Rotation projects 2014

Antonio Giraldez

Genetics Department

Stem Cell Center (associate member)

333 Cedar Street. Shm I room 147

Lab meeting: Friday, 2:00 p.m. SHM I room 143.

Please email Antonio if you are interested.

Rotations available anytime.

The problem: The main goal of my laboratory is to understand the cellular and molecular signals that initiate embryonic development to uncover universal principles that direct the development of a new life. A universal step in all animals is the maternal to zygotic transition, whereby the transcriptionally silent egg activates the new zygotic program and removes the old maternal program. This central step in animal development can be considered the beginning of life from a transcriptional standpoint, whereby subsequent developmental decisions will depend on the correct activation of the zygotic program and regulation of the previous maternal program. 

The questions: Our laboratory aims to understand how does the vertebrate embryo activate the silent zygotic genome to jump start development, how does it regulate the previous developmental program and how do the building blocks in the genome, coding and non-coding elements, orchestrate these processes.

The approaches: We have a multidisciplinary infrastructure (wet/dry) that allows us to combine genomics, embryology, biochemistry and computational biology to leverage the powerful genetics in zebrafish to understand vertebrate development.

The potential projects:

Project 1: How is the genome activated. We have recently identified nanog, oct4 and soxB1 as three factors required to activate the zygotic genome. In this project, we aim to gain mechanistic insights on how these factors establish a competent genome. We will use biochemical approaches (pull down and mass spectrometry) to identify the factors that are recruited by nanog, oct4 and soxB1, and genetic tools (crispr-cas9 loss of function, Chip-seq) to investigate their function in genome activation and development.

Project 2: Computational/experimental analysis of translation regulation. Using ribosome footprinting, we are for the first time able to study how translation is regulated genome wide. This computational project will investigate how translation efficiency changes across development, with the goal of defining co-regulated transcripts and identifying common sequence and structural elements that mediate regulation.

Project 3: Computational/experimental analysis of the RNA structure in the transcriptome. Using high-throughput sequencing tools, we have developed methods to visualize the RNA structure in vivo. This project will investigate how the structure of the transcriptome changes across development and how it influences mRNA turn over and translation, with the goal of defining novel structural elements that regulate gene expression.

Project 4: Uncovering the function of micropeptides in development. Using ribosome foot printing, we have identified a large number of long-noncoding RNAs that encode micropeptides that are conserved and translated during embryogenesis. Using crispr/cas9 mediated mutagenesis and immunoprecipitation in vivo, we will investigate the function of these micropeptides in development, with the goal of identifying new signaling molecules.

Project 5: LincRNAs function in development. We have identified a large number of long non-coding RNAs and have developed crispr-cas9 genome engineering approaches to delete these lincRNAs and identify their partners. We will study their roles in gene regulation and development.

Project 6: Genetic screening to define the factors that initiate vertebrate development. We have identified a set of chromatin remodelers, RNA binding proteins, transcription factors and genes of unknown function that are strongly translated in the early embryo. Using novel approaches developed in our lab, we are beginning a genetic screen to identify their function in vivo.

If you are potentially interested in rotating in our lab and need more information, please feel free to send Antonio an e-mail to arrange for a meeting.

Selected publications:

Bazzini AA‡#, Johnstone TG #,... Giraldez AJ‡. Identification of smallORFs in animals using ribosome footprinting and evolutionary conservation . EMBO J. 2014.

Lee MT#, Bonneau AR#, ... Giraldez AJ‡. Nanog, SoxB1 and Pou5f1/Oct4 regulate widespread zygotic gene activation during the maternal-to-zygotic transition. Nature, 2013.

Stahlhut C, ... Giraldez AJ‡. miR-1/206 regulate angiogenesis by modulating Vegf-A expression. Development, 2012.

Bazzini AA, Lee MT, Giraldez AJ‡. Ribosome Profiling Shows That miR-430 Reduces Translation Before Causing mRNA Decay in Zebrafish. Science 2012.

Cifuentes D, Xue H,… Giraldez AJ‡. A novel miRNA processing pathway independent of Dicer requires Argonaute2. Science. 2010.

Mishima Y, ... Giraldez AJ. Zebrafish miR-1 and miR-133 shape muscle gene expression and regulate sarcomeric actin organization. Genes & Development. 2009

Giraldez AJ‡, et al., Schier AF‡. Zebrafish miR-430 promotes deadenylation and clearance of maternal mRNAs. Science. 2006.