1
|
Bower G, Hollingsworth EW, Jacinto S, Clock B, Cao K, Liu M, Dziulko A, Alcaina-Caro A, Xu Q, Skowronska-Krawczyk D, Lopez-Rios J, Dickel DE, Bardet AF, Pennacchio LA, Visel A, Kvon EZ. Conserved Cis-Acting Range Extender Element Mediates Extreme Long-Range Enhancer Activity in Mammals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.26.595809. [PMID: 38826394 PMCID: PMC11142232 DOI: 10.1101/2024.05.26.595809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
While most mammalian enhancers regulate their cognate promoters over moderate distances of tens of kilobases (kb), some enhancers act over distances in the megabase range. The sequence features enabling such extreme-distance enhancer-promoter interactions remain elusive. Here, we used in vivo enhancer replacement experiments in mice to show that short- and medium-range enhancers cannot initiate gene expression at extreme-distance range. We uncover a novel conserved cis-acting element, Range EXtender (REX), that confers extreme-distance regulatory activity and is located next to a long-range enhancer of Sall1. The REX element itself has no endogenous enhancer activity. However, addition of the REX to other short- and mid-range enhancers substantially increases their genomic interaction range. In the most extreme example observed, addition of the REX increased the range of an enhancer by an order of magnitude, from its native 71kb to 840kb. The REX element contains highly conserved [C/T]AATTA homeodomain motifs. These motifs are enriched around long-range limb enhancers genome-wide, including the ZRS, a benchmark long-range limb enhancer of Shh. Mutating the [C/T]AATTA motifs within the ZRS does not affect its limb-specific enhancer activity at short range, but selectively abolishes its long-range activity, resulting in severe limb reduction in knock-in mice. In summary, we identify a sequence signature globally associated with long-range enhancer-promoter interactions and describe a prototypical REX element that is necessary and sufficient to confer extreme-distance gene activation by remote enhancers.
Collapse
Affiliation(s)
- Grace Bower
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92967, USA
| | - Ethan W. Hollingsworth
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92967, USA
- Medical Scientist Training Program, University of California, Irvine, CA 92967, USA
| | - Sandra Jacinto
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92967, USA
| | - Benjamin Clock
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92967, USA
| | - Kaitlyn Cao
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92967, USA
| | - Mandy Liu
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92967, USA
| | - Adam Dziulko
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ana Alcaina-Caro
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, 41013, Spain
| | - Qianlan Xu
- Department of Physiology and Biophysics, Department of Ophthalmology, Center for Translational Vision Research, School of Medicine, University of California, Irvine, CA, USA
| | - Dorota Skowronska-Krawczyk
- Department of Physiology and Biophysics, Department of Ophthalmology, Center for Translational Vision Research, School of Medicine, University of California, Irvine, CA, USA
| | - Javier Lopez-Rios
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, 41013, Spain
| | - Diane E. Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Anaïs F. Bardet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, CNRS UMR7104, INSERM U1258, 67400 Illkirch, France
| | - Len A. Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
- Comparative Biochemistry Program, University of California, Berkeley, CA 94720, USA
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
- School of Natural Sciences, University of California, Merced, CA 95343, USA
| | - Evgeny Z. Kvon
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92967, USA
| |
Collapse
|
2
|
Ferguson CA, Firulli BA, Zoia M, Osterwalder M, Firulli AB. Identification and characterization of Hand2 upstream genomic enhancers active in developing stomach and limbs. Dev Dyn 2024; 253:215-232. [PMID: 37551791 DOI: 10.1002/dvdy.646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/20/2023] [Accepted: 07/25/2023] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND The bHLH transcription factor HAND2 plays important roles in the development of the embryonic heart, face, limbs, and sympathetic and enteric nervous systems. To define how and when HAND2 regulates these developmental systems, requires understanding the transcriptional regulation of Hand2. RESULTS Remarkably, Hand2 is flanked by an extensive upstream gene desert containing a potentially diverse enhancer landscape. Here, we screened the regulatory interval 200 kb proximal to Hand2 for putative enhancers using evolutionary conservation and histone marks in Hand2-expressing tissues. H3K27ac signatures across embryonic tissues pointed to only two putative enhancer regions showing deep sequence conservation. Assessment of the transcriptional enhancer potential of these elements using transgenic reporter lines uncovered distinct in vivo enhancer activities in embryonic stomach and limb mesenchyme, respectively. Activity of the identified stomach enhancer was restricted to the developing antrum and showed expression within the smooth muscle and enteric neurons. Surprisingly, the activity pattern of the limb enhancer did not overlap Hand2 mRNA but consistently yielded a defined subectodermal anterior expression pattern within multiple transgenic lines. CONCLUSIONS Together, these results start to uncover the diverse regulatory potential inherent to the Hand2 upstream regulatory interval.
Collapse
Affiliation(s)
- Chloe A Ferguson
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Anatomy, Biochemistry, and Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Beth A Firulli
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Anatomy, Biochemistry, and Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Matteo Zoia
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Marco Osterwalder
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
- Department of Cardiology, Bern University Hospital, Bern, Switzerland
| | - Anthony B Firulli
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Anatomy, Biochemistry, and Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| |
Collapse
|
3
|
Monti R, Ohler U. Toward Identification of Functional Sequences and Variants in Noncoding DNA. Annu Rev Biomed Data Sci 2023; 6:191-210. [PMID: 37262323 DOI: 10.1146/annurev-biodatasci-122120-110102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Understanding the noncoding part of the genome, which encodes gene regulation, is necessary to identify genetic mechanisms of disease and translate findings from genome-wide association studies into actionable results for treatments and personalized care. Here we provide an overview of the computational analysis of noncoding regions, starting from gene-regulatory mechanisms and their representation in data. Deep learning methods, when applied to these data, highlight important regulatory sequence elements and predict the functional effects of genetic variants. These and other algorithms are used to predict damaging sequence variants. Finally, we introduce rare-variant association tests that incorporate functional annotations and predictions in order to increase interpretability and statistical power.
Collapse
Affiliation(s)
- Remo Monti
- Max Delbrück Center for Molecular Medicine (MDC), Helmholtz Association of German Research Centers, Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany;
- Digital Health-Machine Learning, Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam, Germany
| | - Uwe Ohler
- Max Delbrück Center for Molecular Medicine (MDC), Helmholtz Association of German Research Centers, Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany;
| |
Collapse
|
4
|
Losa M, Barozzi I, Osterwalder M, Hermosilla-Aguayo V, Morabito A, Chacón BH, Zarrineh P, Girdziusaite A, Benazet JD, Zhu J, Mackem S, Capellini TD, Dickel D, Bobola N, Zuniga A, Visel A, Zeller R, Selleri L. A spatio-temporally constrained gene regulatory network directed by PBX1/2 acquires limb patterning specificity via HAND2. Nat Commun 2023; 14:3993. [PMID: 37414772 PMCID: PMC10325989 DOI: 10.1038/s41467-023-39443-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/14/2023] [Indexed: 07/08/2023] Open
Abstract
A lingering question in developmental biology has centered on how transcription factors with widespread distribution in vertebrate embryos can perform tissue-specific functions. Here, using the murine hindlimb as a model, we investigate the elusive mechanisms whereby PBX TALE homeoproteins, viewed primarily as HOX cofactors, attain context-specific developmental roles despite ubiquitous presence in the embryo. We first demonstrate that mesenchymal-specific loss of PBX1/2 or the transcriptional regulator HAND2 generates similar limb phenotypes. By combining tissue-specific and temporally controlled mutagenesis with multi-omics approaches, we reconstruct a gene regulatory network (GRN) at organismal-level resolution that is collaboratively directed by PBX1/2 and HAND2 interactions in subsets of posterior hindlimb mesenchymal cells. Genome-wide profiling of PBX1 binding across multiple embryonic tissues further reveals that HAND2 interacts with subsets of PBX-bound regions to regulate limb-specific GRNs. Our research elucidates fundamental principles by which promiscuous transcription factors cooperate with cofactors that display domain-restricted localization to instruct tissue-specific developmental programs.
Collapse
Affiliation(s)
- Marta Losa
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Orofacial Sciences and Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Iros Barozzi
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Marco Osterwalder
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department for Biomedical Research (DBMR), University of Bern, Bern, Switzerland
- Department of Cardiology, Bern University Hospital, Bern, Switzerland
| | - Viviana Hermosilla-Aguayo
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Orofacial Sciences and Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Angela Morabito
- Developmental Genetics, Department Biomedicine, University of Basel, Basel, Switzerland
| | - Brandon H Chacón
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Orofacial Sciences and Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Peyman Zarrineh
- School of Medical Sciences, University of Manchester, Manchester, UK
| | - Ausra Girdziusaite
- Developmental Genetics, Department Biomedicine, University of Basel, Basel, Switzerland
| | - Jean Denis Benazet
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Orofacial Sciences and Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Jianjian Zhu
- Cancer and Developmental Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Susan Mackem
- Cancer and Developmental Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Terence D Capellini
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Diane Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nicoletta Bobola
- School of Medical Sciences, University of Manchester, Manchester, UK
| | - Aimée Zuniga
- Developmental Genetics, Department Biomedicine, University of Basel, Basel, Switzerland
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- School of Natural Sciences, University of California, Merced, Merced, CA, 95343, USA
| | - Rolf Zeller
- Developmental Genetics, Department Biomedicine, University of Basel, Basel, Switzerland
| | - Licia Selleri
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Orofacial Sciences and Department of Anatomy, University of California San Francisco, San Francisco, CA, USA.
| |
Collapse
|
5
|
Koyano-Nakagawa N, Gong W, Das S, Theisen JWM, Swanholm TB, Van Ly D, Dsouza N, Singh BN, Kawakami H, Young S, Chen KQ, Kawakami Y, Garry DJ. Etv2 regulates enhancer chromatin status to initiate Shh expression in the limb bud. Nat Commun 2022; 13:4221. [PMID: 35864091 PMCID: PMC9304341 DOI: 10.1038/s41467-022-31848-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 07/05/2022] [Indexed: 12/02/2022] Open
Abstract
Sonic hedgehog (Shh) is essential for limb development, and the mechanisms that govern the propagation and maintenance of its expression has been well studied; however, the mechanisms that govern the initiation of Shh expression are incomplete. Here we report that ETV2 initiates Shh expression by changing the chromatin status of the developmental limb enhancer, ZRS. Etv2 expression precedes Shh in limb buds, and Etv2 inactivation prevents the opening of limb chromatin, including the ZRS, resulting in an absence of Shh expression. Etv2 overexpression in limb buds causes nucleosomal displacement at the ZRS, ectopic Shh expression, and polydactyly. Areas of nucleosome displacement coincide with ETS binding site clusters. ETV2 also functions as a transcriptional activator of ZRS and is antagonized by ETV4/5 repressors. Known human polydactyl mutations introduce novel ETV2 binding sites in the ZRS, suggesting that ETV2 dosage regulates ZRS activation. These studies identify ETV2 as a pioneer transcription factor (TF) regulating the onset of Shh expression, having both a chromatin regulatory role and a transcriptional activation role. The embryonic limb bud is known to be patterned by a Shh morphogen gradient, though how Shh expression is activated remains less clear. Here the authors show that Etv2 acts as a pioneer transcription factor to mediate accessibility of the ZRS enhancer and initiate Shh expression.
Collapse
Affiliation(s)
- Naoko Koyano-Nakagawa
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, 55455, USA.,Stem Cell Institute, University of Minnesota, Minneapolis, MN, 55455, USA.,Hamre, Schumann, Mueller & Larson, P.C., Minneapolis, MN, 55402, USA.,Mitchell Hamline School of Law, St. Paul, MN, 55105, USA
| | - Wuming Gong
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Satyabrata Das
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Joshua W M Theisen
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Tran B Swanholm
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Daniel Van Ly
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Nikita Dsouza
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Bhairab N Singh
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Hiroko Kawakami
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, 55455, USA.,Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Samantha Young
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Katherine Q Chen
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Yasuhiko Kawakami
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, 55455, USA. .,Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, 55455, USA.
| | - Daniel J Garry
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, 55455, USA. .,Stem Cell Institute, University of Minnesota, Minneapolis, MN, 55455, USA.
| |
Collapse
|
6
|
Roscito JG, Sameith K, Kirilenko BM, Hecker N, Winkler S, Dahl A, Rodrigues MT, Hiller M. Convergent and lineage-specific genomic differences in limb regulatory elements in limbless reptile lineages. Cell Rep 2022; 38:110280. [DOI: 10.1016/j.celrep.2021.110280] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 11/24/2021] [Accepted: 12/27/2021] [Indexed: 01/02/2023] Open
|
7
|
Arenas-Mena C, Miljovska S, Rice EJ, Gurges J, Shashikant T, Wang Z, Ercan S, Danko CG. Identification and prediction of developmental enhancers in sea urchin embryos. BMC Genomics 2021; 22:751. [PMID: 34666684 PMCID: PMC8527612 DOI: 10.1186/s12864-021-07936-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 06/28/2021] [Indexed: 11/21/2022] Open
Abstract
Background The transcription of developmental regulatory genes is often controlled by multiple cis-regulatory elements. The identification and functional characterization of distal regulatory elements remains challenging, even in tractable model organisms like sea urchins. Results We evaluate the use of chromatin accessibility, transcription and RNA Polymerase II for their ability to predict enhancer activity of genomic regions in sea urchin embryos. ATAC-seq, PRO-seq, and Pol II ChIP-seq from early and late blastula embryos are manually contrasted with experimental cis-regulatory analyses available in sea urchin embryos, with particular attention to common developmental regulatory elements known to have enhancer and silencer functions differentially deployed among embryonic territories. Using the three functional genomic data types, machine learning models are trained and tested to classify and quantitatively predict the enhancer activity of several hundred genomic regions previously validated with reporter constructs in vivo. Conclusions Overall, chromatin accessibility and transcription have substantial power for predicting enhancer activity. For promoter-overlapping cis-regulatory elements in particular, the distribution of Pol II is the best predictor of enhancer activity in blastula embryos. Furthermore, ATAC- and PRO-seq predictive value is stage dependent for the promoter-overlapping subset. This suggests that the sequence of regulatory mechanisms leading to transcriptional activation have distinct relevance at different levels of the developmental gene regulatory hierarchy deployed during embryogenesis. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07936-0.
Collapse
Affiliation(s)
- César Arenas-Mena
- College of Staten Island, The City University of New York (CUNY), Staten Island, NY, 10314, USA. .,Programs in Biology and Biochemistry, The Graduate Center, CUNY, New York, NY, 10016, USA.
| | - Sofija Miljovska
- Department of Biology, New York University, New York, NY, 10003, USA
| | - Edward J Rice
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Justin Gurges
- College of Staten Island, The City University of New York (CUNY), Staten Island, NY, 10314, USA
| | - Tanvi Shashikant
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Zihe Wang
- College of Staten Island, The City University of New York (CUNY), Staten Island, NY, 10314, USA
| | - Sevinç Ercan
- Department of Biology, New York University, New York, NY, 10003, USA.,Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - Charles G Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA.,Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| |
Collapse
|
8
|
Delgado I, Giovinazzo G, Temiño S, Gauthier Y, Balsalobre A, Drouin J, Torres M. Control of mouse limb initiation and antero-posterior patterning by Meis transcription factors. Nat Commun 2021; 12:3086. [PMID: 34035267 PMCID: PMC8149412 DOI: 10.1038/s41467-021-23373-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 04/21/2021] [Indexed: 12/31/2022] Open
Abstract
Meis1 and Meis2 are homeodomain transcription factors that regulate organogenesis through cooperation with Hox proteins. Elimination of Meis genes after limb induction has shown their role in limb proximo-distal patterning; however, limb development in the complete absence of Meis function has not been studied. Here, we report that Meis1/2 inactivation in the lateral plate mesoderm of mouse embryos leads to limb agenesis. Meis and Tbx factors converge in this function, extensively co-binding with Tbx to genomic sites and co-regulating enhancers of Fgf10, a critical factor in limb initiation. Limbs with three deleted Meis alleles show proximal-specific skeletal hypoplasia and agenesis of posterior skeletal elements. This failure in posterior specification results from an early role of Meis factors in establishing the limb antero-posterior prepattern required for Shh activation. Our results demonstrate roles for Meis transcription factors in early limb development and identify their involvement in previously undescribed interaction networks that regulate organogenesis.
Collapse
Affiliation(s)
- Irene Delgado
- Cardiovascular Development Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Giovanna Giovinazzo
- Cardiovascular Development Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Susana Temiño
- Cardiovascular Development Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Yves Gauthier
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal, Montreal, QC, Canada
| | - Aurelio Balsalobre
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal, Montreal, QC, Canada
| | - Jacques Drouin
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal, Montreal, QC, Canada
| | - Miguel Torres
- Cardiovascular Development Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain.
| |
Collapse
|
9
|
Meyer A, Schloissnig S, Franchini P, Du K, Woltering JM, Irisarri I, Wong WY, Nowoshilow S, Kneitz S, Kawaguchi A, Fabrizius A, Xiong P, Dechaud C, Spaink HP, Volff JN, Simakov O, Burmester T, Tanaka EM, Schartl M. Giant lungfish genome elucidates the conquest of land by vertebrates. Nature 2021; 590:284-289. [PMID: 33461212 PMCID: PMC7875771 DOI: 10.1038/s41586-021-03198-8] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 01/06/2021] [Indexed: 01/29/2023]
Abstract
Lungfishes belong to lobe-fined fish (Sarcopterygii) that, in the Devonian period, 'conquered' the land and ultimately gave rise to all land vertebrates, including humans1-3. Here we determine the chromosome-quality genome of the Australian lungfish (Neoceratodus forsteri), which is known to have the largest genome of any animal. The vast size of this genome, which is about 14× larger than that of humans, is attributable mostly to huge intergenic regions and introns with high repeat content (around 90%), the components of which resemble those of tetrapods (comprising mainly long interspersed nuclear elements) more than they do those of ray-finned fish. The lungfish genome continues to expand independently (its transposable elements are still active), through mechanisms different to those of the enormous genomes of salamanders. The 17 fully assembled lungfish macrochromosomes maintain synteny to other vertebrate chromosomes, and all microchromosomes maintain conserved ancient homology with the ancestral vertebrate karyotype. Our phylogenomic analyses confirm previous reports that lungfish occupy a key evolutionary position as the closest living relatives to tetrapods4,5, underscoring the importance of lungfish for understanding innovations associated with terrestrialization. Lungfish preadaptations to living on land include the gain of limb-like expression in developmental genes such as hoxc13 and sall1 in their lobed fins. Increased rates of evolution and the duplication of genes associated with obligate air-breathing, such as lung surfactants and the expansion of odorant receptor gene families (which encode proteins involved in detecting airborne odours), contribute to the tetrapod-like biology of lungfishes. These findings advance our understanding of this major transition during vertebrate evolution.
Collapse
Affiliation(s)
- Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany.
| | | | - Paolo Franchini
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Kang Du
- Developmental Biochemistry, Biocenter, University of Würzburg, Würzburg, Germany
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA
| | | | - Iker Irisarri
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany
| | - Wai Yee Wong
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
| | | | - Susanne Kneitz
- Biochemistry and Cell Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Akane Kawaguchi
- Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | | | - Peiwen Xiong
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Corentin Dechaud
- Institut de Génomique Fonctionnelle, École Normale Superieure, Université Claude Bernard, Lyon, France
| | - Herman P Spaink
- Faculty of Science, Universiteit Leiden, Leiden, The Netherlands
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle, École Normale Superieure, Université Claude Bernard, Lyon, France
| | - Oleg Simakov
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria.
| | | | - Elly M Tanaka
- Research Institute of Molecular Pathology (IMP), Vienna, Austria.
| | - Manfred Schartl
- Developmental Biochemistry, Biocenter, University of Würzburg, Würzburg, Germany.
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA.
| |
Collapse
|
10
|
A Mutation in the Drosophila melanogaster eve Stripe 2 Minimal Enhancer Is Buffered by Flanking Sequences. G3 (BETHESDA, MD.) 2020; 10:4473-4482. [PMID: 33037064 PMCID: PMC7718739 DOI: 10.1534/g3.120.401777] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Enhancers are DNA sequences composed of transcription factor binding sites that drive complex patterns of gene expression in space and time. Until recently, studying enhancers in their genomic context was technically challenging. Therefore, minimal enhancers, the shortest pieces of DNA that can drive an expression pattern that resembles a gene's endogenous pattern, are often used to study features of enhancer function. However, evidence suggests that some enhancers require sequences outside the minimal enhancer to maintain function under environmental perturbations. We hypothesized that these additional sequences also prevent misexpression caused by a transcription factor binding site mutation within a minimal enhancer. Using the Drosophila melanogastereven-skipped stripe 2 enhancer as a case study, we tested the effect of a Giant binding site mutation (gt-2) on the expression patterns driven by minimal and extended enhancer reporter constructs. We found that, in contrast to the misexpression caused by the gt-2 binding site deletion in the minimal enhancer, the same gt-2 binding site deletion in the extended enhancer did not have an effect on expression. The buffering of expression levels, but not expression pattern, is partially explained by an additional Giant binding site outside the minimal enhancer. Deleting the gt-2 binding site in the endogenous locus had no significant effect on stripe 2 expression. Our results indicate that rules derived from mutating enhancer reporter constructs may not represent what occurs in the endogenous context.
Collapse
|
11
|
Bozek M, Gompel N. Developmental Transcriptional Enhancers: A Subtle Interplay between Accessibility and Activity: Considering Quantitative Accessibility Changes between Different Regulatory States of an Enhancer Deconvolutes the Complex Relationship between Accessibility and Activity. Bioessays 2020; 42:e1900188. [PMID: 32142172 DOI: 10.1002/bies.201900188] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/16/2020] [Indexed: 12/21/2022]
Abstract
Measurements of open chromatin in specific cell types are widely used to infer the spatiotemporal activity of transcriptional enhancers. How reliable are these predictions? In this review, it is argued that the relationship between the accessibility and activity of an enhancer is insufficiently described by simply considering open versus closed chromatin, or active versus inactive enhancers. Instead, recent studies focusing on the quantitative nature of accessibility signal reveal subtle differences between active enhancers and their different inactive counterparts: the closed silenced state and the accessible primed and repressed states. While the open structure as such is not a specific indicator of enhancer activity, active enhancers display a higher degree of accessibility than the primed and repressed states. Molecular mechanisms that may account for these quantitative differences are discussed. A model that relates molecular events at an enhancer to changes in its activity and accessibility in a developing tissue is also proposed.
Collapse
Affiliation(s)
- Marta Bozek
- Department Biochemie, Ludwig-Maximilians Universität München, Genzentrum, 81377, München, Germany
| | - Nicolas Gompel
- Fakultät für Biologie, Ludwig-Maximilians Universität München, Biozentrum, 82152, Planegg-Martinsried, Germany
| |
Collapse
|
12
|
Fu S, Wang Q, Moore JE, Purcaro MJ, Pratt HE, Fan K, Gu C, Jiang C, Zhu R, Kundaje A, Lu A, Weng Z. Differential analysis of chromatin accessibility and histone modifications for predicting mouse developmental enhancers. Nucleic Acids Res 2018; 46:11184-11201. [PMID: 30137428 PMCID: PMC6265487 DOI: 10.1093/nar/gky753] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 07/15/2018] [Accepted: 08/08/2018] [Indexed: 12/11/2022] Open
Abstract
Enhancers are distal cis-regulatory elements that modulate gene expression. They are depleted of nucleosomes and enriched in specific histone modifications; thus, calling DNase-seq and histone mark ChIP-seq peaks can predict enhancers. We evaluated nine peak-calling algorithms for predicting enhancers validated by transgenic mouse assays. DNase and H3K27ac peaks were consistently more predictive than H3K4me1/2/3 and H3K9ac peaks. DFilter and Hotspot2 were the best DNase peak callers, while HOMER, MUSIC, MACS2, DFilter and F-seq were the best H3K27ac peak callers. We observed that the differential DNase or H3K27ac signals between two distant tissues increased the area under the precision-recall curve (PR-AUC) of DNase peaks by 17.5-166.7% and that of H3K27ac peaks by 7.1-22.2%. We further improved this differential signal method using multiple contrast tissues. Evaluated using a blind test, the differential H3K27ac signal method substantially improved PR-AUC from 0.48 to 0.75 for predicting heart enhancers. We further validated our approach using postnatal retina and cerebral cortex enhancers identified by massively parallel reporter assays, and observed improvements for both tissues. In summary, we compared nine peak callers and devised a superior method for predicting tissue-specific mouse developmental enhancers by reranking the called peaks.
Collapse
Affiliation(s)
- Shaliu Fu
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Qin Wang
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Jill E Moore
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Michael J Purcaro
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Henry E Pratt
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Kaili Fan
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Cuihua Gu
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Cizhong Jiang
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Ruixin Zhu
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Anshul Kundaje
- Department of Genetics, School of Medicine, Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Aiping Lu
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Zhiping Weng
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| |
Collapse
|
13
|
Yakushiji-Kaminatsui N, Lopez-Delisle L, Bolt CC, Andrey G, Beccari L, Duboule D. Similarities and differences in the regulation of HoxD genes during chick and mouse limb development. PLoS Biol 2018; 16:e3000004. [PMID: 30475793 PMCID: PMC6283595 DOI: 10.1371/journal.pbio.3000004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 12/06/2018] [Accepted: 11/09/2018] [Indexed: 12/22/2022] Open
Abstract
In all tetrapods examined thus far, the development and patterning of limbs require the activation of gene members of the HoxD cluster. In mammals, they are regulated by a complex bimodal process that controls first the proximal patterning and then the distal structure. During the shift from the former to the latter regulation, this bimodal regulatory mechanism allows the production of a domain with low Hoxd gene expression, at which both telomeric (T-DOM) and centromeric regulatory domains (C-DOM) are silent. These cells generate the future wrist and ankle articulations. We analyzed the implementation of this regulatory mechanism in chicken, i.e., in an animal for which large morphological differences exist between fore- and hindlimbs. We report that although this bimodal regulation is globally conserved between the mouse and the chick, some important modifications evolved at least between these two model systems, in particular regarding the activity of specific enhancers, the width of the TAD boundary separating the two regulations, and the comparison between the forelimb versus hindlimb regulatory controls. At least one aspect of these regulations seems to be more conserved between chick and bats than with mouse, which may relate to the extent to which forelimbs and hindlimbs of these various animals differ in their morphologies. A comparison of Hox gene regulation during the development of limbs in birds and mammals reveals that whereas the characteristic bimodal regulatory system, based on large chromatin domains, is largely conserved between these morphologically distinct structures, some differences are revealed in the way this is implemented in various vertebrates. The shapes of limbs vary greatly among tetrapod species, even between the forelimbs and hindlimbs of the same animal. Hox genes regulate the proper growth and patterning of tetrapod limbs. In order to evaluate whether variations in the complex regulation of a cluster of Hox genes—the Hoxd genes—during limb development contribute to the differences in limb shape, we compared their transcriptional control during limb bud development in the forelimbs and hindlimbs of mouse and chicken embryos. We found that the regulatory mechanism underlying Hoxd gene expression is highly conserved, but some clear differences exist. For instance, we observed a variation in the topologically associating domain (TAD; a self-interacting genomic region) boundary interval between the mouse and the chick, as well as differences in the activity of a conserved enhancer element situated within the telomeric regulatory domain. In contrast to the mouse, the chicken enhancer has a stronger activity in the forelimb buds than in the hindlimb buds, which is correlated with the striking differences in the mRNA levels of the genes. We conclude that differences in both the timing and duration of TAD activities and in the width of their boundary may parallel the important decrease in Hoxd gene transcription in chick hindlimb buds versus forelimb buds. These differences may also account for the slightly distinct regulatory strategies implemented by mammals and birds at this locus.
Collapse
Affiliation(s)
| | - Lucille Lopez-Delisle
- School of Life Sciences, Federal Institute of Technology, Lausanne, Lausanne, Switzerland
| | - Christopher Chase Bolt
- School of Life Sciences, Federal Institute of Technology, Lausanne, Lausanne, Switzerland
| | - Guillaume Andrey
- School of Life Sciences, Federal Institute of Technology, Lausanne, Lausanne, Switzerland
| | - Leonardo Beccari
- Department of Genetics and Evolution, University of Geneva, Geneva 4, Switzerland
| | - Denis Duboule
- School of Life Sciences, Federal Institute of Technology, Lausanne, Lausanne, Switzerland
- Department of Genetics and Evolution, University of Geneva, Geneva 4, Switzerland
- * E-mail:
| |
Collapse
|
14
|
Roscito JG, Sameith K, Parra G, Langer BE, Petzold A, Moebius C, Bickle M, Rodrigues MT, Hiller M. Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution. Nat Commun 2018; 9:4737. [PMID: 30413698 PMCID: PMC6226452 DOI: 10.1038/s41467-018-07122-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 10/15/2018] [Indexed: 02/07/2023] Open
Abstract
Detecting the genomic changes underlying phenotypic changes between species is a main goal of evolutionary biology and genomics. Evolutionary theory predicts that changes in cis-regulatory elements are important for morphological changes. We combined genome sequencing, functional genomics and genome-wide comparative analyses to investigate regulatory elements in lineages that lost morphological traits. We first show that limb loss in snakes is associated with widespread divergence of limb regulatory elements. We next show that eye degeneration in subterranean mammals is associated with widespread divergence of eye regulatory elements. In both cases, sequence divergence results in an extensive loss of transcription factor binding sites. Importantly, diverged regulatory elements are associated with genes required for normal limb patterning or normal eye development and function, suggesting that regulatory divergence contributed to the loss of these phenotypes. Together, our results show that genome-wide decay of the phenotype-specific cis-regulatory landscape is a hallmark of lost morphological traits. Cis-regulatory elements are important factors for morphological changes. Here, the authors show widespread divergence of limb and eye regulatory elements in limb loss in snakes and eye degeneration in subterranean mammals respectively.
Collapse
Affiliation(s)
- Juliana G Roscito
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 01307, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, 01187, Germany.,Center for Systems Biology Dresden, Dresden, 01307, Germany.,Instituto de Biociências, Universidade de São Paulo, São Paulo, 05508-090, Brazil
| | - Katrin Sameith
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 01307, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, 01187, Germany.,Center for Systems Biology Dresden, Dresden, 01307, Germany
| | - Genis Parra
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 01307, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, 01187, Germany.,Center for Systems Biology Dresden, Dresden, 01307, Germany
| | - Bjoern E Langer
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 01307, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, 01187, Germany.,Center for Systems Biology Dresden, Dresden, 01307, Germany
| | - Andreas Petzold
- Center for Regenerative Therapies TU Dresden, Dresden, 01307, Germany
| | - Claudia Moebius
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 01307, Germany
| | - Marc Bickle
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 01307, Germany
| | | | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 01307, Germany. .,Max Planck Institute for the Physics of Complex Systems, Dresden, 01187, Germany. .,Center for Systems Biology Dresden, Dresden, 01307, Germany.
| |
Collapse
|
15
|
Sarro R, Kocher AA, Emera D, Uebbing S, Dutrow EV, Weatherbee SD, Nottoli T, Noonan JP. Disrupting the three-dimensional regulatory topology of the Pitx1 locus results in overtly normal development. Development 2018; 145:dev.158550. [PMID: 29549111 DOI: 10.1242/dev.158550] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 03/09/2018] [Indexed: 12/28/2022]
Abstract
Developmental gene expression patterns are orchestrated by thousands of distant-acting transcriptional enhancers. However, identifying enhancers essential for the expression of their target genes has proven challenging. Maps of long-range regulatory interactions may provide the means to identify enhancers crucial for developmental gene expression. To investigate this hypothesis, we used circular chromosome conformation capture coupled with interaction maps in the mouse limb to characterize the regulatory topology of Pitx1, which is essential for hindlimb development. We identified a robust hindlimb-specific interaction between Pitx1 and a putative hindlimb-specific enhancer. To interrogate the role of this interaction in Pitx1 regulation, we used genome editing to delete this enhancer in mouse. Although deletion of the enhancer completely disrupts the interaction, Pitx1 expression in the hindlimb is only mildly affected, without any detectable compensatory interactions between the Pitx1 promoter and potentially redundant enhancers. Pitx1 enhancer null mice did not exhibit any of the characteristic morphological defects of the Pitx1-/- mutant. Our results suggest that robust, tissue-specific physical interactions at essential developmental genes have limited predictive value for identifying enhancer mutations with strong loss-of-function phenotypes.
Collapse
Affiliation(s)
- Richard Sarro
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Acadia A Kocher
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Deena Emera
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Severin Uebbing
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Emily V Dutrow
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Scott D Weatherbee
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Timothy Nottoli
- Department of Comparative Medicine, Yale School of Medicine, New Haven, CT 06520, USA.,Yale Genome Editing Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - James P Noonan
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| |
Collapse
|
16
|
Ecker JR, Geschwind DH, Kriegstein AR, Ngai J, Osten P, Polioudakis D, Regev A, Sestan N, Wickersham IR, Zeng H. The BRAIN Initiative Cell Census Consortium: Lessons Learned toward Generating a Comprehensive Brain Cell Atlas. Neuron 2017; 96:542-557. [PMID: 29096072 PMCID: PMC5689454 DOI: 10.1016/j.neuron.2017.10.007] [Citation(s) in RCA: 163] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 10/01/2017] [Accepted: 10/03/2017] [Indexed: 10/25/2022]
Abstract
A comprehensive characterization of neuronal cell types, their distributions, and patterns of connectivity is critical for understanding the properties of neural circuits and how they generate behaviors. Here we review the experiences of the BRAIN Initiative Cell Census Consortium, ten pilot projects funded by the U.S. BRAIN Initiative, in developing, validating, and scaling up emerging genomic and anatomical mapping technologies for creating a complete inventory of neuronal cell types and their connections in multiple species and during development. These projects lay the foundation for a larger and longer-term effort to generate whole-brain cell atlases in species including mice and humans.
Collapse
Affiliation(s)
- Joseph R Ecker
- Genomic Analysis Laboratory and Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Daniel H Geschwind
- Program in Neurogenetics, Departments of Neurology and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Arnold R Kriegstein
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Neurology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - John Ngai
- Department of Molecular and Cell Biology, Helen Wills Neuroscience Institute, QB3 Functional Genomics Laboratory, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Pavel Osten
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Damon Polioudakis
- Program in Neurogenetics, Departments of Neurology and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Department of Biology, Koch Institute of Integrative Cancer Research, and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Nenad Sestan
- Departments of Neuroscience, Genetics, Psychiatry and Comparative Medicine, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale Child Study Center, Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Ian R Wickersham
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| |
Collapse
|