The intersectional genetics landscape for humans

BACKGROUND: The human body is made up of hundreds-perhaps thousands-of cell types and states, most of which are currently inaccessible genetically. Intersectional genetic approaches can increase the number of genetically accessible cells, but the scope and safety of these approaches have not been systematically assessed. A typical intersectional method acts like an "AND" logic gate by converting the input of 2 or more active, yet unspecific, regulatory elements (REs) into a single cell type specific synthetic output. RESULTS: Here, we systematically assessed the intersectional genetics landscape of the human genome using a subset of cells from a large RE usage atlas (Functional ANnoTation Of the Mammalian genome 5 consortium, FANTOM5) obtained by cap analysis of gene expression sequencing (CAGE-seq). We developed the heuristics and algorithms to retrieve and quality-rank "AND" gate intersections. Of the 154 primary cell types surveyed, >90% can be distinguished from each other with as few as 3 to 4 active REs, with quantifiable safety and robustness. We call these minimal intersections of active REs with cell-type diagnostic potential "versatile entry codes" (VEnCodes). Each of the 158 cancer cell types surveyed could also be distinguished from the healthy primary cell types with small VEnCodes, most of which were robust to intra- and interindividual variation. Methods for the cross-validation of CAGE-seq-derived VEnCodes and for the extraction of VEnCodes from pooled single-cell sequencing data are also presented. CONCLUSIONS: Our work provides a systematic view of the intersectional genetics landscape in humans and demonstrates the potential of these approaches for future gene delivery technologies.publishersversionpublishe

Mutations in genes involved in nonsense mediated decay ameliorate the phenotype of sel-12 mutants with amber stop mutations in Caenorhabditis elegans

<p>Abstract</p> <p>Background</p> <p>Presenilin proteins are part of a complex of proteins that can cleave many type I transmembrane proteins, including Notch Receptors and the Amyloid Precursor Protein, in the middle of the transmembrane domain. Dominant mutations in the human presenilin genes PS1 and PS2 lead to Familial Alzheimer's disease. Mutations in the <it>Caenorhabditis elegans sel-12 </it>presenilin gene cause a highly penetrant egg-laying defect due to reduction of signalling through the <it>lin-12</it>/Notch receptor. Mutations in six <it>spr </it>genes (for suppressor of presenilin) are known to strongly suppress <it>sel-12</it>. Mutations in most strong <it>spr </it>genes suppress <it>sel-12 </it>by de-repressing the transcription of the largely functionally equivalent <it>hop-1 </it>presenilin gene. However, how mutations in the <it>spr-2 </it>gene suppress <it>sel-12 </it>is unknown.</p> <p>Results</p> <p>We show that <it>spr-2 </it>mutations increase the levels of <it>sel-12 </it>transcripts with Premature translation Termination Codons (PTCs) in embryos and L1 larvae. mRNA transcripts from <it>sel-12 </it>alleles with PTCs undergo degradation by a process known as Nonsense Mediated Decay (NMD). However, <it>spr-2 </it>mutations do not appear to affect NMD. Mutations in the <it>smg </it>genes, which are required for NMD, can restore <it>sel-12(PTC) </it>transcript levels and ameliorate the phenotype of <it>sel-12 </it>mutants with amber PTCs. However, the phenotypic suppression of <it>sel-12 </it>by <it>smg </it>genes is nowhere near as strong as the effect of previously characterized <it>spr </it>mutations including <it>spr-2</it>. Consistent with this, we have identified only two mutations in <it>smg </it>genes among the more than 100 <it>spr </it>mutations recovered in genetic screens.</p> <p>Conclusion</p> <p><it>spr-2 </it>mutations do not suppress <it>sel-12 </it>by affecting NMD of <it>sel-12(PTC) </it>transcripts and appear to have a novel mechanism of suppression. The fact that mutations in <it>smg </it>genes can ameliorate the phenotype of <it>sel-12 </it>alleles with amber PTCs suggests that some read-through of <it>sel-12(amber) </it>alleles occurs in <it>smg </it>backgrounds.</p

5′ flanking region of var genes nucleate histone modification patterns linked to phenotypic inheritance of virulence traits in malaria parasites

In the human malaria parasite Plasmodium falciparum antigenic variation facilitates long-term chronic infection of the host. This is achieved by sequential expression of a single member of the 60-member var family. Here we show that the 5′ flanking region nucleates epigenetic events strongly linked to the maintenance of mono-allelic var gene expression pattern during parasite proliferation. Tri- and dimethylation of histone H3 lysine 4 peak in the 5′ upstream region of transcribed var and during the poised state (non-transcribed phase of var genes during the 48 h asexual life cycle), ‘bookmarking’ this member for re-activation at the onset of the next cycle. Histone H3 lysine 9 trimethylation acts as an antagonist to lysine 4 methylation to establish stably silent var gene states along the 5′ flanking and coding region. Furthermore, we show that competition exists between H3K9 methylation and H3K9 acetylation in the 5′ flanking region and that these marks contribute epigenetically to repressing or activating var gene expression. Our work points to a pivotal role of the histone methyl mark writing and reading machinery in the phenotypic inheritance of virulence traits in the malaria parasite

The steroid-hormone ecdysone coordinates parallel pupariation neuromotor and morphogenetic subprograms via epidermis-to-neuron Dilp8-Lgr3 signal induction

Funding Information: We thank Drs. Carlos Ribeiro, Christen Mirth, Elio Sucena, Filip Port, Frank Schnorrer, Julien Colombani, Maria Dominguez, Maria Luisa Vasconcelos, Pierre Leopold, Simon Bullock, Rita Teodoro, Gerald Rubin, Melissa Harrison, Kate O’Connor-Giles, Jill Wildonger, Mariana Melani, Pablo Wappner, and Christian Wegener for fly stocks and reagents. We thank Ryohei Yagi and Konrad Basler for the LHV2 plasmid and Brain McCabe for the mhc-Gateway destination plasmid. We thank Carlos Ribeiro and Dennis Goldschmidt for help in designing and constructing one of the pupariation arenas and Mariana Melani, Pablo Wappner, Arash Bashirullah, and Filip Port for sharing resources and unpublished data. We thank Arash Bashirullah, Fillip Port, and Carlos Ribeiro for discussions and/or comments on the manuscript, and Jim Truman for discussions on Fraenkel’s pupariation factors. Stocks obtained from the Bloomington Drosophila Stock Center (NIH P40OD018537) were used in this study. Work in the Integrative Biomedicine Laboratory was supported by the European Commission FP7 (PCIG13-GA-2013-618847), by the FCT (IF/00022/2012; Congento LISBOA-01-0145-FEDER-022170, cofinanced by FCT/Lisboa2020; UID/Multi/04462/2019; PTDC/BEXBCM/1370/2014; PTDC/MED-NEU/30753/2017; PTDC/BIA-BID/31071/2017; FCT SFRH/BPD/94112/ 2013; SFRH/BD/94931/2013), the MIT Portugal Program (MIT-EXPL/BIO/0097/2017), and FAPESP (16/09659-3, 16/10342-4, and 17/17904-0). AG is a CONICET researcher, YV holds a CONICET postdoctoral fellowship and FPS and MJD hold a PhD fellowship from CONICET. Work in the Garelli lab was supported by ANPCyT (Agencia Nacional para la Promoción de la Ciencia y la Tecnología, PICT 2014-2900 and PICT 2017-0254) and CONICET (PIP11220150100182CO). Publisher Copyright: © 2021, The Author(s). Copyright: Copyright 2021 Elsevier B.V., All rights reserved.Innate behaviors consist of a succession of genetically-hardwired motor and physiological subprograms that can be coupled to drastic morphogenetic changes. How these integrative responses are orchestrated is not completely understood. Here, we provide insight into these mechanisms by studying pupariation, a multi-step innate behavior of Drosophila larvae that is critical for survival during metamorphosis. We find that the steroid-hormone ecdysone triggers parallel pupariation neuromotor and morphogenetic subprograms, which include the induction of the relaxin-peptide hormone, Dilp8, in the epidermis. Dilp8 acts on six Lgr3-positive thoracic interneurons to couple both subprograms in time and to instruct neuromotor subprogram switching during behavior. Our work reveals that interorgan feedback gates progression between subunits of an innate behavior and points to an ancestral neuromodulatory function of relaxin signaling.publishersversionpublishe

The biology and evolution of the Dilp8-Lgr3 pathway: A relaxin-like pathway coupling tissue growth and developmental timing control

Many insects, like cockroaches, moths, and flies, can regenerate tissues by extending the growth-competent phases of their life cycle. The molecular and cellular players mediating this coordination between tissue growth and developmental timing have been recently discovered in Drosophila. The insulin/relaxin-like peptide, Dilp8, was identified as a factor communicating abnormal growth status of Drosophila larval imaginal discs to the neuroendocrine centers that control the timing of the onset of metamorphosis. Dilp8 requires a neuronal relaxin receptor for this function, the Leucine rich repeat containing G protein coupled receptor, Lgr3. A review of current data supports a model where imaginal disc-derived Dilp8 acts on four central nervous system Lgr3-positive neurons to activate cyclic-AMP signaling in an Lgr3-dependent manner. This causes a reduction in ecdysone hormone production by the larval endocrine prothoracic gland, which leads to a delay in the onset of metamorphosis and a simultaneous slowing down in the growth rates of healthy imaginal tissues, promoting the generation of proportionate individuals. We discuss reports indicating that the Dilp8-Lgr3 pathway might have other functions at different life history stages, which remain to be elucidated, and review molecular evolution data on invertebrate genes related to the relaxin-pathway. The strong conservation of the relaxin pathway throughout animal evolution contrasts with instances of its complete loss in some clades, such as lepidopterans, which must coordinate growth and developmental timing using another mechanism. Research into these areas should generate exciting new insights into the biology of growth coordination, the evolution of the relaxin signaling pathway, and likely reveal unforeseen functions in other developmental stages.Fil: Gontijo, Alisson M.. Universidade Nova de Lisboa; PortugalFil: Garelli, Andres. Universidade Nova de Lisboa; Portugal. Universidad Nacional del Sur; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto de Investigaciones Bioquímicas de Bahía Blanca. Universidad Nacional del Sur. Instituto de Investigaciones Bioquímicas de Bahía Blanca; Argentin

Correlations between pre-and post-fasting growth in Nile tilapia

We tested the correlation between growth rate before and after a food deprivation phase in twelve single held Nile tilapias, Oreochromis niloticus. The experiment was divided into three phases: Before food deprivation (phase 1: 15 d), food deprivation (phase 2: 12 d) and refeeding (phase 3: 15 d). The specific growth rate - SGR, food conversion efficiency - FCE and feed ingestion increased significantly during phase 3. Positive and significant correlations were found either to SGR or to feed ingestion between Phase 1 and 3 but not for FCE. The SGR on phase 3, moreover, were positively correlated to FCE and feed ingestion, while on phase 1 SGR was positively correlated to FCE only. Thus, high pre-fasting SGR or feed ingestion reflects in likewise high post-fasting SGR or feed ingestion values. Moreover, since SGR and FCE are correlated to each other in both phase 1 and 3, but phase 3 SGR is also correlated to feed ingestion; We could suppose that hyperphagic behaviour could be the main compensatory mechanism. Accordingly, we suggest that a fish with an elevated growth performance shall display a proportionally raised post-fasting growth response in order to normalize its predetermined growth trajectory and resume its normal growth rate. © GSP.Peer Reviewe

Imaginal discs secrete insulin-like peptide 8 to mediate plasticity of growth and maturation

Developing animals frequently adjust their growth programs and/or their maturation or metamorphosis to compensate for growth disturbances (such as injury or tumor) and ensure normal adult size. Such plasticity entails tissue and organ communication to preserve their proportions and symmetry. Here, we show that imaginal discs autonomously activate DILP8, a Drosophila insulin-like peptide, to communicate abnormal growth and postpone maturation. DILP8 delays metamorphosis by inhibiting ecdysone biosynthesis, slowing growth in the imaginal discs, and generating normal-sized animals. Loss of dilp8 yields asymmetric individuals with an unusually large variation in size and a more varied time of maturation. Thus, DILP8 is a fundamental element of the hitherto ill-defined machinery governing the plasticity that ensures developmental stability and robustness.Ministerio de Ciencia e Innovación BFU2009-09074, MEC-CONSOLIDER/CSD2007-00023. Generalitat Valenciana PROMETEO/2008/134. European Commission HEALTH-F2-2008-201666. Marie Curie Fellowship. Fundacion Botín.Peer Reviewe

Natural-geographic characteristics of Bjelovar-bilogora County in the function of tourism development

Bjelovarsko-bilogorska županija smještena je u Središnjoj hrvatskoj zavali te ima povoljne prirodnogeografske uvjete za razvoj turizma. Županija ima dobar geoprometni položaj prema najvećoj urbanoj aglomeraciji koja je ujedno i najveće turističko središte kontinentalne Hrvatske. Usprkos bogatoj i raznolikoj prirodnogeografskoj samo je zdravstveno-lječilišni turizam sustavno razvijan od druge polovice 20. stoljeća, a sve veća važnost pridaje se lovnom i ruralnom turizmu. Za potrebe istraživanja provedeno je kvantitativno anketno istraživanje na neprobabilistički odabranom, prigodnom uzorku koji čine građani Republike Hrvatske sa stalnim prebivalištem na području Bjelovarsko-bilogorske županije i oni koji nemaju stalno prebivalište na području Bjelovarsko-bilogorske županije. Na temelju rezultata ankete i analize statističkih podataka utvrđeno je da su posjetitelji uglavnom zadovoljni cjelokupnom turističkom ponudom, no nedostaje im više manifestacija i zabavnih sadržaja. Budući razvoj turizma Bjelovarsko-bilogorske županije trebao bi se temeljiti na nadopuni postojeće turističke ponude koja ima brojne neiskorištene prirodne potencijale, te što boljom promocijom istih.Bjelovar-bilogora County is located in central Croatian basin and has favourable natural-geographical conditions for the tourism development. County has a good geographic position towards the largest urban agglomeration in Croatia, which is also the largest source of domestic travel demand. Despite its rich and diverse natural resource basis, only medical and health tourism has been systematically developed, while the increasing importance is given to hunting and rural tourism. For the purpose of this study quantitative survey on a nonprobabilistic sample consisting of Croatian citizens who have permanent residence in the area of Bjelovar County and others who have not, was conducted. Visitors are mostly satisfied with the overall tourist offer, but they have expressed a desire for a larger number of cultural and entertainment events. Further development of tourism in Bjelovar-bilogora County should be based on the upgrading and better promotion of the existing touristic offer that has many unexploited natural resources