Katz, David et al. (2021) International Worm Meeting "The Pipeline CURE: lowering institutional barriers to research by reiteratively incorporating original C. elegans experiments throughout a biology curriculum"

Lee, Teresa, Schmeichel, Karen, Katz, David, Carpenter, Brandon

[International Worm Meeting, 2021]

Participation in research provides personal and professional benefits for undergraduates. However, some students face institutional barriers that prevent their entry into research, particularly those from underrepresented groups who may stand to gain the most from research experiences. Course-based undergraduate research experiences (CUREs) effectively scale research availability, but many only last for a single semester, which is rarely enough time for a novice to develop proficiency. To address these challenges, we established a Pipeline CURE. The Pipeline CURE integrates C. elegans epigenetics research being conducted by the Katz Lab at Emory University throughout the biology curriculum at Oglethorpe University, a nearby liberal arts college. Students are introduced to C. elegans with their first course in the major. After revisiting the research system in several subsequent courses, students can choose to participate in an upper-level research experience, led by an NIH Institutional Research and Academic Career Development Award (IRACDA) postdoctoral fellow from the Katz Lab. Preliminary data taken during implementation of The Pipeline CURE suggests that the reiterative CURE strategy can recapitulate benefits of a traditional apprenticeship lab experience entirely within the curriculum in a classroom setting. These benefits associated with The Pipeline Cure include including replacing beginner confidence with mastery and resilience via repeated exposure to the same research system. As a result, the Pipeline CURE levels the playing field by giving underrepresented students the chance to experience original research, and potentially conduct honors thesis research, without having to seek out a traditional apprenticeship lab experience. The research experience gained by students can serve as an entry to STEM careers, or provide a platform for competing for admission to graduate programs. In addition, the data generated can open new areas of research and help facilitate publication of manuscripts. As an added benefit, The Pipeline CURE also exposes postdoctoral fellows to challenges that underrepresented groups face in the classroom. Thus, by uniting evidence-based teaching methods with ongoing scientific research, the Pipeline CURE provides a new model for overcoming barriers to participation in undergraduate research, that is flexible enough to be implemented at a range of institutions using a variety of research questions.

(2021) Development "The people behind the papers - Brandon Carpenter and David Katz."

[Development, 2021]

A dynamic pattern of histone methylation and demethylation controls gene expression during development, with some processes such as formation of the zygote involving large-scale reprogramming of methylation states. A new paper in Development investigates how inherited histone methylation regulates developmental timing and the germline/soma distinction in <i>Caenorhabditis elegans</i> To hear more about the story we caught up with first author and postdoctoral researcher Brandon Carpenter, and his supervisor David Katz, Associate Professor in the Department of Cell Biology at Emory University School of Medicine in Atlanta, Georgia.

David Katz et al. (2006) Development & Evolution Meeting "Histone H3 Lysine 4 Guards The Immortality Of The Germline"

William Kelly, David Katz, Thomas Edwards

[Development & Evolution Meeting, 2006]

In the C. elegans early embryo, the chromatin in all blastomeres initially contain the euchromatic mark, di-methylation of histone H3 on lysine 4 (H3K4me2). However, upon their birth, the primordial germ cells Z2 and Z3 uniquely lose this mark. This appears to be a conserved characteristic of primordial germ cells as Drosophila pole cells also initially lack this modification. The loss of H3K4me2 has been proposed to be necessary for protecting the totipotency of the germline through chromatin-based transcriptional repression, but the mechanism of its removal is not understood. Recently, Shi et al. demonstrated that the mammalian amine oxidase LSD1 can specifically demethylate H3K4me2 (Shi et al. 2004). C. elegans has three lsd1 homologs : spr-5, amx-1 and T08D10.2. In order to ask if these genes play a role in the chromatin remodeling of Z2 and Z3, we inactivated them individually and in combination. RNAi or genetic mutation of any of these genes individually has no affect on H3K4me2 levels in Z2 and Z3. To test for redundant roles in the chromatin remodeling of Z2 and Z3, we generated a spr-5;amx-1 double mutant from two existing putative null mutations. Although the double mutants display multiple pleiotropic phenotypes, we observed no immediate effects on H3meK4 levels in Z2 and Z3. However, after multiple generations the double mutant exhibits a germline mortality phenotype, in which an increasing fraction of progeny in the population grow up sterile(black sterile phenotype). Strikingly, in these later generations, the double mutants exhibit retention of H3K4me2 in Z2 and Z3, further correlating repressive chromatin with maintenance of the germ cell lineage. In addition, the multiple generations that are required for this phenotype suggest that there can be stable inheritance of epigenetic defects through the germline and that the H3K4 demethylases may play a role in resetting H3K4 methylation at each generation.

David Katz et al. (2008) Development & Evolution Meeting "Epigenetic Reprogamming by LSD1 Contributes to Germline Immortality in C. elegans"

T. Mathhew Edwards, David Katz, William Kelly

[Development & Evolution Meeting, 2008]

Upon their specification, the two primordial germ cells (PGCs) in C. elegans, Z2 and Z3, rapidly lose the euchromatic mark di-methylation of histone H3 on lysine 4 (H3K4me2). This epigenetic erasure has been suggested to contribute to embryonic germline maintenance through chromatin-based transcriptional repression. The mammalian protein LSD1 has been shown to demethylate H3K4me2. Here we show that mutants in the C. elegans LSD1 ortholog, spr-5, exhibit progressive sterility over many generations due to defects in oogenesis and a delay in spermatogenesis. The progressive sterility correlates with increased retention of H3K4me2 in the PGCs, suggesting that SPR-5 mediated H3K4 demethylation is essential for germline immortality. In addition, microarray analysis and quantitative rt-PCR in spr-5 mutants demonstrate that the progressive sterility corresponds with a heritable build up of expression in spermatogenesis genes. Taken together, these results suggest that failure to erase H3K4me2 in the germline cycle causes a progressive failure of epigenetic erasure in the PGCs which leads to inappropriate expression of spermatogenesis genes and increasing sterility. Therefore, we propose that H3K4me2 can serve as an epigenetic memory and that LSD1 demethylases play an important role in the reprogramming of this memory in the germline, preventing inappropriate epigenetic information from being propagated from one generation to the next.

David J Katz et al. (2005) International Worm Meeting "Investigating the link between NANOS and chromatin for germ cell maintenance in C. elegans"

William G Kelly, David J Katz

[International Worm Meeting, 2005]

In Drosophila, nanos is required for primordial germ cells (PGCs) to differentiate into a functional germ line. Lack of NANOS function causes defects in germ cell migration, differentiation, and quiescence and ultimately leads to sterility in both males and females. Similarly, in mice a lack of nanos3 results in the complete loss of germ cells in both sexes (Tsuda et al. 2003) and functional loss of two of the three nanos genes in C. elegans, nos1 and nos2, also results in sterility (Subramaniam and Seydoux, 1999). It has therefore been proposed that nanos is a conserved master regulator of the germ cell fate. In the C. elegans early embryo, the chromatin in all cells contain the active chromatin mark, histone H3 methylated on lysine 4 (H3meK4). However upon their birth, the primordial germ cells Z2 and Z3 dramatically lose this mark. This loss of the active H3meK4 mark has been suggested to be part of a chromatin-based transcriptional repression mechanism. Remarkably, absence of the H3meK4 mark has been shown to be dependent upon nanos activity (Schaner et al. 2003). Thus it is possible that nanos may be partially affecting its role in maintaining the undifferentiated germ cell fate through a chromatin-based mechanism. We aim to explore this potential link by further characterizing the role of C. elegans nanos in germ cell fate. To this end, we are taking both forward and reverse genetic approaches as well as conducting ectopic expression studies.

Zarkower D et al. (1994) Worm Breeder's Gazette "mab-3 YAC Rescue"

De Bono M, Hodgkin JA, Zarkower D

[Worm Breeder's Gazette, 1994]

mab-3 YAC rescue David Zarkower, Mario de Bono, and Jonathan Hodgkin MRC Laboratory of Molecular Biology, Cambridge, England

Carpenter, Brandon et al. (2021) International Worm Meeting "C. elegans establishes germline versus soma by balancing histone methylation"

Carpenter, Brandon, Katz, David

[International Worm Meeting, 2021]

Embryos undergo extensive reprogramming at fertilization to prevent the inappropriate inheritance of histone methylation. In C. elegans, the H3K4me2 demethylase, SPR-5, and the H3K9 methyltransferase, MET-2, are maternally deposited into the oocyte where they cooperate to reestablish the epigenetic ground state of the newly formed zygote. Previous work from the Strome and Kelly Labs demonstrates that maternally deposited MES-4 maintains H3K36me2/3 at germline genes between generations to help re-establish the germline. To determine whether the MES-4 germline inheritance system antagonizes spr-5; met-2 maternal reprogramming, we examined the interaction between these two systems. Here, we show that the progeny of spr-5; met-2 mutants display a severe developmental delay that is associated with the ectopic expression of MES-4 germline genes in somatic tissues. By performing ChIP-seq on L1 progeny from spr-5; met-2 mutants, we find that MES-4 germline genes ectopically accumulate H3K36me3 in somatic tissues. Additionally, knocking down MES-4 suppresses the ectopic expression of MES-4 germline genes and rescues the developmental delay. We also show that the developmental delay is dependent upon the H3K4 methyltransferase, SET-2. More recent data from our lab uncovered a synergistic interaction between SPR-5; MET-2 maternal reprogramming and MEC Complex member, MEP-1. This interaction links maternal reprogramming of histone methylation to the somatic mechanisms that suppress germline gene expression in somatic tissues. Together, these data suggest a model where SPR-5; MET-2 maternal reprogramming antagonizes H3K36me2/3 to enable the proper transgenerational control of germline versus somatic cell fates. Without SPR-5; MET-2 reprogramming, somatic cells struggle to specify their proper cell fate amongst the noise of inappropriate germline gene transcription, leading to developmental delay. A similar mechanism may underlie the developmental delay of Soto and Kabuki Syndrome patients who have mutations in histone modifying enzymes.

Birol, Onur et al. (2021) International Worm Meeting "The effect of age on epigenetic transgenerational reprogramming in the C. elegans germline"

Birol, Onur, Katz, David

[International Worm Meeting, 2021]

In 1972 Beguet observed that parental age affects fertility of the following generation in wild type worms (C. elegans). Offspring from the older hermaphrodites had a smaller brood size compared to their siblings from younger parents. To determine if this effect of age on the fertility of progeny is due to defects in maternal epigenetic reprogramming, I performed the analogous experiments in spr-5 mutant worms. SPR-5 (LSD1/KDM1A) is a histone demethylase that removes the methylation on histone 3 lysine 4 (H3K4me2) from actively transcribed genes between generations. Our lab has previously shown that spr-5 mutant C. elegans have a transgenerational sterility phenotype, due to increasing H3K4me2. Remarkably, I found that progeny of spr-5 mutant worms have a further compromised fertility with advanced maternal age (AMA) compared to wild type. In addition, I found that progeny of spr-5 mutant worms from young maternal age (YMA) also have reduced fertility. To further address whether these defects may be due to increasing H3K4me2, I determined whether they are exacerbated in later generation spr-5 mutants that have increased H3K4me2. Consistent with this possibility, the difference between the YMA and AMA groups from the peak maternal age progeny (PMA) is exacerbated progressively in later generations. My results confirm Beguet's original findings and suggest that the effect of parental age on reduced fecundity in the offspring may be through compromised H3K4me2 reprogramming at fertilization. Understanding the potential link between maternal age and maternal epigenetic reprogramming is important because a) the effect of age on fecundity that I observe is reminiscent of the maternal age effect on the rate of autism, b) mice that are mutant maternally for the SPR-5 homolog LSD1 have autism-like behavior, and c) patients with LSD1 mutations display autism-like symptoms. Thus, these experiments may provide a foundation for understanding these potential connections.

Weinkove D (2018) BMC Biol "On microbes, aging and the worm: an interview with David Weinkove."

Weinkove D

[BMC Biol, 2018]

David Weinkove is an associate professor at Durham University, UK, studying host-microbe interactions in the model organism Caenorhabditis elegans. David has been focusing on the way microbes affect the physiology of their hosts, including the process of aging. In this interview, he discusses the questions shaping his research, how they evolved over the years, and his guiding principles for leading a lab.

Miller DM et al. (1992) Worm Breeder's Gazette "unc-4 LacZ Expression in A-Type Motor Neurons"

Miller DM, Niemeyer CJ

[Worm Breeder's Gazette, 1992]

unc-4 LacZ expression in A-type motor neurons David M. Miller and Charles J. Niemeyer, Dept. of Cell Biology, Duke Univ. Medical Ctr, Durham, NC 27710