Menu

Close

Rapid embryonic cell cycles defer the establishment of heterochromatin by Eggless/SetDB1 in Drosophila

Charles A Seller, Chun-Yi Cho, Patrick H O'Farrell

Preprint posted on November 22, 2018 https://www.biorxiv.org/content/early/2018/10/22/450155

Cell cycle speed sets the pace for heterochromatin formation

Selected by Gabriel Aughey

Background

Regulation of gene expression is controlled by chromatin environments that are either permissive to transcription or else transcriptionally silent. The formation of heterochromatin, characterised by presence of the protein HP1 and H3K9 histone methylation, is required to establish and maintain cell identity. Heterochromatin is largely absent in the earliest stages of a developing embryo in which transcription is minimal and cell fate is not yet firmly established. Therefore, heterochromatin formation can be viewed as one of the first steps in initiating the transcriptional programme that decides a cell’s developmental trajectory.

Although heterochromatin is well studied, very little is currently known about the mechanisms by which the naïve cells of the early embryo establish heterochromatin. Furthermore, it is difficult to use genetics to study the early embryo due to the presence of a large amount of maternally contributed material. In this preprint, Seller et al. use innovative approaches to identify a key factor involved in deposition of heterochromatin, and point towards a mechanism that implicates cell cycle rate in the regulation of this process.

 

Key findings

Jabba-trap can be used to mislocalise nuclear proteins in early development

The early stages of embryogenesis are difficult to study using classical genetics as a large amount of maternally contributed proteins coordinate the majority of developmental processes before the start of zygotic transcription. These proteins can be removed by creating germline mutants, but this is not feasible if the gene is required for oogenesis. To circumvent these problems, Seller et al. explore a nanobody-mediated mis-localisation system (Jabba-trap). This approach relies on a previously published observation that histone proteins (initially present in excess due to maternal contribution), are stored in lipid droplets during early embryogenesis to overcome toxicity until their redistribution to the nucleus later in development (Li et al. 2012). The authors use a nanobody fused to a lipid droplet targeting protein (Jabba) to sequester proteins of interest to these lipid droplets. The authors use Jabba trap to successfully target nuclear proteins to lipid droplets either when injected into embryos or supplied transgenically. As the nanobody targets GFP, this approach could be used to mislocalise any GFP fused protein of interest.

eggless is required to establish heterochromatin

The authors then apply their new technique to the question of heterochromatin formation in early embryogenesis. Of three known histone methyltransferases, the authors observe that one in particular, eggless (egg), is required for heterochromatin formation, whilst the other two (G9a and Su(var)3-9) are dispensable. Satellite repeats associated with constitutive heterochromatin are shown to colocalise with egg and display a loss of HP1 and H3K9 methylation when egg is mislocalised. An egg cofactor, windei (wde) is also shown to colocalise at these regions and is similarly mislocalised when egg is sequestered from the nucleus, indicating that wde forms a complex with egg at heterochromatin. egg localisation in the nucleus preceded HP1 foci formation, indicating that egg is initiating the formation of heterochromatin.

eggless mediated heterochromatin formation is regulated by interphase duration

One of the authors’ most interesting findings comes from the observation that more egg protein is seen to accumulate as the length of cell cycles increases during embryogenesis (cell cycle 14 is approximately 6-7-fold longer than cell cycle 11, and a concomitant increase of egg is observed at stage 14). The authors hypothesise that longer cell cycles later in embryogenesis allow for greater accumulation of egg, which therefore allows for the formation of more heterochromatin. This hypothesis is tested by using RNAi against cell cycle regulators to artificially alter cell cycle duration. Shortening interphase resulted in less egg and heterochromatin formation, whereas cell cycle arrest resulted in greater accumulation of egg and corresponding heterochromatin markers.

(Fig 6. from Seller et al. – Model depicting heterochromatin formation in relation to interphase duration.)

Why I like this preprint

This preprint has several features that I admire. Firstly, the authors have pioneered an innovative approach using nanobodies to mislocalise proteins of interest. This allowed them to study a fundamental period of development that was previously relatively inaccessible to experimental interventions of this nature. This technique is one of several recent studies leveraging nanobodies in creative ways to answer interesting questions (Caussinus et al., Harmansa et al.), and I think the principles that underlie these techniques are useful to many researchers.

Secondly, I am struck by the idea that the slowing of cell cycles is sufficient to kick-start heterochromatin formation at this fundamental juncture in development. Often, I think that as biologists we are predisposed to imagining complex mechanisms to explain our observations. In this case, it is pleasing that an idea as simple as a slowing of cell division could be sufficient to result in a fundamental shift in the gene-regulatory programme of a developing animal.

 

Open questions

  • How does the Jabba-trap technique compare to other nanobody mediated methods? For example, what is the advantage of mislocalisation of nuclear proteins over degradation techniques such as the degradFP system (Caussinus et al, 2011)?
  • What is the mechanism by which egg is recruited to heterochromatin regions? Are the physical properties of repeat DNA regions sufficient for recognition by egg? Does egg alone recognise sequence features associated with heterochromatin or is there a preceding cofactor (chicken perhaps!?) that comes before egg?
  • What happens if cell cycle rate is altered by other means? It is well known that the rate of Drosophila development is temperature dependent. If the temperature is decreased, does slowed diffusion of egg result in HP1 recruitment at a proportionally reduced rate?
  • Is early embryogenesis the only developmental stage in which cell cycle speed affects heterochromatin formation? Could increased cell cycle speed or unusual cell cycles such as endoreplication influence heterochromatin later in development?

 

References

Li Z, Thiel K, Thul PJ, Beller M, Kühnlein RP, Welte MA. (2012). Lipid Droplets Control the Maternal Histone Supply of Drosophila Embryos. Current Biology 22:2104–2113.

Caussinus E, Kanca O, Affolter M. (2011). Fluorescent fusion protein knockout mediated by anti-GFP nanobody. Nat Struct Mol Biol. 19(1):117-21.

Harmansa S, Alborelli I, Bieli D, Caussinus E, Affolter M. (2017) A nanobody-based toolset to investigate the role of protein localization and dispersal in Drosophila. Elife. Apr 11;6. pii: e22549. doi: 10.7554/eLife.22549

Tags: drosophila, embryogenesis, fly, heterochromatin

Posted on: 22nd November 2018

Read preprint (No Ratings Yet)




  • Have your say

    Your email address will not be published. Required fields are marked *

    This site uses Akismet to reduce spam. Learn how your comment data is processed.

    Sign up to customise the site to your preferences and to receive alerts

    Register here

    Also in the developmental biology category:

    The cell wall regulates dynamics and size of plasma-membrane nanodomains in Arabidopsis.

    Joseph Franics McKenna, Daniel Rolfe, Stephen E D Webb, et al.



    Selected by Marc Somssich

    Psychiatric risk gene NT5C2 regulates protein translation in human neural progenitor cells

    Rodrigo R.R. Duarte, Nathaniel D. Bachtel, Marie-Caroline Cotel, et al.



    Selected by Joanna Cross

    A Scube2-Shh feedback loop links morphogen release to morphogen signaling to enable scale invariant patterning of the ventral neural tube

    Zach Collins, Kana Ishimatsu, Tony Tsai, et al.



    Selected by Teresa Rayon

    1

    Epiblast formation by Tead-Yap-dependent expression of pluripotency factors and competitive elimination of unspecified cells

    Masakazu Hashimoto, Hiroshi Sasaki



    Selected by Sarah Bowling, Teresa Rayon

    Single cell transcriptomics reveals spatial and temporal dynamics of gene expression in the developing mouse spinal cord

    Julien Delile, Teresa Rayon, Manuela Melchionda, et al.



    Selected by Reena Lasrado

    1

    The Toll pathway inhibits tissue growth and regulates cell fitness in an infection-dependent manner

    Federico Germani, Daniel Hain, Denise Sternlicht, et al.



    Selected by Rohan Khadilkar

    A histidine kinase gene is required for large radius root tip circumnutation and surface exploration in rice

    Kevin R Lehner, Isaiah Taylor, Erin N McCaskey, et al.



    Selected by Martin Balcerowicz

    Actomyosin-driven tension at compartmental boundaries orients cell division independently of cell geometry in vivo

    Elena Scarpa, Cedric Finet, Guy Blanchard, et al.



    Selected by Ivana Viktorinová

    Molecular organization of integrin-based adhesion complexes in mouse Embryonic Stem Cells

    Shumin Xia, Evelyn K.F. Yim, Pakorn Kanchanawong

    AND

    Superresolution architecture of pluripotency guarding adhesions

    Aki Stubb, Camilo Guzmán, Elisa Närvä, et al.



    Selected by Nicola Stevenson, Amanda Haage

    Transcriptional initiation and mechanically driven self-propagation of a tissue contractile wave during axis elongation

    Anais Bailles, Claudio Collinet, Jean-Marc Philippe, et al.



    Selected by Sundar Naganathan

    1

    Revealing the nanoscale morphology of the primary cilium using super-resolution fluorescence microscopy

    Joshua Yoon, Colin J. Comerci, Lucien E. Weiss, et al.



    Selected by Gautam Dey

    Signaling dynamics control cell fate in the early Drosophila embryo

    Heath E Johnson, Stanislav Y Shvartsman, Jared E Toettcher



    Selected by Yara E. Sánchez Corrales

    1

    Three-dimensional tissue stiffness mapping in the mouse embryo supports durotaxis during early limb bud morphogenesis

    Min Zhu, Hirotaka Tao, Mohammad Samani, et al.



    Selected by Natalie Dye

    PUMILIO hyperactivity drives premature aging of Norad-deficient mice

    Florian Kopp, Mehmet Yalvac, Beibei Chen, et al.



    Selected by Carmen Adriaens

    Synergy with TGFβ ligands switches WNT pathway dynamics from transient to sustained during human pluripotent cell differentiation

    Joseph Massey, Yida Liu, Omar Alvarenga, et al.



    Selected by Pierre Osteil

    1

    3D Tissue elongation via ECM stiffness-cued junctional remodeling

    Dong-Yuan Chen, Justin Crest, Sebastian J Streichan, et al.



    Selected by Sundar Naganathan

    Also in the genetics category:

    Psychiatric risk gene NT5C2 regulates protein translation in human neural progenitor cells

    Rodrigo R.R. Duarte, Nathaniel D. Bachtel, Marie-Caroline Cotel, et al.



    Selected by Joanna Cross

    The Toll pathway inhibits tissue growth and regulates cell fitness in an infection-dependent manner

    Federico Germani, Daniel Hain, Denise Sternlicht, et al.



    Selected by Rohan Khadilkar

    Rapid embryonic cell cycles defer the establishment of heterochromatin by Eggless/SetDB1 in Drosophila

    Charles A Seller, Chun-Yi Cho, Patrick H O'Farrell



    Selected by Gabriel Aughey

    Evidence for an Integrated Gene Repression Mechanism based on mRNA Isoform Toggling in Human Cells

    Ina Hollerer, Juliet C Barker, Victoria Jorgensen, et al.



    Selected by Clarice Hong

    Signaling dynamics control cell fate in the early Drosophila embryo

    Heath E Johnson, Stanislav Y Shvartsman, Jared E Toettcher



    Selected by Yara E. Sánchez Corrales

    1

    PUMILIO hyperactivity drives premature aging of Norad-deficient mice

    Florian Kopp, Mehmet Yalvac, Beibei Chen, et al.



    Selected by Carmen Adriaens

    Arterio-Venous Remodeling in the Zebrafish Trunk Is Controlled by Genetic Programming and Flow-Mediated Fine-Tuning

    Ilse Geudens, Baptiste Coxam, Silvanus Alt, et al.



    Selected by Andreas van Impel

    CRISPR/Cas9-mediated gene deletion of the ompA gene in an Enterobacter gut symbiont impairs biofilm formation and reduces gut colonization of Aedes aegypti mosquitoes

    Shivanand Hegde, Pornjarim Nilyanimit, Elena Kozlova, et al.



    Selected by Snehal Kadam

    millepattes micropeptides are an ancient developmental switch required for embryonic patterning

    Suparna Ray, Miriam I Rosenberg, Hélène Chanut-Delalande, et al.



    Selected by Erik Clark

    Neural crest cells regulate optic cup morphogenesis by promoting extracellular matrix assembly

    Chase Dallas Bryan, Rebecca Lynne Pfeiffer, Bryan William Jones, et al.



    Selected by Ashrifia Adomako-Ankomah

    1

    The cis-regulatory logic underlying abdominal Hox-mediated repression versus activation of regulatory elements in Drosophila

    Arya Zandvakili, Juli Uhl, Ian Campbell, et al.



    Selected by Clarice Hong

    1

    Dynamic control of proinflammatory cytokines Il-1β and Tnf-α by macrophages is necessary for functional spinal cord regeneration in zebrafish

    Themistoklis M. Tsarouchas, Daniel Wehner, Leonardo Cavone, et al.



    Selected by Shikha Nayar

    1

    JNK-mediated spindle reorientation in stem cells promotes dysplasia in the aging intestine

    Daniel Hu, Heinrich Jasper



    Selected by Maiko Kitaoka

    Phenotypic landscape of schizophrenia-associated genes defines candidates and their shared functions

    Summer B. Thyme, Lindsey M. Pieper, Eric H. Li, et al.



    Selected by Daniel Grimes

    Super-Mendelian inheritance mediated by CRISPR/Cas9 in the female mouse germline

    Hannah A. Grunwald, Valentino M. Gantz, Gunnar Poplawski, et al.



    Selected by Rebekah Tillotson

    1

    The Ly6/uPAR protein Bouncer is necessary and sufficient for species-specific fertilization

    Sarah Herberg, Krista R Gert, Alexander Schleiffer, et al.



    Selected by James Gagnon

    Also in the molecular biology category:

    The modular mechanism of chromocenter formation in Drosophila

    Madhav Jagannathan, Ryan Cummings, Yukiko M Yamashita



    Selected by Maiko Kitaoka

    1

    The structural basis for release factor activation during translation termination revealed by time-resolved cryogenic electron microscopy

    Ziao Fu, Gabriele Indrisiunaite, Sandip Kaledhonkar, et al.



    Selected by David Wright

    The cell wall regulates dynamics and size of plasma-membrane nanodomains in Arabidopsis.

    Joseph Franics McKenna, Daniel Rolfe, Stephen E D Webb, et al.



    Selected by Marc Somssich

    Psychiatric risk gene NT5C2 regulates protein translation in human neural progenitor cells

    Rodrigo R.R. Duarte, Nathaniel D. Bachtel, Marie-Caroline Cotel, et al.



    Selected by Joanna Cross

    DNA microscopy: Optics-free spatio-genetic imaging by a stand-alone chemical reaction

    Joshua A. Weinstein, Aviv Regev, Feng Zhang



    Selected by Theo Sanderson

    2

    Rapid embryonic cell cycles defer the establishment of heterochromatin by Eggless/SetDB1 in Drosophila

    Charles A Seller, Chun-Yi Cho, Patrick H O'Farrell



    Selected by Gabriel Aughey

    Signaling dynamics control cell fate in the early Drosophila embryo

    Heath E Johnson, Stanislav Y Shvartsman, Jared E Toettcher



    Selected by Yara E. Sánchez Corrales

    1

    PUMILIO hyperactivity drives premature aging of Norad-deficient mice

    Florian Kopp, Mehmet Yalvac, Beibei Chen, et al.



    Selected by Carmen Adriaens

    Target-specific precision of CRISPR-mediated genome editing

    Anob M Chakrabarti, Tristan Henser-Brownhill, Josep Monserrat, et al.



    Selected by Rob Hynds

    1

    Transient intracellular acidification regulates the core transcriptional heat shock response

    Catherine G Triandafillou, Christopher D Katanski, Aaron R Dinner, et al.



    Selected by Srivats Venkataramanan

    1

    Memory sequencing reveals heritable single cell gene expression programs associated with distinct cellular behaviors

    Sydney M Shaffer, Benjamin L Emert, Ann E. Sizemore, et al.



    Selected by Leighton Daigh

    2

    Site-specific K63 ubiquitinomics reveals post-initiation regulation of ribosomes under oxidative stress

    Songhee Back, Christine Vogel, Gustavo M Silva



    Selected by Srivats Venkataramanan

    1

    Quantitative, real-time, single cell analysis in tissue reveals expression dynamics of neurogenesis

    Cerys S Manning, Veronica Biga, James Boyd, et al.



    Selected by Teresa Rayon

    The cis-regulatory logic underlying abdominal Hox-mediated repression versus activation of regulatory elements in Drosophila

    Arya Zandvakili, Juli Uhl, Ian Campbell, et al.



    Selected by Clarice Hong

    1

    Moving beyond P values: Everyday data analysis with estimation plots

    Joses Ho, Tayfun Tumkaya, Sameer Aryal, et al.



    Selected by Gautam Dey

    1

    A limited number of double-strand DNA breaks are sufficient to delay cell cycle progression.

    Jeroen van den Berg, Anna G. Manjon, Karoline Kielbassa, et al.



    Selected by Leighton Daigh
    Close