Echinoderms Part B

Echinoderms, Volume 151, the latest release in the Methods in Cell Biology series, highlights advances in the field, with this update presenting chapters on Echinoderm Genome Databases, analysis of gene regulatory networks, using ATAC-seq and RNA-seq to increase resolution in GRN connectivity, multiplex cis-regulatory analysis, experimental approaches GRN/signal pathways, BACs, analysis of chromatin accessibility using ATAC-seq, analysis of sea urchin proteins /Click IT, CRISPR/Cas9-mediated genome editing in sea urchins, super-resolution and in toto imaging of echinoderm embryos, and methods for analysis of intracellular ion signals in sperm, eggs and embryos.

1. Fertilization When sperm meets egg—Fifty years of surprises David Epel Early and later studies on action potential and fertilization potential of echinoderm oocytes and Ca²⁺ response of mammalian oocytes Shunichi Miyazaki My research career on (mainly) sea urchins Victor D. Vacquier

2. Cytokenesis and Embryology Echinoderm eggs as a model for discoveries in cell biology David R. Burgess Unlocking mechanisms of development through advances in tools David McClay From hemoglobin to urchin spicules Fred Wilt

3. Genomics and Morphogenesis The causes of things Robert D. Burke A personal history of the echinoderm genome sequencing R. Andrew Cameron

Section 1 - Methods for genome and transcriptome analysis 1. Genomic resources for the study of echinoderm development and evolution Gregory A. Cary, R. Andrew Cameron and Veronica F. Hinman 2. Methods for the experimental and computational analysis of gene regulatory networks in sea urchins Isabelle S. Peter 3. Using ATAC-seq and RNA-seq to increase resolution in GRN connectivity Elijah K. Lowe, Claudia Cuomo, Danila Voronov and Maria I. Arnone 4. Identifying gene expression from single cells to single genes Nathalie Oulhen, Stephany Foster, Greg Wray and Gary Wessel 5. Multiplex cis-regulatory analysis Jongmin Nam 6. Whole mount in situ hybridization techniques for analysis of the spatial distribution of mRNAs in sea urchin embryos and early larvae Eric M. Erkenbrack, Jenifer C. Croce, Esther Miranda, Sujan Gautam, Marina Martinez-Bartolome, Shunsuke Yaguchi and Ryan C. Range 7. Techniques for analyzing gene expression using BAC-based reporter constructs Katherine M. Buckley and Charles A. Ettensohn 8. Genome-wide analysis of chromatin accessibility using ATAC-seq Tanvi Shashikant and Charles A. Ettensohn

Section 2 - Genome-editing and proteomics 9. Expression of exogenous mRNAs to study gene function in echinoderm embryos Maria Dolores Molina, Christian Gache and Thierry Lepagef 10. Trapping, tagging and tracking: Tools for the study of proteins during early development of the sea urchin Michelle M. Roux-Osovitz, Kathy R. Foltz, Nathalie Oulhen and Gary Wessel 11. CRISPR/Cas9-mediated genome editing in sea urchins Che-Yi Lin, Nathalie Oulhen, Gary Wessel and Yi-Hsien Su 12 .Analysis of microRNA functions Carolyn Remsburg, Kalin Konrad, Nina Faye Sampilo and Jia L. Song 13. In vivo analysis of protein translation activity in sea urchin eggs and embryos Héloïse Chassé, Sandrine Boulben, Virginie Glippa, Florian Pontheaux, Patrick Cormier and Julia Morales 14. Generation, expression and utilization of single-domain antibodies for in vivo protein localization and manipulation in sea urchin embryos Catherine S. Schrankel, Tufan Gökirmak, Chang-Wook Lee, Geoffrey Chang and Amro Hamdoun

Section 3 - Imaging of echinoderm embryos 15. Live-cell fluorescence imaging of echinoderm embryos Silvia P. Sepúlveda-Ramírez, Leslie Toledo-Jacobo, Chelsea Garno, Debadrita Pal, Clara Ross, Andrea Ellis and Charles B. Shuster 16. 3D + time imaging of normal and twin sea urchin embryos for the reconstruction of their cell lineage Antonio Ortiz, Elena Kardash and Nadine Peyriéras 17. High resolution imaging of the cortex isolated from sea urchin eggs and embryos J.H. Henson, Bakary Samasa and E.C. Burg 18. Spatially mapping gene expression in sea urchin primary mesenchyme cells Daniel T. Zuch and Cynthia A. Bradham

Section 4 - Methods for measurement of intracellular signals in eggs, sperm and embryos 19. Probing Ca²⁺ release mechanisms using sea urchin egg homogenates Yu Yuan, Gihan S. Gunaratne, Jonathan S. Marchant and Sandip Patel 20. Measuring voltage and ion concentrations in live embryos Nahomie Rodriguez-Sastre, Christopher F. Thomas and Cynthia A. Bradham 21. Analysis of sperm chemotaxis Héctor Vicente Ramírez-Gómez, Idán Tuval, Adán Guerrero and Alberto Darszon 22. Kinetic and photonic techniques to study chemotactic signaling in sea urchin sperm Hussein Hamzeh, Luis Alvarez, Timo Strünker, Michelina Kierzek, Christoph Brenker, Parker E. Deal, Evan W. Miller, Reinhard Seifert and U. Benjamin Kaupp 23. Analysis of neural activity with fluorescent protein biosensors Robert D. Burke and Shunsuke Yaguchi