The Genomics Lab – Details, episodes & analysis

In today's episode I spoke again to Dr Christopher Todd from the Babraham institute. Chris is a postdoctoral researcher in Wolf Reiks lab who talked to me about transposable elements and epigenetic priming of enhancers with human embryonic development. Chris gave a great talk at GREECS 2022 where he discussed his research and I absolutely loved his talk, so immediately messaged him to join me on the podcast! 

If like me, you feel unclear on what exactly are transposable elements, the details of their function & classification and want to learn more about enhancer priming, stay tuned to learn lots! Even if you do know these things, I guarantee you will still learn so much from Chris! Hope you all enjoy!

Chris' twitter: https://twitter.com/C_D_Todd

Reik lab twitter: https://twitter.com/ReikLab

Chris profile on Babraham website: https://www.babraham.ac.uk/people/member/746

Google scholar: https://scholar.google.com/citations?user=WPqJa6QAAAAJ&hl=en

TGL made it to 2022! On todays episode, I spoke to Dr Benjamin Rein, a neuroscientist all the way from Stanford.  We speak all about Bens experience of science communication on social media, Ben uses Tik Tok & instagram to make awesome short videos on scientific papers and topics and has gained a following of +600,000 on tik tok! He also talks all about his passion for neuroscience, his PhD research and then we talked a lot about stuff we dont know a lot about! 

Hope you enjoy this conversation & be sure to check Ben out on social media using the links below!

Bens tik tok - https://www.tiktok.com/@dr.brein?lang=en

Bens instagram - https://www.instagram.com/doctor.brein/?hl=en

Bens website - https://www.benrein.com

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!

Kats twitter: https://twitter.com/KatIvey2

Kats publications : https://scholar.google.com/citations?user=wVZuQykAAAAJ&hl=en

Kats instagram: https://www.instagram.com/blondetravelingcircus/?hl=en

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! 

Publication relevant to todays discussion: https://www.nature.com/articles/s41559-020-01293-z?proof=t

Blog post relevant to todays discussion: https://lms.mrc.ac.uk/epigenetics-evolution-in-the-fast-lane/

Lab website: https://psarkies.wixsite.com/epievo

Contact Peter on twitter here: https://twitter.com/PSarkies 

On todays episode, we talk to Dr Sarah Marzi from Imperial College London all about her work into the epigenetic regulation in neurodegenerative diseases like Alzheimers and Parkinsons. Sarah tells us about her journey into this field and describes what exactly neurodegenerative diseases are?! She also talks to us about her contributions to the field so far, including her work on epigenetic modifications, more specifically histone acetylation differences in people with and without Alzheimers and what these histone modifications mean for gene regulation. She also tells us all about the current and future plans for her research and her lab, which sounds very promising and exciting. 

Contact Sarah on twitter here: https://twitter.com/sj_marzi

Read the paper in nature neuroscience here: https://www.nature.com/articles/s41593-018-0253-7?WT.feed_name=subjects_dementia

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!

You can contact Andy via twitter here : https://twitter.com/AndrewJLee90

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.

Ozren's recent publication we discuss can be found here.

If you want to find out more, contact Ozren on Twitter or via email.

On todays episode we speak to Dr Adam Wende and Dr Mark Pepin! We discuss their recent publication which has been all over twitter recently! During the research, they identified an association between socioeconomic factors, the methylome, & heart failure. We discuss all of the motivations, methodological techniques and interesting findings from the study! Adam and Mark previously worked together, with Adam being Marks doctoral supervisor, but they tell us about their common interest for running & the future plans for their research and careers. Stay tuned to find out more.

Find the publication here: https://journals.physiology.org/doi/full/10.1152/ajpheart.00036.2021

Contact Adam here: adamwende@uabmc.edu or https://twitter.com/AdamWende

Contact Mark here: pepinme@gmail.com or https://twitter.com/MarkEPepin

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. 

Contact the lab here https://twitter.com/regenberg_lab

Find the labs website here https://www.regenberglab.net/

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.

Contact Cátia here

Cátia's Twitter

Cátia's LinkedIn

https://www.catiamoutinho.com/

Listen to Ellie's 3-Minute-Thesis here

Listen to Liv's 3-Minute-Thesis here