically with ord, suggesting an important functional relationship between them in meiotic chromosome dynamics. The dcap-g and incenp mutations cause maternal effect lethality, with embryos from mutant mothers arrested in the initial mitotic divisions.

Control of centromere localization of the MEI-S332 cohesion protection protein

Current biology: CB, Jan 1, 2004

In mitosis and meiosis, cohesion is maintained at the centromere until sister-chromatid separatio... more In mitosis and meiosis, cohesion is maintained at the centromere until sister-chromatid separation. Drosophila MEI-S332 is essential for centromeric cohesion in meiosis and contributes to, though is not absolutely required for, cohesion in mitosis. It localizes specifically to centromeres in prometaphase and delocalizes at the metaphase-anaphase transition. In mei-S332 mutants, centromeric sister-chromatid cohesion is lost at anaphase I, giving meiosis II missegregation. MEI-S332 is the founding member of a family of proteins important for chromosome segregation. One likely activity of these proteins is to protect the cohesin subunit Rec8 from cleavage at the metaphase I-anaphase I transition. Although the family members do not show high sequence identity, there are two short stretches of homology, and mutations in conserved residues affect protein function. Here we analyze the cis- and trans-acting factors required for MEI-S332 localization. We find a striking correlation between domains necessary for MEI-S332 centromere localization and conserved regions within the protein family. Drosophila MEI-S332 expressed in human cells localizes to mitotic centromeres, further highlighting this functional conservation. MEI-S332 can localize independently of cohesin, assembling even onto unreplicated chromatids. However, the separase pathway that regulates cohesin dissociation is needed for MEI-S332 delocalization at anaphase.

Undergraduate Essay Writing: Online and Face-to-Face Peer Reviews

CELT: Collected Essays on Learning and Teaching, 2012

We implemented two different approaches of using peer review to support undergraduate essay assig... more We implemented two different approaches of using peer review to support undergraduate essay assignments for students taking large second-year courses in life sciences and biology: a web-based online peer review (OPR) approach and a more traditional face-to-face peer review (FPR) approach that was conducted in tutorial settings. The essays consisted of a review of current literature to discuss the molecular involvement of cancer development or stem-cell growth. Following implementation of the peer reviews, we conducted a preliminary analysis of the pros and cons of using the two methods. Student and instructor feedback suggested that the activity of peer review was generally perceived as valuable regardless of which approach was used. OPR was convenient and saved time and resources relative to FPR, but the technical drawbacks using the OPR approach made it challenging for some students to use. A subsequent investigation using alternative OPR programs that offer additional functionality is planned.

The E2F cell cycle regulator is required for Drosophila nurse cell DNA replication and apoptosis

Mechanisms of …, Jan 1, 2002

During Drosophila oogenesis nurse cells become polyploid, enabling them to provide the developing... more During Drosophila oogenesis nurse cells become polyploid, enabling them to provide the developing oocyte with vast amounts of maternal messages and products. The nurse cells then die by apoptosis. In nurse cells, as in many other polyploid or polytene tissues, replication is differentially controlled and the heterochromatin is underreplicated. The nurse cell chromosomes also undergo developmentally induced morphological changes from being polytene, with tightly associated sister chromatids, to polyploid, with dispersed sister chromatids. We used female-sterile dE2F1 and dDP mutants to assess the role of the E2F cell cycle regulator in oogenesis and the relative contributions of transcriptional activation versus repression during nurse cell development. We report here that E2F1 transcriptional activity in nurse cells is essential for the robust synthesis of S-phase transcripts that are deposited into the oocyte. dE2F1 and dDP are needed to limit the replication of heterochromatin in nurse cells. In dE2F1 mutants the nurse cell chromosomes do not properly undergo the transition from polyteny to polyploidy. We also find that dDP and dE2F1 are needed for nurse cell apoptosis, implicating transcriptional activation of E2F target genes in this process.

Characterization and Reconstitution of Drosophila y-Tubulin Ring Complex Subunits

Journal of Cell Biology, Dec 25, 2000

The γ-tubulin ring complex (γTuRC) is important for microtubule nucleation from the centrosome. I... more The γ-tubulin ring complex (γTuRC) is important for microtubule nucleation from the centrosome. In addition to γ-tubulin, the Drosophila γTuRC contains at least six subunits, three of which [Drosophila gamma ring proteins (Dgrips) 75/d75p, 84, and 91] have been characterized previously. Dgrips84 and 91 are present in both the small γ-tubulin complex (γTuSC) and the γTuRC, while the remaining subunits are found only in the γTuRC. To study γTuRC assembly and function, we first reconstituted γTuSC using the baculovirus expression system. Using the reconstituted γTuSC, we showed for the first time that this subcomplex of the γTuRC has microtubule binding and capping activities. Next, we characterized two new γTuRC subunits, Dgrips128 and 163, and showed that they are centrosomal proteins. Sequence comparisons among all known γTuRC subunits revealed two novel sequence motifs, which we named grip motifs 1 and 2. We found that Dgrips128 and 163 can each interact with γTuSC. However, this interaction is insufficient for γTuRC assembly.