Rodriguez Crespo, David et al. (2021) International Worm Meeting "Chromatin context in the regulation of germline genes by the zinc-finger transcription factor LSL-1"

Rodriguez Crespo, David, Wicky, Chantal, Rajopadhye, Shweta, Nanchen, Magali

[International Worm Meeting, 2021]

Epigenetic and transcription factors control specific gene transcription profiles that instruct cells to proliferate and differentiate throughout development. Underlying this process the chromatin structure is dynamically shaped by different enzymatic complexes called chromatin remodelers. Among them, the C. elegans Mi2 homolog LET-418/Mi2 is required for post-embryonic development and ensures that the germline-specific transcriptional program is silent in somatic cells. By performing a genome-wide RNAi screen, we identified a let-418 genetic interactor, lsl-1, which encodes a close homolog of the human ZFP57 zinc-finger transcription factor involved in imprinting. LSL-1 is a germ cell specific protein, whose expression is first observed in the P4 blastomere and maintained in the germ cells through adulthood. Absence of LSL-1 activity leads to various defects. Germline nuclei do not progress normally through meiotic prophase and aberrant chromatin organization and nuclear morphology is observed during homologous chromosome pairing in lsl-1 mutants. Furthermore, an increased level of apoptosis, that relies on pairing and DNA damage checkpoints, is indicative of a high level of genome instability. By analysing the transcriptome of LSL-1 together with the ChIP-seq data available from the modERN (ENCODE) resource, we found out that LSL-1 is acting as a transcriptional activator of germline genes which are involved in different aspects of germline development, including meiotic chromosomes pairing and genome stability. Finally, we show that these defects are partially dependent on the chromatin proteins LET-418/Mi2 and HPL-2/HP1. We propose a model where the transcription factor LSL-1 is antagonizing repressive chromatin formation by LET-481/Mi2 and/or HPL-2/HP1 at germline gene promoters to allow expression of the proper gene repertoire for gamete production. In the other hand, absence of LSL-1 from somatic cells ensures that germline genes remain silent. Further molecular analysis of this interaction will let us know how LSL-1 is modifying chromatin accessibility to allow transcription.

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

Munro E (2017) Dev Cell "Protein Clustering Shapes Polarity Protein Gradients."

Munro E

[Dev Cell, 2017]

In this issue of Developmental Cell, Dickinson etal. (2017) and Rodriguez etal. (2017), along with Wang etal. (2017) in Nature Cell Biology, show how PAR protein oligomerization can dynamically couple protein diffusion and transport by cortical flow to control kinase activity gradients and polarity in the C.elegans zygote.

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

Grenache DG et al. (1993) Worm Breeder's Gazette "Differential Effects of Dauer-Defective Mutations in L1-Specific Surface Antigen Switching"

Politz SM, Grenache DG

[Worm Breeder's Gazette, 1993]

DIFFERENTIAL EFFECTS OF DAUER-DEFECTIVE MUTATIONS ON L1- SPECIFIC SURFACE ANTIGEN SWITCHING. David G. Grenache and Samuel M. Politz, Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA.

Emmons SW et al. (1994) Worm Breeder's Gazette "Strain Names for non-C. elegans Species."

Emmons SW, Fitch DHA, Leroi AM

[Worm Breeder's Gazette, 1994]

Strain names for non-C. elegans species Scott W. Emmonst, Armand Leroit, and David Fitch, Department of Molecular Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, Department of Biology, New York University, RmlOO9 Main Bldg., Washington Square, New York, NY 10003

Hall DH et al. (1994) Worm Breeder's Gazette "Cytology of Degenerin-Induced Cell Death in the PVM Neuron"

Driscoll MA, Chalfie M, Gu GQ, Hall DH, Gong L

[Worm Breeder's Gazette, 1994]

Cytology of degenerin-induced cell death in the PVM neuron David H. Hall, Guoqiang Gu+, Lei Gong#, Monica Driscoll#, and Martin Chalfie+, * Dept. Neuroscience, Albert Einstein College of Medicine, Bronx, N.Y. 10461 + Dept. Biological Sciences, Columbia University, New York, N.Y. 10027 # Dept. Molecular Biology and Biochemistry, Rutgers University, Piscataway, N.J. 08855

Amrit FRG et al. (2017) J Vis Exp "Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project."

Ghazi A, Amrit FRG

[J Vis Exp, 2017]

Next generation sequencing (NGS) technologies have revolutionized the nature of biological investigation. Of these, RNA Sequencing (RNA-Seq) has emerged as a powerful tool for gene-expression analysis and transcriptome mapping. However, handling RNA-Seq datasets requires sophisticated computational expertise and poses inherent challenges for biology researchers. This bottleneck has been mitigated by the open access Galaxy project that allows users without bioinformatics skills to analyze RNA-Seq data, and the Database for Annotation, Visualization, and Integrated Discovery (DAVID), a Gene Ontology (GO) term analysis suite that helps derive biological meaning from large data sets. However, for first-time users and bioinformatics' amateurs, self-learning and familiarization with these platforms can be time-consuming and daunting. We describe a straightforward workflow that will help C. elegans researchers to isolate worm RNA, conduct an RNA-Seq experiment and analyze the data using Galaxy and DAVID platforms. This protocol provides stepwise instructions for using the various Galaxy modules for accessing raw NGS data, quality-control checks, alignment, and differential gene expression analysis, guiding the user with parameters at every step to generate a gene list that can be screened for enrichment of gene classes or biological processes using DAVID. Overall, we anticipate that this article will provide information to C. elegans researchers undertaking RNA-Seq experiments for the first time as well as frequent users running a small number of samples.

Vogel G (2002) Science "Neuroscience. Genes keep neurons' house in order."

Vogel G

[Science, 2002]

As any homeowner knows, timely maintenance is vital for keeping a building functioning properly after construction is finished. The same is evidently true for the complex architecture of the nervous system - at least in the roundworm. On page 686, neuroscientists Oliver Hobert, Oscar Aurelio, and David Hall describe a new family of proteins that help keep the wiring of the worm's nervous system tangle free.