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Seminars

Institute of Cell Biology Seminar Series

 

Seminars will be held on Mondays at 12.05 pm in Lecture Theatre 1, Daniel Rutherford Building.

Seminars in May are held on Wednesdays.

Everyone is welcome to attend.

Semester Two:  January - June 2016

 

Date

Speaker

Host

11 Jan 2016

Geert Kops

University Medical Center, Utrecht, The Netherlands

Andrew Goryachev

18 Jan 2016

Paul Lehner

Cambridge Institute for Medical Research, University of Cambridge

Robin Allshire

25 Jan 2016

Ronald Pierik

Institute of Environmental Biology, Utrecht University, The Netherlands

 

Gerben van Ooijen

1 Feb 2016

Jonathan Higgins

Institute for Cell & Molecular Biosciences, Newcastle University

JP

8 Feb 2016

Kiyoshi Nagai

MRC Laboratory of Molecular Biology, Cambridge

Jean Beggs

15 Feb 2016

Matthias Hentze

EMBL, Heidelberg, Germany

Jean Beggs

22 Feb 2016

Simon Bullock

MRC-LMB, Cambridge University

Hiro Okhura

29 Feb 2016

Thomas Greb

Ruprecht-Karls-Universitat, Heidelberg, Germany

Naomi Nakayama

7 March 2016

KJ Patel

 MRC-LMB, Cambridge

Adrian Bird

14 March 2016

Anna Akhmanova

Department of Biology, Utrecht University, The Netherlands

Julie Welburn

21 March 2016

Renata Basto

Institut Curie, CNRS, Paris, France

Ken Sawin

28 March 2016

Easter Monday

 

4 April 2016

No seminar (School holidays)

 

11 April 2016

Jerome Dujardin

Institute of Human Genetics, CNRS

Robin Allshire

18 April 2016

Ioannis.Vakonakis

Department of Biochemistry, University of Oxford

Paul Barlow

25 April 2016

To be confirmed

 

Wed 4 May 2016

Thijn Brummelkamp

The Netherlands Cancer Institute, Amsterdam

Adrian Bird

Wed 11 May 2016

Mary Herbert

Institute of Genetic Medicine, Newcastle University

Adele Martson

Wed 18 May 2016

Dónal O'Carroll

MRC Centre for Regenerative Medicine, University of Edinburgh

David Tollervey

Wed 25 May 2016

Jane Mellor - Seminar cancelled

Department of Biochemistry, University of Oxford

Jean Beggs

6 June 2016

Lori Passmore

MRC-LMB, University of Cambridge

Gracjan Michlewski

13 June 2016

Melike Lakadamyali

Institute of Photonic Sciences, Barcelona, Spain

Julie Welburn

20 June 2016

Helder Maiato

IBMC, Porto, Portugal

 

Bill Earnshaw

27 June 2016

To be confirmed

 

 
 
 

 

Other seminars

Date Event
24th Jun 2016
16:00
Michael Swann Building
Main Lecture Theatre

Steve Jacobsen, University of California, Los Angeles

Mechanisms of DNA methylation and gene silencing

Our laboratory is using genetic and genomic techniques to study cytosine DNA methylation and gene silencing in the model plant Arabidopsis thaliana. The initiation of DNA methylation requires the DNA methyltransferase DRM2 which is guided by 24 nucleotide small RNAs and several RNA silencing proteins including Pol IV, RDR2, DCL3, Pol V, and AGO4. Pol IV is required for the synthesis of 24 nucleotide small RNAs and Pol V is required for the synthesis of non-coding RNAs that serve as a scaffold to recruitment of these small RNAs.   The coincidence of Pol IV and Pol V transcription in the genome dictates the location of RNA directed DNA methylation.  Recent work has uncovered mechanisms in which Pol IV and Pol V are recruited back to epigenetic marks in the genome, creating a self reinforcing loop which helps explain the stability and heritability of DNA methylation.  We are also interested in the processes downstream of DNA methylation.  The MORC ATPase proteins act to silence transposons and other DNA methylated loci, but morc mutants do not change the underlying epigenetic marks, indicating that they work downstream of the methylation signal.  MORCs are conserved in many eukaryotic organisms, and play roles in gene silencing in different developmental contexts.

Host: Justin Goodrich and Adrian Bird


26th May 2016
12:00
Michael Swann Building
7.20

Helen McNeil, Lunenfeld Institute, University of Toronto

Drosophila Speg: roles in nuclear stress and fertility

Host: Eric Schirmer


18th May 2016
12:00
Daniel Rutherford
Lecture Theatre 1 G.27

Dr Dónal O’Carroll- MRC Centre for Regenerative Medicine, University of Edinburgh

WT PhD Programme Seminar - "Non-coding solutions to developmental challenges"

The integrity of the genome transmitted to the next generation intrinsically relies on cells of the germ line. Processes that ensure germ cell development, genomic stability, and reproductive lifespan are essential for the long-term success of a species. We are interested in characterising spermatogonial stem cell (SSC) populations that support fertility as well the regenerative capacity of the testis throughout adult life. In addition, we tackle fundamental questions regarding the mammalian male germ line and heredity from an RNA perspective. Specifically, our research explores the contribution of non-coding RNA and RNA modification pathways within germ cell development as well as testicular homeostasis/regeneration. Our research objectives focus on the contribution of these emerging pathways on the underlying circuitry of self-renewal that underpins the SSC, as well as the coordination of the various cellular/differentiation processes of spermatogenesis.

Host: David Tollervey

Host: WTCCB


11th May 2016
12:00
Daniel Rutherford
Lecture Theatre 1 G.27

Prof Mary Herbert- Institute of Genetic Medicine, Newcastle University

WT PhD Programme Seminar - "Can reproductive technologies prevent maternal transmission of mitochondrial DNA disease?"

Summary:

Mitochondrial DNA (mtDNA) mutations are maternally inherited and are associated with a broad range of debilitating and fatal diseases. Reproductive technologies designed to uncouple the inheritance of mtDNA from nuclear DNA may enable affected women to have a genetically related child with a greatly reduced risk of mtDNA disease. To this end, we have performed preclinical studies to test the likely safety and efficacy of pronuclear transplantation (PNT). Surprisingly, techniques we previously developed using abnormally fertilized human zygotes were not well tolerated by those that undergo normal fertilisation. We have therefore developed an alternative approach based on transplanting pronuclei shortly after completion of meiosis rather than shortly before the first mitotic division. This approach promotes efficient development of human embryos to the blastocyst stage with no detectable effect on aneuploidy or gene expression. However, the efficacy of PNT in preventing transmission of mtDNA disease depends on minimal carryover of mtDNA during pronuclear transplantation.  Following optimisation, we found that mtDNA carryover was reduced to <5% in all PNT and was <2% in the majority (79%).  These levels are well below the threshold for disease symptoms. We therefore propose that the PNT procedures we have developed have the potential to reduce the risk of disease transmission for women with high mutation loads. 

Host: WTCCB


4th May 2016
12:00
Daniel Rutherford
Lecture Theatre 1 G.27

Dr Thijn Brummelkamp: The Netherlands Cancer Institute, Amsterdam

WT PhD Programme Seminar - "Haploid genetics in human cells to unravel disease relevant networks"

Our group uses genetics in mammalian cells to study human disease. Unfortunately only few biological processes that operate in human cells have been subjected to extensive, mutation-based, genetic analysis. Moreover, even when genes have been linked to a particular phenotype, their genetic interactions are rarely known. This is a bottleneck in today’s biomedical research because a detailed understanding of the genes involved in a disease phenotype as well as their genetic interactions could suggest new avenues for therapeutic intervention.

The goal of our laboratory is to use genetics in cultured human cells to generate accurate and complete overviews of genes that play a role in phenotypes of interest. In addition, we are interested in studying genetic interactions between human genes. In the last years we have developed a new genetic model system that allows yeast-like genetics in haploid human cells. We have used this to identify host factors that are used by diverse pathogens, which led to the identification of a new class of intracellular receptors required for the entry of Ebola and Lassa virus. Furthermore, we use extensive mutagenesis in haploid cells to identify genes that are required for optimal cell viability as well as genes that are only required for viability in specific genetic backgrounds.

To study the principles of genetic interactions in human cells we created a synthetic lethality network focused on the secretory pathway based exclusively on mutations. The synthetic lethality map can be used to assign functions to orphan genes, parallels observations made in yeast in terms of numbers and network organization and projects a route forward to reveal genetic interactions affecting diverse aspects of human cell biology.

Host: WTCCB


28th Apr 2016
16:30
Michael Swann Building
Main Lecture Theatre

Margaret Fuller, Stanford University of Medicine

Regulation of differentiation in an adult stem cell lineage

Host: David Tollervey


20th Apr 2016
16:00
Michael Swann Building
Main Lecture Theatre

Ben Martynoga, Francis Crick Institute, London

Molecular Tinkering: the Edinburgh scientists who changed the face of modern biology

During the 1960s Edinburgh became a hotbed for a forward-thinking group of molecular biologists. These scientists played a key role in biology’s molecular revolution. They invented gene cloning techniques, made epigenetics tangible and launched genomics and systems biology. Ben Martynoga will describe the pivotal innovations and the unique individuals who devised them. He will explain how expertise mastered decades ago still resonates in Edinburgh’s thriving research scene today. He will explore what the resource-intensive machine of modern biology can learn from the curiosity-driven, often craft-like approach of Edinburgh’s molecular pioneers.

Brief biography:
Ben Martynoga gained his PhD in developmental neuroscience from Edinburgh University in 2006. During postdoctoral work in Mumbai and London’s National Institute for Medical Research he used genomics approaches to understand the brain’s stem cells. He’s currently a visiting scientist at the Francis Crick Institute in London and a freelance science writer. His journalistic work has appeared in various publications including the Financial Times, the Long+Short magazine and the Guardian. He is currently writing a book about Edinburgh’s history of pioneering molecular approaches to biology.

Host: Adrian Bird


12th Apr 2016
11:00
Michael Swann Building
S7.20

Marvin Tanenbaum, Hubrecht Institute, Utrecht, Netherlands

Dynamics of translation of single mRNA molecules in vivo

Regulation of mRNA translation, the process by which ribosomes decode mRNAs into polypeptides, is used to tune cellular protein levels. Currently, methods for observing the complete process of translation from single mRNAs in vivo are unavailable. We have developed a single molecule imaging approach, which allows long-term (>1 hr) imaging of single mRNAs undergoing hundreds of rounds of translation in live cells, enabling quantitative measurements of ribosome initiation, elongation and stalling. This approach reveals a surprising heterogeneity in the translation of individual mRNAs within the same cell, including rapid and reversible transitions between a translating and non-translating state. Applying this method to the cell cycle gene Emi1, we find strong overall repression of translation initiation by specific 5’UTR sequences, but individual mRNA molecules in the same cell can exhibit dramatically different translational efficiencies. The ability to observe translation of single mRNA molecules in live cells provides a powerful tool to unravel mechanisms of translation regulation.

 

Host: Julie Welburn


7th Apr 2016
13:00
Michael Swann Building
S7.20

Masato Kanemaki

Auxin-inducible degron (AID) technology in human cells

Studies of protein function in vivo are greatly helped by systems that allow the conditional depletion of a protein of interest. Conditional depletion can be achieved by fusing a destabilizing domain (so called degron) that can be conditionally controlled. We developed the auxin-inducible degron (AID) technology by transplanting a plant-specific degradation pathway to non-plant cells. Crucially, the AID technology allows for conditional depletion that is very rapid, typically with a half-life of 10–20 min. This is much quicker than any of the other depletion technologies, which typically yield half-lives of several hours to days. By using the AID technology, it is possible to analyse the direct consequences of depletion, before they are obscured by secondary effects. However, even though the AID system represents a very promising technology for the analysis of proteins in human cells, its use has been severely limited until now, because it is difficult to fuse endogenous proteins with the AID tag.

To overcome this problem, we developed a simple and scalable CRISPR/Cas-based tagging method for the construction of human AID cells. We also improved the AID technology by making smaller and efficient degrons. These technical breakthroughs enabled us to generate human conditional cells within three weeks. As an example, I would like to show conditional mutants of essential complexes for cell proliferation, such as Cohesin and Dynein. In order to demonstrate the power of the AID technology, we applied it to study chromosome maintenance in yeast and in human cells. In particular, we recently found a non-canonical pathway for DNA synthesis in human cells that was induced when the active replication forks were artificially destroyed by degrading the replicative MCM helicase in S phase. In this process, we revealed that the MCM8-9 complex, which is involved in recombination-dependent repair, was playing an important role.

In this seminar, I would like to share our latest findings and to discuss possible contributions of degron-based genetics for stem cell biology and other fields in the future

Host: Bill Earnshaw


16th Mar 2016
16:00
Rutherford Building
G.27

Thomas C. Mettenleiter, President of the Friedrich-Loeffler-Institut, Greifswald and Head of the Institute of Molecular Virology and Cell Biology

Molecular Basis of Herpesvirus Nuclear Egress – the Prototypic Vesicular Nucleo-Cytoplasmic Transport

Herpesvirus nucleocapsids are assembled in the nucleus but mature to infectious virions in the cytosol. To gain access to the maturation compartment intranuclear capsids have to cross the nuclear envelope (NE). While nucleo-cytoplasmic transport usually occurs through nuclear pore complexes (NPC), the ca. 120nm capsids are too large to pass through NPC. Thus, herpesviruses use a vesicle-mediated nucleo-cytoplasmic transport by budding of nucleocapsids at the inner nuclear membrane thereby obtaining a primary envelope, which then fuses with the outer nuclear membrane to release the capsid into the cytosol. Nuclear egress is mediated by the heterodimeric viral nuclear egress complex (NEC) which alone is sufficient for membrane bending and scission in artificial membrane systems as well as authentic nuclear envelopes. We have analyzed vesicle formation by the NEC in situ by multimodal imaging and determined the crystal structure of the NEC of the alphaherpesvirus pseudorabies virus. Our data unravel basic principles of vesiculation from the INM including the formation of two hexagonal lattices composed of multiple copies of the NEC which induce bending of the INM resulting in the formation of vesicles of distinct size capable to accommodate the viral nucleocapsid for transport. Although this herpesvirus-induced vesicular transfer through the NE has been thought unique, it may actually also be used for transport of other large cellular cargo, e.g. RNP complexes, through the NE.

Host: Eric Schirmer


23rd Feb 2016
12:30
Michael Swann Building
S7.15

Tony Ly, Centre for Gene Regulation and Expression, University of Dundee

Proteomic approaches to study cell cycle regulation

Understanding how carcinogenesis disrupts cell cycle control has important implications in human biology and anti-cancer therapy. A key feature of cell cycle control, conserved from yeast to human, is the periodic fluctuation in protein abundances and their PTMs. In this seminar, I will present how recent technological advances in mass spectrometry (MS)-based proteomics enable large scale characterisation of the cell cycle regulatory network in human cells. I will show how the proteomes of synchronised human cells, namely via serum starvation, hydroxyurea, and CDK1 inhibition, compare with cells fractionated with minimal physiological perturbation into different cell cycle stages. Finally, I will present work in progress combining intracellular immunostaining, FACS and MS to analyse protein cell cycle regulation with improved resolution, which I have used to characterise the temporal switch in substrate specificity of the anaphase promoting complex/cyclosome (APC/C) E3 ligase during mitosis.

Host: Patrick Heun


23rd Feb 2016
16:00
Michael Swann Building
S7.15

Monica Justice, SickKids Research Institute, Toronto, Canada

A suppressor screen in Mecp2 mice reveals pathways for Rett Syndrome pathogenesis

Mutations in the methyl CpG binding protein 2 (MeCP2) cause Rett Syndrome, an X-linked neurological disease with autistic features and developmental regression. Mecp2 mouse mutants provide an excellent animal model to identify molecules that are important for disease pathogenesis. A modifier screen is an unbiased forward-genetic approach to find mutations that suppress or enhance a phenotype of interest, allowing the organism to reveal important pathways for morbidity. We used random unbiased mutagenesis to isolate mutations that suppressed clinical signs and improved overall health in a Mecp2 mouse model. MeCP2 is central to the brain epigenome, so tipping the scale using modifier mutagenesis is highly informative, revealing key pathways for pathology. One modifying mutation showed that cholesterol synthesis was abnormal in Mecp2 mice, and revealed the importance of brain lipid homeostasis to neurological disease. Surprisingly, metabolic syndrome also develops in Mecp2 mice, which can be ameliorated by the administration of statin drugs. Altogether, our data suggest that multiple factors will be required to reverse disease entirely.

Host: Adrian Bird


15th Feb 2016
12:05
Daniel Rutherford
Lecture Theatre 1 G.27

Matthias Henze, EMBL, Heidelberg

WT PhD Programme Seminar - "A new view on RNA-binding proteins and RNA"

We recently discovered that hundreds of cellular proteins, previously well known for other biological functions, also unexpectedly bind RNA (termed “enigmRBPs” for enigmatic RNA-Binding Proteins)(1-4). Since many enigmRBPs are conserved from yeast to humans, their existence raises pressing questions. One of the most stunning surprises was the discovery that almost all enzymes of the glycolytic pathway are conserved as enigmRBPs. Overall, more than 50 metabolic enzymes were found to bind RNA. Could the combination of enzymatic and RNA-binding functions represent a general biological principle for coordination between gene expression and metabolism? (5). Applying a newly developed technique, RBDmap, to identify the RNA-binding domains of enigmRBPs, we uncovered new RNA-binding architectures yielding functional insights (6). Integrating all information, we discuss a possible new function for genomes in addition to their classical role in driving protein biosynthesis via mRNAs, rRNAs, and tRNAs and their associated modifying and regulatory RNAs.

 

(1)   Castello et al., Cell 149, 1393-1406, 2012

(2)   Castello et al., Nature Protoc. 8, 491-500, 2013

(3)   Kwon et al., Nature Struc. Mol. Biol. 20, 1122-1132, 2013

(4)   Beckmann, Horos et al., submitted

(5)   Hentze and Preiss, TiBS 35, 423-426, 2010

(6)   Castello et al., submitted

 

 

Host: Jean Beggs


11th Feb 2016
12:30
Michael Swann Building
S7.20

John Weir, MPI of Molecular Physiology, Dortmund, Germany

Biochemical reconstitution and characterisation of a human kinetochore

Chromosomes are carriers of the genetic material and their accurate transfer from a mother cell to its two daughters during cell division is of paramount importance for life. Kinetochores are crucial for this process, as they connect chromosomes with microtubules in the mitotic spindle. Kinetochores are multi-subunit complexes that assemble on specialized chromatin domains, the centromeres, whose unique feature is the enrichment of nucleosomes containing the histone H3 variant centromeric protein A (CENP-A). A group of several additional CENPs, collectively known as constitutive centromere associated network (CCAN), establish the inner kinetochore, whereas a 10-subunit assembly known as the KMN network creates a microtubule-binding site in the outer kinetochore.

 

Interactions between CENP-A and two CCAN subunits, CENP-C and CENP-N, have been previously described, but a comprehensive understanding of CCAN organization, of how it contributes to selective recognition of CENP-A, and of how it may contribute to propagate centromere identity through subsequent cell generations has been missing. Here, we use biochemical reconstitution of recombinant material to unveil fundamental principles of kinetochore organization and function. We show that cooperative interactions of a 7-subunit CCAN sub-complex, the CHIKMLN complex, determine binding selectivity for CENP-A over H3-nucleosomes The CENP-A:CHIKMLN complex binds directly to the KMN network, resulting in a 21-subunit kinetochore complex. Using a cross-linking and mass-spec approach we elucidate the topology of the complex. Finally we prove that the reconstituted kinetochores are functional, translocating CENP-A nucleosomes to microtubules and that the strength of microtubule binding is influenced by CCAN composition.

Host: Adele Marston


18th Jan 2016
12:00
Daniel Rutherford
Lecture Theatre 1 G.27

Paul Lehner, Cambridge Institute for Medical Research, University of Cambridge

WT PhD Programme Seminar - "Complementary genetic and proteomic approaches to viral evasion"

The goal of our work is to identify novel genes and map intracellular pathways involved in virus:host cell interactions. Viruses manipulate host cell signaling pathways to enable viral replication and evade immune recognition. In turn, infected cells need to sense and respond appropriately to intracellular viral infections. We have developed a gene discovery platform that involves functional proteomic approaches to identify receptors manipulated by viruses and genome-wide genetic screens to identify key components of intracellular signalling pathways. We use ‘Plasma Membrane Profiling’ to gain an unprecedented overview of cellular receptors manipulated by viruses. TMT-based quantitation allows us to create a temporal cell surface map of receptors manipulated by both integrating (HIV) and non-integrating viruses (HCMV) and established a novel paradigm of viral interference with immunometabolism, through downregulation of amino acid carriers and transporters.

 

To complement this proteomic approach we use fluorescence-based phenotypic selection for forward genetic screens in human haploid cells. This identified novel genes including (i) ERAD E3 ubiquitin ligases and (ii) the transcriptional repressor complex we termed ‘HUSH’ (Human Silencing Hub) a widely active epigenetic repressor complex that plays a major role in somatic transgene silencing, including the silencing of newly inserted retroviruses.

Host: Robin Allshire


23rd Sep 2015
12:00
Daniel Rutherford Building
G27, Lecture Theatre 1

Elena Conti

Structural insights into the molecular mechanisms of RNA helicase

RNA helicases are present in all domains of life and participate in virtually all aspects of RNA metabolism. Members of this protein family act as RNA-dependent ATPases in promoting rearrangements of RNAs and/or ribonucleoprotein particles, but are remarkable diverse in their individual functions. Although they share the same catalytic core formed by two domains homologous to the bacterial RecA recombination protein, they are often characterised by additional domains that impart specificity and/or regulation. The talk will address the molecular mechanisms we learnt from studying the structures of DEAD-box and DExH-box helicases, with a particular focus on the exosome-associated helicases Ski2 and Mtr4 and the Drosophila dosage compensation helicase MLE.

Host: Atlanta Cook


13th Jul 2015
11:00
Daniel Rutherford Building
Lecture Theatre 1 (G27)

Peter Fraser

Nuclear organization and gene expression control

Host: Eric Schirmer and Philipp Voigt


3rd Jul 2015
13:00
Daniel Rutherford Building
Lecture Theatre 1

Chris Ponting, MRC Functional Genomics Unit, University of Oxford

Short steps along the long road to long non-coding RNA function

Thousands of human lncRNA loci have been documented yet only a handful have had their functions experimentally defined.  A large-scale lncRNA knockout project will be required exploiting multiple targeting strategies to determine the full range of contributions that lncRNAs make to human biology and disease.  In the meantime, either computational or experimental investigation of lncRNA loci can provide insights into lncRNA mechanism.

Our investigations of sequence conservation and constraint on lncRNA sequence have previously provided scant evidence for much of this sequence being functional. Nevertheless, we found that such patterns across multi-exonic lncRNA loci mirror those of protein coding genes, although to a lesser degree. Additionally we report strong evidence for the action of purifying selection to preserve exonic splicing enhancers within human multi-exonic lncRNAs and nucleotide composition in fruitfly lncRNAs. Our findings provide evidence for selection for more efficient rates of transcription and splicing within lncRNA loci.

Careful experimental investigations of single lncRNA loci are essential if we are to appreciate the breadth of lncRNA mechanisms. We have identified a mammalian-conserved lncRNA which acts as a microRNA sponge thereby increasing the transcript and protein abundance of mitochondrial oxidative phosphorylation subunits, and hence complex I enzymatic activity. Our experimental and computational approaches demonstrate that many lncRNAs are biologically consequential by regulating gene expression levels in trans either by regulating rates of transcription or levels of transcripts.

Host: David Tollervey


23rd Jun 2015
16:00
Darwin Building
Darwin Lecture Theatre (G10)

Professor Tom Owen-Hughes, Centre for Gene Regulation and Expression, University of Dundee

Wellcome Trust PhD Programme in Cell Biology Symposium Lecture - How are nucleosomes organised?

 

The fundamental subunit of eukaryotic chromatin in the nucleosome consisting of four core histones and 147 bp of DNA. The positions at which nucleosomes deposited on DNA are not random. Arrays of spaced nucleosomes are aligned with genomic features such as transcriptional start sites and the binding sites for sequence specific DNA binding proteins. ATP-dependent motor proteins contribute to the organisation of nucleosomes. To understand how these motors work, we are using combined structural approaches to determine how they engage and alter nucleosomes. We are also studying which motor proteins are responsible for organising nucleosomes in different regions of genomes. For example, in human cells nucleosomes are exceptionally well organised adjacent to the architectural regulator CTCF. We find that complexes containing the enzyme SNF2H play a major role in the organisation of nucleosomes at these sites. A major challenge to the maintenance of stably organised chromatin is the separation of DNA strands during DNA replication. To investigate this we have devised approaches to study how nucleosomes are organised on newly replicated DNA. In budding yeast we find that nucleosomes are organised with respect to transcriptional start sites within minutes of replication. This process does not require transcription indicating the existence of a distinct replication coupled programme for organising nucleosomes. The rate at which nucleosomes are aligned to the transcriptional start site is enhanced at transcribed genes. This supports the existence of periods of increased chromatin organisation activity coupled to the transit of DNA and RNA polymerases. The rapid re-establishment of nucleosome organisation following replication ensures that the chromatin landscape is re-established before newly replicated chromosomes are separated into daughter cells.

 

Host: Wellcome Trust PhD Programme in Cell Biology


27th May 2015
12:00
Daniel Rutherford
Lecture Theatre 1 G.27

Tony Carr - University of Sussex

WT PhD Programme Seminar - "Mechanisms of replication-associated genome rearrangement"

A common feature of most cancer cells is genetic instability. We are interested in how this genetic instability occurs. When cancer is initiated by oncogene expression, DNA replication is perturbed and cells experience "oncogene-induced stress" (OIS) during which replication generates DNA damage which activates the p53 checkpoint. This results in a barrier to cancer progression that must be overcome (i.e. through loss of p53) if carcinogenesis is to progress. If this occurs, the resulting cells have an increased propensity to accumulate mutations.

 

OIS can result in the dissociation of the DNA replication machinery from the site of DNA synthesis. If this occurs, replication can be restarted by homologous recombination (HR). Our previous work has demonstrated that HR-restarted DNA replication is intrinsically error prone. We are currently examining the consequences of replicating a region of DNA with a fork that has been correctly restarted by HR. Using DNA polymerase mutants that incorporate excess ribonucleotides we have shown that, following replication restart by HR-dependent mechanisms within S phase, replication is semi-conservative and both strands are synthesises by polymerase delta. We have developed a protocol (Pu-Seq) to map, genome-wide, the usage of Polymerase delta and Polymerase epsilon. Our data plot, at very high resolution, the location of the replication origins and identify regions of the genome where there is increased usage of polymerase delta to replicate the duplex DNA. Such sites may represent regions prone to genome instability.

Host: Kevin Hardwick


20th May 2015
12:00
Daniel Rutherford
Lecture Theatre 1 G.27

Shona Murphy - Sir William Dunn School of Pathology, Oxford

WT PhD Programme Seminar - "The point of no return: a novel Poly(A)-associated elongation checkpoint"

We have uncovered a hitherto-unsuspected kinase-controlled transcription-elongation checkpoint associated with polyadenylation signals at the end of human protein-coding genes. This functions in addition to the well-known CDK9-dependent early-elongation checkpoint at the beginning of genes, and the failure of RNA polymerase II to negotiate this polyadenylation-associated checkpoint aborts transcription elongation prematurely. This checkpoint may provide a final quality-control step for mRNAs at the point of no return, after which a potentially functional mRNA is produced. Polyadenylation-associated checkpoints could therefore provide a powerful and rapid mechanism for the control of transcription in response to a range of signals, such as during development, where synchronous activation and repression of gene expression is required.

Host: Jean Beggs


13th May 2015
12:00
Daniel Rutherford
Lecture Theatre 1 G.27

Cristina Cardoso - Technische Universität Darmstadt, Germany

WT PhD Programme Seminar - "Functional units of DNA replication and repair"

Since the pioneering proposal of the replicon model of DNA replication 50 years ago, the predicted replicons have not been identified and quantified at the cellular level. Here, we combined conventional and super-resolution microscopy of replication sites in live and fixed cells with computational image analysis. We complemented these data with genome size measurements, comprehensive analysis of S-phase dynamics and quantification of replication fork speed and replicon size in human and mouse cells. These multidimensional analyses demonstrated that replication foci in 3D preserved mammalian cells could be optically resolved down to single replicons throughout S-phase. This sets aside the conventional view of replication foci as complex entities corresponding to clustered replicons and establishes the replicon as the elementary functional unit of 3D genome organization. Furthermore, we have combined super-resolution microscopy of DNA damage repair sites with genome-wide ChIP-seq analysis and are testing whether the same elementary units of genome organization underly multiple DNA metabolic processes.

Host: Irina Stancheva


12th Jan 2015
12:00
Michael Swann
Main Lecture Theatre

Ana Pombo - Berlin Institute for Medical Systems Biology

WT PhD Programme Seminar - "Hierarchical organization of chromosome folding during mammalian cell differentiation"

Chromosomes have a complex spatial organization within the cell nucleus. They are folded into an array of megabase-sized regions, known as topologically associated domains (TADs), marked by locally enriched chromatin interactions. TADs have internal sub-structures, but their higher-order organization and folding into chromosome territories remains elusive.

 

We have investigated interactions between TADs and find that, far from being isolated structures, they form a functional hierarchy of domains-within-domains (metaTADs), which extends across genomic scales up to entire chromosomes. We map chromatin contacts with Hi-C along a differentiation time-course from proliferating murine embryonic stem cells, through neuronal precursors cells, and terminally differentiated neurons. We find that TAD-TAD interactions generate a hierarchical folding structure irrespective of cell type, reflecting a general organizational principle of the mammalian genome. We explore the mechanisms of hierarchical folding using polymer modelling, and demonstrate that it can promote efficient chromatin packaging without loss of contact specificity. We find that the structures of metaTAD trees correlate with genetic, epigenetic and expression features. The structural rearrangements in metaTAD trees observed during differentiation correlate with changes in transcriptional state, highlighting a functional role for hierarchical chromatin organization far beyond simple packing efficiency.

Host: Adrian Bird


25th Jun 2014
16:45
Michael Swann Building
Main Lecture Theatre

Professor Caroline Dean - John Innes Centre, Norwich

Wellcome Trust PhD Programme in Cell Biology Symposium Lecture - Chromatin and antisense transcript dynamics underlying seasonal timing.

The study of adaptation in plants has led us into the dissection of conserved mechanisms that link antisense transcripts with chromatin dynamics. This work emerged from genetic and molecular analysis of flowering pathways that quantitatively modulate expression of the flowering repressor FLC in response to different environmental and developmental cues.

The antisense transcripts, collectively called COOLAIR, are alternatively spliced and polyadenylated, initiate in an R-loop covering the 3’ end of FLC and encompass the whole FLC sense transcription unit. The differentially processed forms of COOLAIR are associated with different FLC chromatin states via changes in recruitment of chromatin modifying complexes. The talk will describe our current understanding of these mechanisms.

Host: Wellcome Trust PhD Programme in Cell Biology