Recent CIG publications Archive


Elife.: auth.: group Benton

Elife. 2021 Mar 5;10:e63036. doi: 10.7554/eLife.63036. Online ahead of print.

Targeted molecular profiling of rare olfactory sensory neurons identifies fate, wiring and functional determinants

J Roman Arguello 1Liliane Abuin 1Jan Armida 1Kaan Mika 1Phing Chian Chai 1Richard Benton 1Affiliations expand

Free article


Determining the molecular properties of neurons is essential to understand their development, function and evolution. Using Targeted DamID (TaDa), we characterize RNA polymerase II occupancy and chromatin accessibility in selected Ionotropic receptor (Ir)-expressing olfactory sensory neurons in Drosophila. Although individual populations represent a minute fraction of cells, TaDa is sufficiently sensitive and specific to identify the expected receptor genes. Unique Ir expression is not consistently associated with differences in chromatin accessibility, but rather to distinct transcription factor profiles. Genes that are heterogeneously-expressed across populations are enriched for neurodevelopmental factors, and we identify functions for the POU-domain protein Pdm3 as a genetic switch of Ir neuron fate, and the atypical cadherin Flamingo in segregation of neurons into discrete glomeruli. Together this study reveals the effectiveness of TaDa in profiling rare neural populations, identifies new roles for a transcription factor and a neuronal guidance molecule, and provides valuable datasets for future exploration.

Keywords: D. melanogaster; developmental biology; neuroscience.


Methods Mol Biol.: auth.: group Fankhauser

Methods Mol Biol. 2021;2297:21-31. doi: 10.1007/978-1-0716-1370-2_3.

Analysis of Shade-Induced Hypocotyl Elongation in Arabidopsis

Yetkin Çaka Ince 1Vinicius Costa Galvão 2Affiliations expand


The presence of neighbor or overtopping plants is perceived by changes in light quality, which lead to several growth and developmental changes known as shade avoidance syndrome (SAS). Among them, the analysis of hypocotyl elongation is an important SAS physiological output that has been successfully used to investigate photoreceptors and downstream signaling components. Here we describe the experimental setup and growth conditions used to investigate photoreceptors and their signaling mechanisms through the analysis of hypocotyl elongation in laboratory, using simulated low R/FR ratio, low blue light, and true/deep shade conditions.

Keywords: Hypocotyl; Low R/FR ratio; Low blue; Shade avoidance; True shade.


Nat Commun.: auth.: group Vastenhouw

Nat Commun. 2021 Mar 1;12(1):1360. doi: 10.1038/s41467-021-21589-3.

Transcription organizes euchromatin via microphase separation

Lennart Hilbert 1 2 3 4 5Yuko Sato # 6Ksenia Kuznetsova # 2Tommaso Bianucci # 2 3Hiroshi Kimura 6Frank Jülicher 1 3 7 8Alf Honigmann 2Vasily Zaburdaev 1 3 9Nadine L Vastenhouw 10 11

Free article


In eukaryotes, DNA is packed inside the cell nucleus in the form of chromatin, which consists of DNA, proteins such as histones, and RNA. Euchromatin, which is permissive for transcription, is spatially organized into transcriptionally inactive domains interspersed with pockets of transcriptional activity. While transcription and RNA have been implicated in euchromatin organization, it remains unclear how their interplay forms and maintains transcription pockets. Here we combine theory and experiment to analyze the dynamics of euchromatin organization as pluripotent zebrafish cells exit mitosis and begin transcription. We show that accumulation of RNA induces formation of transcription pockets which displace transcriptionally inactive chromatin. We propose that the accumulating RNA recruits RNA-binding proteins that together tend to separate from transcriptionally inactive euchromatin. Full phase separation is prevented because RNA remains tethered to transcribed euchromatin through RNA polymerases. Instead, smaller scale microphases emerge that do not grow further and form the typical pattern of euchromatin organization.


Hum Brain Mapp.: co-auth.: A.Reymond

Hum Brain Mapp. 2021 Feb 21. doi: 10.1002/hbm.25354. Online ahead of print.

Effects of copy number variations on brain structure and risk for psychiatric illness: Large-scale studies from the ENIGMA working groups on CNVs

Ida E Sønderby 1 2 3Christopher R K Ching 4Sophia I Thomopoulos 4Dennis van der Meer 2 5Daqiang Sun 6 7Julio E Villalon-Reina 4Ingrid Agartz 8 9 10Katrin Amunts 11 12Celso Arango 13 14Nicola J Armstrong 15Rosa Ayesa-Arriola 14 16Geor Bakker 17 18Anne S Bassett 19 20 21Dorret I Boomsma 22 23Robin Bülow 24Nancy J Butcher 21 25Vince D Calhoun 26Svenja Caspers 11 27Eva W C Chow 19 21Sven Cichon 11 28 29Simone Ciufolini 30Michael C Craig 31Benedicto Crespo-Facorro 32Adam C Cunningham 33Anders M Dale 34 35Paola Dazzan 36Greig I de Zubicaray 37Srdjan Djurovic 1 38Joanne L Doherty 33 39Gary Donohoe 40Bogdan Draganski 41 42Courtney A Durdle 43Stefan Ehrlich 44Beverly S Emanuel 45Thomas Espeseth 46 47Simon E Fisher 48 49Tian Ge 50 51David C Glahn 52 53Hans J Grabe 54 55Raquel E Gur 56 57Boris A Gutman 58Jan Haavik 59 60Asta K Håberg 61 62Laura A Hansen 63Ryota Hashimoto 64 65Derrek P Hibar 66Avram J Holmes 67 68Jouke-Jan Hottenga 22Hilleke E Hulshoff Pol 69Maria Jalbrzikowski 70Emma E M Knowles 51 71Leila Kushan 72David E J Linden 73 74Jingyu Liu 26 75Astri J Lundervold 76Sandra Martin-Brevet 41Kenia Martínez 13 14 77Karen A Mather 78 79Samuel R Mathias 53 71Donna M McDonald-McGinn 45 80 81Allan F McRae 82Sarah E Medland 83Torgeir Moberget 84Claudia Modenato 41 85Jennifer Monereo Sánchez 73 86 87Clara A Moreau 88Thomas W Mühleisen 11 12 29Tomas Paus 89 90Zdenka Pausova 91Carlos Prieto 92Anjanibhargavi Ragothaman 93Céline S Reinbold 29 94Tiago Reis Marques 30 95Gabriela M Repetto 96Alexandre Reymond 97David R Roalf 56Borja Rodriguez-Herreros 98James J Rucker 36Perminder S Sachdev 78 99James E Schmitt 100Peter R Schofield 79 101Ana I Silva 74 102Hreinn Stefansson 103Dan J Stein 104Christian K Tamnes 2 9 105Diana Tordesillas-Gutiérrez 14 106Magnus O Ulfarsson 103 107Ariana Vajdi 72Dennis van ‘t Ent 22Marianne B M van den Bree 33Evangelos Vassos 108Javier Vázquez-Bourgon 14 16 109Fidel Vila-Rodriguez 110G Bragi Walters 103 111Wei Wen 78Lars T Westlye 3 46 112Katharina Wittfeld 54 55Elaine H Zackai 45 80Kári Stefánsson 103 111Sebastien Jacquemont 88 113Paul M Thompson 4Carrie E Bearden 6 114Ole A Andreassen 2ENIGMA-CNV Working GroupENIGMA 22q11.2 Deletion Syndrome Working GroupAffiliations expand


The Enhancing NeuroImaging Genetics through Meta-Analysis copy number variant (ENIGMA-CNV) and 22q11.2 Deletion Syndrome Working Groups (22q-ENIGMA WGs) were created to gain insight into the involvement of genetic factors in human brain development and related cognitive, psychiatric and behavioral manifestations. To that end, the ENIGMA-CNV WG has collated CNV and magnetic resonance imaging (MRI) data from ~49,000 individuals across 38 global research sites, yielding one of the largest studies to date on the effects of CNVs on brain structures in the general population. The 22q-ENIGMA WG includes 12 international research centers that assessed over 533 individuals with a confirmed 22q11.2 deletion syndrome, 40 with 22q11.2 duplications, and 333 typically developing controls, creating the largest-ever 22q11.2 CNV neuroimaging data set. In this review, we outline the ENIGMA infrastructure and procedures for multi-site analysis of CNVs and MRI data. So far, ENIGMA has identified effects of the 22q11.2, 16p11.2 distal, 15q11.2, and 1q21.1 distal CNVs on subcortical and cortical brain structures. Each CNV is associated with differences in cognitive, neurodevelopmental and neuropsychiatric traits, with characteristic patterns of brain structural abnormalities. Evidence of gene-dosage effects on distinct brain regions also emerged, providing further insight into genotype-phenotype relationships. Taken together, these results offer a more comprehensive picture of molecular mechanisms involved in typical and atypical brain development. This “genotype-first” approach also contributes to our understanding of the etiopathogenesis of brain disorders. Finally, we outline future directions to better understand effects of CNVs on brain structure and behavior.


Genes Dev.: co-auth.: group Franken

Genes Dev. 2021 Feb 18. doi: 10.1101/gad.346460.120. Online ahead of print.

Circadian hepatocyte clocks keep synchrony in the absence of a master pacemaker in the suprachiasmatic nucleus or other extrahepatic clocks

Flore Sinturel # 1 2 3 4Pascal Gos # 5Volodymyr Petrenko 1 2 3 4Claudia Hagedorn 6Florian Kreppel 6Kai-Florian Storch 7Darko Knutti 7Andre Liani 5Charles Weitz 7Yann Emmenegger 8Paul Franken 8Luigi Bonacina 9Charna Dibner 1 2 3 4Ueli Schibler 5


It has been assumed that the suprachiasmatic nucleus (SCN) synchronizes peripheral circadian oscillators. However, this has never been convincingly shown, since biochemical time series experiments are not feasible in behaviorally arrhythmic animals. By using long-term bioluminescence recording in freely moving mice, we show that the SCN is indeed required for maintaining synchrony between organs. Surprisingly, however, circadian oscillations persist in the livers of mice devoid of an SCN or oscillators in cells other than hepatocytes. Hence, similar to SCN neurons, hepatocytes can maintain phase coherence in the absence of Zeitgeber signals produced by other organs or environmental cycles.

Keywords: circadian gene expression; in vivo bioluminescence recording; liver; suprachiasmatic nucleus.


Curr Top Dev Biol.: auth.: group Vastenhouw

Curr Top Dev Biol. 2020;140:209-254. doi: 10.1016/bs.ctdb.2020.02.002. Epub 2020 Feb 26.

From mother to embryo: A molecular perspective on zygotic genome activation

Edlyn Wu 1Nadine L Vastenhouw 2Affiliations expand


In animals, the early embryo is mostly transcriptionally silent and development is fueled by maternally supplied mRNAs and proteins. These maternal products are important not only for survival, but also to gear up the zygote’s genome for activation. Over the last three decades, research with different model organisms and experimental approaches has identified molecular factors and proposed mechanisms for how the embryo transitions from being transcriptionally silent to transcriptionally competent. In this chapter, we discuss the molecular players that shape the molecular landscape of ZGA and provide insights into their mode of action in activating the transcription program in the developing embryo.

Keywords: Chromatin; Embryo development; Maternal-to-zygotic transition; Nuclear organization; Pioneer factors; Transcription factors; Transcriptional regulation; Zygotic genome activation.