Davis, Richard E. et al. (2013) International Worm Meeting "Significant Transcription in Zygote Pronuclei and 1-4 Cell Embryos Drives Early Development in the Nematode, Ascaris suum."

Davis, Richard E., Wang, Jianbin, Roy, Julianne

[International Worm Meeting, 2013]

During early C. elegans development, zygote maturation and early embryonic development are typically characterized by an absence of mRNA transcription, and regulation of gene expression during this period is primarily post-transcriptional. We took advantage of the availability of distinct stages of zygote maturation (prior to pronuclear fusion) and early embryo development to provide a unique and comprehensive time course of mRNA expression, turnover, and translation in early development of the parasitic nematode Ascaris suum. RNA-seq data on zygotes undergoing maturation prior to pronuclear fusion and 1, 2, 4-cell, and later stages of early development strikingly demonstrate that a large number of genes are transcribed during zygote maturation and in the 1-4 cell embryos of A. suum. This differs from C. elegans and the general view that transcription is quiescent until at least the 2-cell stage in metazoa. Much less maternal mRNA is contributed from the oocytes in Ascaris compared to that in C. elegans. We find that the orthologs of many maternal C. elegans mRNAs are not maternally contributed in A. suum, but are transcribed during A. suum zygote maturation prior to pronuclear fusion and in the early embryo. Ribosome profiling of 1-cell, 4-cell, 32-64 cell, and 250 cell embryos mRNAs demonstrated that, in general, mRNAs do not appear to be made and stored for subsequent translation, but are directly translated following their synthesis. Our data indicate that the roles of maternally contributed and zygote transcribed genes differs between A. suum and C. elegans despite the fact that the two nematodes appear to exhibit identical morphological patterns in early development. In Ascaris, maternal mRNA contribution is minimal, and newly transcribed genes appear to drive early development. This suggests that mechanisms used for controlling the timing of the expression of key conserved genes has been altered between the two nematodes, illustrating significant plasticity in the regulatory networks that play important roles in developmental outcomes in nematodes.

Davis, Richard E et al. (2013) International Worm Meeting "Silencing of Germline-Expressed Genes by DNA Elimination in Somatic Cells and a Mechanism for Selective DNA Segregation."

Kratzer, Stella, Wang, Jianbin, Koutsovoulos, Georgios, Blaxter, Mark, Beriman, Matthew, Mitreva, Makedonka, Thorne, Alicia, Kumar, Sujai, Balas, Maggie, Magrini, Vincent, Davis, Richard E

[International Worm Meeting, 2013]

Chromatin diminution is the programmed elimination of specific DNA sequences during development. It occurs in diverse species, but the function(s) of diminution and the specificity of sequence loss remain largely unknown. Diminution in the nematode Ascaris suum occurs during early embryonic cleavages and leads to the loss of germline genome sequences and the formation of a distinct genome in somatic cells. We found that ~43 Mb (~13%) of genome sequence is eliminated in A. suum somatic cells, including ~12.7 Mb of unique sequence. The eliminated sequences and location of the DNA breaks are the same in all somatic lineages from a single individual, and between different individuals. At least 685 genes are eliminated. These genes are preferentially expressed in the germline and during early embryogenesis. Soma-specific elimination provides a unique mechanism of gene repression and differentiation between germline and soma. We found no temporal or any other correlation of small RNAs with diminution. Preliminary data suggest that a possible mechanism of differential segregation of DNA following the breaks may be due to differential deposition of CenpA (as well as other histone marks) on retained vs eliminated DNA sequences. For comparison, we have also sequenced the germline and somatic genomes of a second nematode with a single large haploid chromosome that undergoes DNA elimination, Parascaris univalens. These data will be discussed. Overall, our studies suggest that diminution is a unique mechanism of germline gene regulation that specifically silences genes involved in gametogenesis and early embryogenesis through their elimination and that this process contributes to the soma-germline differentiation.

Townsend SR et al. (1994) Worm Breeder's Gazette "C. elegans Molecular Genetics and Long PCR."

Finelli AL, Savage C, Xie T, Padgett RW, Townsend SR

[Worm Breeder's Gazette, 1994]

C. elegans Molecular Genetics and Long PCR Scott R. Townsend, Cathy Savage, Alyce L. Finelli, Ting Xie, and Richard W. Padgett, Waksman Institute and Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08855

Streit Adrian et al. (2016) "Chromatin Diminution"

Streit Adrian, Davis Richard E

[2016]

Chromatin diminution is defined as chromosomal fragmentation, followed by the elimination of part of the chromosome during mitosis. The process was first observed in early cleavage divisions of the parasitic nematode Parascaris equorum embryo by Boveri in 1887. It was later found to also occur in some other parasitic nematodes, as well as a number of unicellular and metazoan species in diverse taxonomic groups. While chromatin diminution occurs in diverse higher order taxa, within individual taxa, it occurs only in a rather small number of species. The process appears to play different biological roles in different organisms, may use different mechanisms and is likely to have arisen multiple times during evolution.

Davis RE (1996) Parasitol Today "Spliced leader RNA trans-splicing in metazoa."

Davis RE

[Parasitol Today, 1996]

Spliced leader trans-splicing is a form of RNA processing originally described and studied in parasitic kinetoplastida. This mechanism of gene expression also occurs in parasitic and free-living metazoa. In this review, Dick Davis describes current knowledge of the distribution, substrates, specificity and functional significance of trans-splicing in metazoa.

Starr, D. et al. (2015) International Worm Meeting "UC Davis-University of Maryland Eastern Shore Graduate Admissions Pathway: Collaborating to broaden participation in molecular and cellular biology."

Starr, D., Hom, C.

[International Worm Meeting, 2015]

STEM professionals in the 21st century remain predominantly Caucasian/white, in spite of decades of work by professional societies, colleges and universities, and individual scientists to broaden participation. This multifaceted problem includes concerns among students and faculty at minority-serving institutions about the economics of career choice, family pressure to pursue a career in a biomedical field, and limited exposure to natural history. Further, institutional efforts in recruitment by research universities remain rooted in graduate fairs that target senior undergraduates from groups underrepresented in science, whereas connections made via shared research networks provide a more sure means to admission in molecular and cell biology. The UC Davis-University of Maryland Eastern Shore (UMES) Molecular and Cellular Biology Graduate Admissions Pathways (MCBGAP) program addresses this challenge via collaborations between faculty at the two institutions and a research co-mentoring program that brings UMES undergraduates to UC Davis for summer research. The program is funded by a grant from the University of California Office of the President and the UC Davis College of Biological Sciences.MCBGAP supported two cohorts of five UMES students in the summers of 2014 and 2015. The MCBGAP program consists of reciprocal student-faculty visits, close interactions between key UC Davis and UMES faculty, monthly Skype meetings that involve mentors and students, and research, professional development, and field trips in the summer. MCBGAP has catalyzed change both at UMES, where students are given the opportunity to self-identify as researchers at a tier 1 research university, and at UC Davis, where increased numbers of faculty recognize the need to be proactive in graduate recruiting and admissions, and multiple deans have committed time to mentor students and funds to support additional undergraduates from Historically Black Colleges and Universities for summer research and mentoring. The experience has also inspired us to apply for a Postbaccalaureate Research Education Program (PREP) from the NIH.

Zagoskin, Maxim et al. (2021) International Worm Meeting "Programmed DNA Elimination in the parasitic nematode Ascaris: Are Argonautes and their associated small RNAs involved?"

Zagoskin, Maxim, Davis, Richard, Wang, Jianbin

[International Worm Meeting, 2021]

Programmed DNA elimination in the nematode Ascaris is a developmentally regulated process that reduces the somatic genome, while leaving the germline genome intact. It occurs in early embryogenesis at 4 to 16 cell stage in all somatic lineages. The eliminated DNA consist of repetitive sequence as well as ~1,000 germline-expressed genes. The biological role of this process appears in part to be a gene silencing mechanism. Ascaris DNA elimination involves specific chromosomal DNA breaks and changes in the holocentric chromosomes. The DNA breaks and loss of CENP-A in specific chromosomal regions defines the retained and eliminated regions of chromosomes. In ciliate programmed DNA elimination, small RNAs are known to mark retained or eliminated genome regions during DNA elimination. To examine if small RNAs contribute to Ascaris programmed DNA elimination, we identified Ascaris small RNAs, 10 Argonautes, and characterized Ascaris small RNAs associated with 7 Argonaut proteins including all WAGOs. Immunostaining of embryos during programmed DNA elimination indicated that WAGO-2 specifically stains retained DNA while WAGO-3 predominantly localizes to chromosome fragments that will be eliminated. ChIP-seq data also showed some enrichment of WAGO-3 Argonaute on eliminated DNA regions. We also carried out small RNA sequencing and analysis in embryos enriched for DNA elimination mitoses by sorting with H3S10p labeled embryos or chromatin IP with WAGO-2 and WAGO-3. Small RNA sequencing of embryos enriched for DNA elimination (sorted) did not identify any small RNAs associated with the sites of chromosome breaks or changes in CENP-A localization that contribute to DNA elimination. Chromatin IP identified specific sets of small RNAs corresponding to repeats for WAGO-2 and mRNAs for WAGO-3. Overall, however, these small RNAs do not appear to specifically target retained vs eliminated regions as anticipated. WAGO-3 small RNAs appears to be enriched for nascent RNAs associated the eliminated regions. The possible role of WAGO-2 and WAGO-3 and small RNAs in Ascaris programmed DNA elimination will be further discussed.

Martinelli SD et al. (1995) International C. elegans Meeting "ACEDB"

Durbin RM, Martinelli SD

[International C. elegans Meeting, 1995]

We hope to provide a demonstration of the current state of the ACeDB worm database on Unix workstations, and if possible Apple Macintosh, throughout the poster sessions. This will be based on the new version 4 release of the acedb software (Jean Thierry-Mieg, Richard Durbin and numerous others), which contains many new features for greater efficiency, more flexible printing, and display of new features.

(2024) Development "The people behind the papers - Thomas Mullan and Richard Poole."

[Development, 2024]

Asymmetric cell divisions can produce daughter cells of different sizes, but it is unclear whether unequal cell cleavage is important for cell fate decisions. A new paper in Development explores the role of unequal cleavages in Caenorhabditis elegans embryos. To learn more about the story behind the paper, we caught up with first author Thomas Mullan and corresponding author Richard Poole, Associate Professor of Developmental Biology at University College London, UK.

Wang, Jianbin et al. (2021) International Worm Meeting "Plasticity of Argonautes and their associated small RNA pathways in nematodes"

Breda Veronezi, Giovana, Zagoskin, Maxim, Davis, Richard, Wang, Jianbin

[International Worm Meeting, 2021]

Nematoda is a diverse phylum that includes many free-living as well as parasitic species. The model nematode C. elegans has a diverse set of small RNAs and an expanded group of Argonautes, particularly the worm-specific clade Argonautes (WAGOs) and their endogenous siRNAs that are largely amplified by RNA-dependent RNA Polymerases (RdRPs). Our understanding of small RNA types, Argonautes, and pathways in other nematodes is limited. We carried out comparative studies of the small RNA pathways in the Clade III parasitic nematode Ascaris. Ascaris has 10 Argonautes. However, a PIWI Argonaute and piRNAs are absent. Five of the Argonautes are from the WAGO clade. We generated antibodies against all five Ascaris WAGOs as well as AsALG-1 (miRNAs) and AsALG-4 (26G-RNAs) and used them to identify their associated small RNAs in the early embryo, ovary, and testis including discrete developmental stages during spermatogenesis. We found that in general, AsALG-4, AsCSR-1 and AsWAGO-3 small RNAs target mRNAs while AsWAGO-1, AsWAGO-2 and AsNRDE-3 small RNAs target repetitive sequences. Notably, AsNRDE-3 small RNAs change their targets from repetitive sequences to mRNAs during male meiosis at the pachytene stage. RNA-seq data identified a group of genes expressed at pachytene during spermatogenesis which are rapidly degraded at the end of pachytene. Degradation of these mRNAs is associated with AsALG-4 26G-RNAs specifically expressed only in late pachytene and diplotene. The timing and expression of AsCSR-1 and AsALG-4 Argonautes and their small RNAs during spermatogenesis suggests they likely function independently, with AsCSR-1 and its 22-24G-RNAs fine-tuning expression of a broad set of transcripts and AsALG-4 and its 26G-RNAs down-regulating male meiosis-specific mRNAs. Genomic regions with transposons and their derivates are in general enriched for H3K9me3 and are targeted by an expansive set of 22G-RNAs associated with AsWAGO-1, AsWAGO-2 and AsNRDE-3 throughout development. Overall, there is clear conservation in the miRNA, 22G-RNA, and 26G-RNA pathways between the distantly related Ascaris and C. elegans nematodes. However, our data demonstrate the complexity and plasticity of small RNA pathways in a Clade III nematode without PIWI and a piRNA pathway and provide an in depth of analysis of the dynamics of small RNA pathways throughout spermatogenesis.