Wellcome Sanger Institute

Vertebrate Genetics and Genomics

Parasites and Microbes

We explore molecular phenotypes through the transcript sequencing of whole vertebrate embryos and tissues either by traditional RNA-seq or 3' end transcript counting. Taking advantage of the high quality reference genomes of the zebrafish and mouse, we are able to capture the full complement of polyadenylated transcripts. This allows us to establish a baseline of gene expression across the development of unperturbed organisms or explore the transcriptional consequences of loss of gene function or environmental disturbance.

Genetic perturbation screens have generated large collections of morphological phenotypes, playing a fundamental role in our understanding of gene function in development and disease. The observed morphological changes are the manifestation of molecular phenotypes such as altered genomic sequence and transcriptional variation. Changes in transcription levels can be due to gene regulatory events, genomic variation and other non-genetic factors. Untangling the different contributions is critical for understanding the relationship between molecular and morphological phenotype.

We explore these molecular phenotypes through the transcript sequencing of whole vertebrate embryos and tissues either by traditional RNA-seq or 3′ end transcript counting. Taking advantage of the high quality reference genomes of the zebrafish and mouse, we are able to capture the full complement of polyadenylated transcripts, establishing a baseline of gene expression across the development of unperturbed organisms.

Foremost, we are exploring the level of gene expression variation that can be tolerated by a particular biological system and when this variation leads to phenotypic changes. We are able to manipulate these systems through specific genome engineering or gene knockout, exposure to chemical compounds or infection challenges. Following perturbations we are then able to measure the changes in transcript abundance across the entire organism and simultaneously link them to genotype information.

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    [excerpt] => We explore molecular phenotypes through the transcript sequencing of whole vertebrate embryos and tissues either by traditional RNA-seq or 3' end transcript counting. Taking advantage of the high quality reference genomes of the zebrafish and mouse, we are able to capture the full complement of polyadenylated transcripts. This allows us to establish a baseline of gene expression across the development of unperturbed organisms or explore the transcriptional consequences of loss of gene function or environmental disturbance.
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    [introduction] => We explore molecular phenotypes through the transcript sequencing of whole vertebrate embryos and tissues either by traditional RNA-seq or 3' end transcript counting. Taking advantage of the high quality reference genomes of the zebrafish and mouse, we are able to capture the full complement of polyadenylated transcripts. This allows us to establish a baseline of gene expression across the development of unperturbed organisms or explore the transcriptional consequences of loss of gene function or environmental disturbance.
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                            [post_content] => <p><img class="wp-image-105180 alignright" src="/wp-content/uploads/ensembl_1.gif" alt="" width="300" height="152" data-credit="" /></p><p>Ensembl was established in 1999, towards the end of the Human Genome Project, in response to a recognition that understanding the genetic code of organisms is as important as reading it. However, purely manual curation of all genome sequences is an unthinkable task, given the labour-intensive and time-consuming nature of such work. To overcome this problem, the Ensembl project team developed new software pipelines to automatically generate evidence-based annotation of genome sequences.</p><p>Since its inception, the Ensembl project has expanded from the curation of the human genome to embrace more than 80 vertebrate species. These include many model organisms central to the study of human diseases. Ensembl has participated in many genome consortia, producing annotation used in the initial genomic analyses of newly sequenced organisms.</p><p>The project provides an expanding wealth of information for a diverse list of species, including:</p><p>Intron and exon structure for protein-coding and non-coding genes</p><p>Genomic variations and somatic mutations and their consequences on genes and genotypes in populations and individuals</p><p>Cross-species gene trees and whole genome alignments</p><p>Functional genomic data - including regulatory region annotation.</p><h6>Ensembl website</h6><p>To provide the data in the most useful format for researchers, Ensembl provides several means of access including the Ensembl website, which is the public face of the project. It is highly customisable, interactive and presents a track-based genome browser location view as the major entry point. Many additional displays supply specialised and highly integrated views of genomic annotation.</p><h6>Rapid and open data access</h6><p>Free and unrestricted access to the information held in Ensembl is one of the foundational principles of the project and supports our vision to enable genomic science and promote rapid research into all areas of human and animal disease.</p><p>All Ensembl code is open source.</p>
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    [secondary_title] => Parasites and Microbes
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    [title] => Vertebrate Genetics and Genomics
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                    [content] => <p>Genetic perturbation screens have generated large collections of morphological phenotypes, playing a fundamental role in our understanding of gene function in development and disease. The observed morphological changes are the manifestation of molecular phenotypes such as altered genomic sequence and transcriptional variation. Changes in transcription levels can be due to gene regulatory events, genomic variation and other non-genetic factors. Untangling the different contributions is critical for understanding the relationship between molecular and morphological phenotype.</p>
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Previous team members

Photo of Neha Wali

Neha Wali

Advanced Research Assistant

Photo of Dr Christopher M. Dooley

Dr Christopher M. Dooley

Postdoctoral Staff Scientist

Partners

We work with the following groups

 

Publications

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