The Genomics Lab

On todays episode, I speak to Sudarshan Pinglay, a PhD student from NYU medical center. Sudarshan is involved in the dark matter project- we talk about the dark matter of the genome, where introns, repetitive and regulatory elements reside. Sudarshan works specifically on the HOXA locus. The Hox family of genes pattern the head to tail axis in the developing embryo. In mammals, there are are four separate clusters (HoxA,B,C and D). Both space and time of Hox gene expression is colinear to their sequence in the genome. Loss of this leads to serious defects. 

Sudarshan talks about his wet lab and dry lab work, where he has been using the HoxA cluster as a model to understand how the expression of Hox genes is regulated in order to pattern the developing nervous system. He tells us about his work aiming to build the HoxA cluster from the ground up so that he could manipulate the various players that have been implicated in Hox gene regulation and understand the pattern of Hox gene expression and embryonic development.

In todays episode, I speak to Dr Hamish King, a Sir Henry Wellcome Fellow affiliated with the Blizard Institute at Queen Mary University of London. Hamish is interested in how errors in gene regulation lead to changes in the behaviour and function of B cells, an important cell type in our immune system that makes antibodies to fight and remember infections. Hamish talks about how he uses wet lab and bioinformatic techniques to answer these questions. Dr King is also due to become a laboratory head at WEHI in early 2022, where his lab will focus on answering a range of questions including:

1. How immune-specific chromatin-based mechanisms regulate gene expression
2. Whether autoimmune-associated genetic risk loci disrupt regulatory function of enhancers
3. If disease-specific epigenomic networks exist in autoimmunity

Welcome to Episode 28 of The Genomics Lab! On today's episode we talk to Dr.Patrick CN Martin who is a postdoctoral researcher at the University of Copenhagen. He completed his PhD in Dr Radu Zabets lab in 2020 where he investigated the binding mechanisms of transcription factors to DNA. His research involved development of an R package, ChIPAnalyser. A user-friendly, versatile and powerful R/Bioconductor package predicting and modelling the binding of TFs to DNA. ChIPanalyser performs similarly to state-of-the-art tools, but is an explainable model and provides biological insights into binding mechanisms of transcription factors to DNA. His research focused on investigating the binding mechanisms of three TFs that are known architectural proteins CTCF, BEAF-32 and su(Hw) in three Drosophila cell lines (BG3, Kc167 and S2). Aside from his research, Patrick enjoys coding, astrophysics and is now working in the exciting field of spatial transcriptomics! We also discuss the use of clinical data in genomics research, learning to code and bioinformatics. Hope you all enjoy! (See below for links)

This week we are honoured to host Professor Wendy Bickmore, the Director of the MRC Human Genetics unit at the University of Edinburgh. Wendys research laboratory focuses on trying to better understand the 3D organisation of the genome, and how this controls how the genome functions during normal development. They are further interested in how this may be perturbed into disease. Wendy talks to us about some of her recent work which has been extremely important for better understanding enhancer function and also, some of the challenges and questions which remain to be answered in the field. She also provides some great insight into the experiments and methods ongoing in her lab now. 

Welcome back! Today we are talking to Kathleen Ivey, a PhD student from the University of Texas at Arlington in the Castoe Lab. Kat talks to us all about her journey to her PhD, with a background in vet tech & herpetology. Kat now focuses on population genomics, with a particular interest in Rattlesnakes. She tells us all about being out in the field collecting the species right through to the laboratory investigation of gene expression! Find links to Kats socials below!

Welcome back for another episode! This week we chat to Dr Peter Sarkies from Imperial College London / MRC LMS! Peter is a senior lecturer running his own laboratory which aims to make connections between epigenetic gene regulation and evolution. Peter talks to us all about his research involving investigation of a wide range of epigenetic pathways including small RNA's such as Piwi interacting RNAs (piRNAs), DNA methylation and histone modification. Talking about RNAs is a first for us on the podcast, so we really enjoyed listening to everything Peter had to say! 

This week we took a slight detour away from our normal topic of conversation (Genomics) and immersed ourselves into the world of DNA nanotechnology with Dr Andrew J Lee, the centre manager of the Bragg Centre for materials research. Andy is a weaver of DNA and nanoscale filmaker in the Bioelectronics group. He develops nanostructures that are self assembled from DNA molecules to template, control and study a variety of single biological entities and inorganic processes. We spoke about Andrews academic background, what DNA nanotechnology is, its methods AND its applications. This episode was so fascinating and Andy explains a very complex topic in a very simple and accessible way! If you're keen to hear more about DNA origami and smiley face emojis made out of DNA, then stay tuned!

Our second guest from the Garvan Institute of Medical Research in Sydney, is DrOzren Bogdanovic. We are so privileged to talk today to Ozren about his work in developmental epigenetics which covers how DNA methylation participates in diverse developmental processes, and how deposition and removal of the methylation mark impacts upon embryonic and germline integrity. 

We discuss his recent publication on non-CG methylation at satellite DNA repeats - something a little different this week! Widespread non-CG methylation occurs in mammalian embryonic stem cells and in the brain. In mammals, it is found at CAC trinucleotides in the nervous system, and is associated with transcriptional repression. It is found at CAG trinucleotides in embryonic stem cells, and CAC methylation is a known conserved feature of adult vertebrate brains. However, in his recent work, Ozren describes how, as opposed to any of these established methylation signatures, a novel form of non-CG methylation occurs in the TGCT context within zebrafish mosaic satellite repeats. TGCT methylation is inherited from both male and female gametes, and is critical for development. Ozren also discusses enzymes responsible for this observed novel methylation mark.

We hope you enjoy listening as much as we enjoyed talking to Ozren.

In today's episode we speak to Dr Birgitte Regenberg and Dr Sam Keating from the Regenberg Lab, University of Copenhagen, about extrachromosomal circular DNA and it's significance in human disease.

Circular DNA originates from chromosomes but differs from linear chromosomes as  they mostly don’t have centromeres - so if a gene is trapped on a circle, it can amplify its copy number to much above the normal 2 copies in a few cell cycles. If the gene is expressed, this means that much more protein is produced than it should be. 

The Regenberg lab aims to understand how circular DNA is formed, maintained and how it affects the biology of the cell - thereby looking at eccDNA growth advantages or disadvantages in things such as aging and cancer. 

We've reached episode 20!!!

In celebration of our twentieth episode, we are speaking today to Dr Cátia Moutinho about single cell sequencing and spatial omics - two up and coming techniques that everyone seems to be talking about at the moment. Cátia is Group Leader of the Single Cell Technology Development in the Garvan Institute in Sydney, Australia.

The aim of Cátia's lab is to perform and optimise single-cell-related experiments, to develop the latest methods and approaches in molecular cellular genomics. We talk today about the importance of the development of these techniques, how her lab works, and why these techniques are so 'in demand' at the moment.

We're back after the Easter Break with an extremely interesting episode with Dr Peter Ellis from the School of Biosciences at the University of Kent! Dr.Ellis is a Lecturer in Molecular Genetics and Reproduction at the University of Kent. His research thus far has involved the identification of novel genes on the mouse Y chromosome that affect sperm head shape and fertility; the discovery of a genomic conflict between the mice sex chromosomes as they compete to influence offspring sex ratio. Also the identification of mechanisms regulating meiotic and post-meiotic transcriptional silencing of the sex chromosomes. His lab investigates the molecular biology of reproduction, the conflicting roles played by sex-linked genes in regulating this process, and the relationship between DNA damage repair mechanisms and the checkpoints governing meiotic progression. 

Join us today as we speak to Dr Maxim Greenberg, located at the Institut Jacques Monod in the heart of Paris. IJM is one of the premier institutes for fundamental research in the life sciences in France. Maxim's lab aims to better understand the epigenetic consequences of DNA methylation during a specific window of development which occurs in the first week of embryogenesis but ripples throughout life. Another aim of the Greenberg lab is to better understand what DNAme is doing when it is not at promoters? And its corollary: how do promoters stay DNA methylation free?

Today we discuss several of Maxims publications (linked below), the function of DNA methylation and the process of DNA methylation deposition and removal. Maxim also gives us an interesting insight into the details of how his lab aim to better understand epigenetic reprogramming in development. 

Join us today as we speak to Dr David Tumbarello, from the University of Southampton, as he talks to us about his dynamic and varied academic career that has taken him from New York, to Southampton, stopping off at a number of places in between!! David's lab currently focuses on understanding the cellular mechanisms and molecular machinery required for subcellular trafficking of membrane associated and cytosolic cargo via endocytosis and autophagy. Knowledge of these mechanisms is critical for understanding the molecular mechanisms of cancer and neurodegenerative diseases , which stem from defects in various membrane trafficking and cell signalling pathways.

Today we discuss one of David's lab's recent papers, published June 2020, which looks at multiple mitochondrial quality control pathways that exist to maintain the health of mitochondria, the mitochondrial stress response and identify the interaction of molecules associated with this response with E3 ubiquitin ligase Parkin - involved in Parkinson's disease.

In today's episode, we speak to Dr Jordi Paps-Montserrat, lecturer in the School of Biological Sciences at the University of Bristol. Jordi did his PhD at the University of Barcelona, before completing his post-doc at the University of Oxford. We talk with Jordi today about his work on evolutionary genomics, and how we can elucidate biological adaptations and the origins on animals and plants throughout evolution by looking at the genomic and molecular pathways underlying these evolutionary shifts.

Join us today as we speak to an inspirational Woman in STEM, Sethlina Naa Dodua Aryee, raised in Ghana, who moved to the University of Cambridge to complete her PhD in sustainable food production through the use of genomic and bioinformatic tools - a global issue that she has been passionate about for her whole life. Sethlina speaks to us today about her research into the genomics of the indigenous Ashanti Dwarf pig, following cross-breeding of the indigenous species with some overseas species, as well as the differences between studying in Ghana and the UK. The indigenous Ashanti dwarf pig is hugely disease-resistant, so it is of great importance to harness this trait for sustainable food security.

In order to celebrate International Women's Day 2021, we have picked two inspirational role models at our University and invited them to speak to us about their experiences of being a woman in science. We learn about their varied and exciting careers, and then we discuss all of our personal experiences of being a woman in science - from how we were inspired into the field, what we feel are the biggest barriers and how to overcome them, as well as some really great advice from both Dr Louise Beard and Dr Michelle Taylor on all stages of the academic journey. We are very lucky at the University of Essex to be working within a hugely inclusive and supportive environment, but it is important to recognise not all women are this lucky. We discuss the Athena Swan charter, an initiative in academia and the workplace to increase equality for all people, in all roles, and how some of the specific action plans within the charter have directly impacted the University of Essex in order to make it a more inclusive workplace.

In today's episode, we are excited to be talking to Dr Christopher Clarkson, currently based at UCL, where he has just started a post-doctoral research position.

In 2020, Dr. Clarkson completed his PhD at the University of Essex where he investigated changes of nucleosome positioning and 3D chromatin organization! In today's episode, we discuss how CTCF binding strength correlates with nucleosome repeat length and what the implications are of this on gene regulation. We further discuss how regions in the genome where CTCF is able to bind are extremely important for cellular differentiation and boundary formation within the genome.

In today's episode, we are privileged to be speaking to Professor Darren Griffin, who is currently based at the University of Kent, where he is the director of the Centre for Interdisciplinary Studies of Reproduction, and Professor of Genetics.

Darren is President of the International Chromosome and Genome Society, and is a world leader in the field of cytogenetics, performing the first successful cytogenetic preimplantation genetic diagnosis, as well as playing a large role in the development of a universal test for genetic disease in IVF, known as karyomapping. Darren also sits on the faculty of CoGen (controversies in genetics), so we were able to have some really interesting discussions with him, not only on the scientific side of his work but also on the ethical implications.

Welcome to Episode 1 of The Genomics Lab! On today's episode we talk to Jess Chadwick who is a third year PhD researcher at Imperial College London. She is doing her PhD in molecular neuroscience, investigating the molecular mechanisms of axonal regeneration after spinal cord injury. Jess talks to us about how axonal injury in the spinal cord usually results in no regeneration, but how in the peripheral nervous system, neurons can re-grow and regenerate to a certain extent. Jess explains how her research aims to study the regenerative mechanisms in peripheral neurons, and identifying which molecular targets need to be activated to achieve regenerative effects, which become promising targets for boosting spinal cord regeneration. We also discuss the role that epigenetics plays in this neurological research. Jess predominantly works in the mouse nervous system, and she discusses with us some of the limitations, ethical considerations and benefits of a mouse model for this line of research. Jess will welcome any questions or feedback so we have provided her contact information below. Hope you all enjoy our first episode! (See below for links)

Welcome to Episode 3 of The Genomics Lab! On today's episode we talk to Laura Whelan, who is a PhD researcher at the School of Genetics & Microbiology at the Trinity College Dublin. Laura is part of the Target 5000 programme; the first large-scale study to apply next generation sequencing to the Irish inherited retinal diseases (IRD) patient population. Laura discusses with us some of the causes of IRDs, the different types of IRD, the kind of inheritance involved in these diseases, and how her lab and the Target 5000 initiative use sequencing techniques to both discover novel genetic variants, and validate previous findings of genetic variants involved in the cause of IRDs. Laura discusses the impact of IRD on quality of life, the scale of the problem and the future of this work in terms of improving the diagnostics of IRDs.