Ahmad MS (1970) Development, structure and composition of lampbrush chromosomes in domestic fowl. Can J Genet Cytol 12:728–737. https://doi.org/10.1139/g70-095

Article  PubMed  Google Scholar 

Angelier N, Bonnanfant-Ja’s ML, Moreau N, et al (1986) DNA methylation and RNA transcriptional activity in amphibian lampbrush chromosomes. Chromosoma 94:169–182. https://doi.org/10.1007/BF00288491

Article  Google Scholar 

Beagan JA, Phillips-Cremins JE (2020) On the existence and functionality of topologically associating domains. Nat Genet 52:8–16. https://doi.org/10.1038/s41588-019-0561-1

Article  PubMed  PubMed Central  Google Scholar 

Bickmore WA, van Steensel B (2013) Genome architecture: domain organization of interphase chromosomes. Cell 152:1270–1284. https://doi.org/10.1016/j.cell.2013.02.001

Article  PubMed  Google Scholar 

Bintu B, Mateo LJ, Su J-H, et al (2018) Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells. Science 362:eaau1783. https://doi.org/10.1126/science.aau1783

Bione S, Sala C, Manzini C et al (1998) A human homologue of the Drosophila melanogaster diaphanous gene is disrupted in a patient with premature ovarian failure: evidence for conserved function in oogenesis and implications for human sterility. The American Journal of Human Genetics 62:533–541. https://doi.org/10.1086/301761

Article  PubMed  Google Scholar 

Bouwman BA, de Laat W (2015) Getting the genome in shape: the formation of loops, domains and compartments. Genome Biol 16:154. https://doi.org/10.1186/s13059-015-0730-1

Article  PubMed  PubMed Central  Google Scholar 

Buchwalter A, Kaneshiro JM, Hetzer MW (2019) Coaching from the sidelines: the nuclear periphery in genome regulation. Nat Rev Genet 20:39–50. https://doi.org/10.1038/s41576-018-0063-5

Article  PubMed  PubMed Central  Google Scholar 

Burt DW (2002) Origin and evolution of avian microchromosomes. Cytogenet Genome Res 96:97–112. https://doi.org/10.1159/000063018

Article  PubMed  Google Scholar 

Callebaut M (1973) Correlation between germinal vesicle and oocyte development in the adult Japanese quail (Coturnix coturnix japonica). A Cytochemical and Autoradiographic Study Development 29:145–157. https://doi.org/10.1242/dev.29.1.145

Article  Google Scholar 

Carreira-Rosario A, Bhargava V, Hillebrand J et al (2016) Repression of Pumilio protein expression by Rbfox1 promotes germ cell differentiation. Dev Cell 36:562–571. https://doi.org/10.1016/j.devcel.2016.02.010

Article  PubMed  PubMed Central  Google Scholar 

Chelysheva LA, Solovei IV, Rodionov AV et al (1990) The lampbrush chromosomes of the chicken. Cytological maps of the macrobivalents. Tsitologiia 32:303–316

PubMed  Google Scholar 

Conboy JG (2017) Developmental regulation of RNA processing by Rbfox proteins: Rbfox regulation of RNA processing. Wires RNA 8:e1398. https://doi.org/10.1002/wrna.1398

Article  Google Scholar 

Cremer M, Grasser F, Lanctôt C et al (2012) Multicolor 3D fluorescence in situ hybridization for imaging interphase chromosomes. In: Hancock R (ed) The Nucleus. Humana Press, Totowa, NJ, pp 205–239

Chapter  Google Scholar 

Cremer M, Brandstetter K, Maiser A et al (2020) Cohesin depleted cells rebuild functional nuclear compartments after endomitosis. Nat Commun 11:6146. https://doi.org/10.1038/s41467-020-19876-6

Article  PubMed  PubMed Central  Google Scholar 

Daks AA, Deriusheva SE, Krasikova AV et al (2010) Lampbrush chromosomes of the Japanese quail (Coturnix coturnix japonica): a new version of cytogenetic maps. Genetika 46:1335–1338

PubMed  Google Scholar 

Dekker J (2016) Mapping the 3D genome: aiming for consilience. Nat Rev Mol Cell Biol 17:741–742. https://doi.org/10.1038/nrm.2016.151

Article  PubMed  Google Scholar 

Derjusheva S, Kurganova A, Krasikova A et al (2003) Precise identification of chicken chromosomes in the lampbrush form using chromosome painting probes. Chromosome Res 11:749–757. https://doi.org/10.1023/B:CHRO.0000005778.72909.4d

Article  PubMed  Google Scholar 

Deryusheva S, Krasikova A, Kulikova T, Gaginskaya E (2007) Tandem 41-bp repeats in chicken and Japanese quail genomes: FISH mapping and transcription analysis on lampbrush chromosomes. Chromosoma 116:519–530. https://doi.org/10.1007/s00412-007-0117-5

Article  PubMed  Google Scholar 

Dixon JR, Selvaraj S, Yue F et al (2012) Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485:376–380. https://doi.org/10.1038/nature11082

Article  PubMed  PubMed Central  Google Scholar 

Dixon JR, Gorkin DU, Ren B (2016) Chromatin domains: the unit of chromosome organization. Mol Cell 62:668–680. https://doi.org/10.1016/j.molcel.2016.05.018

Article  PubMed  PubMed Central  Google Scholar 

Du Z, Zheng H, Kawamura YK et al (2020) Polycomb group proteins regulate chromatin architecture in mouse oocytes and early embryos. Mol Cell 77:825-839.e7. https://doi.org/10.1016/j.molcel.2019.11.011

Article  PubMed  Google Scholar 

Eagen KP, Hartl TA, Kornberg RD (2015) Stable chromosome condensation revealed by chromosome conformation capture. Cell 163:934–946. https://doi.org/10.1016/j.cell.2015.10.026

Article  PubMed  PubMed Central  Google Scholar 

Filippova D, Patro R, Duggal G, Kingsford C (2014) Identification of alternative topological domains in chromatin. Algorithms Mol Biol 9:14. https://doi.org/10.1186/1748-7188-9-14

Article  PubMed  PubMed Central  Google Scholar 

Fishman V, Battulin N, Nuriddinov M et al (2019) 3D organization of chicken genome demonstrates evolutionary conservation of topologically associated domains and highlights unique architecture of erythrocytes’ chromatin. Nucleic Acids Res 47:648–665. https://doi.org/10.1093/nar/gky1103

Article  PubMed  Google Scholar 

Flyamer IM, Gassler J, Imakaev M et al (2017) Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition. Nature 544:110–114. https://doi.org/10.1038/nature21711

Article  PubMed  PubMed Central  Google Scholar 

Freshney R (2010) Culture of animal cells: a manual of basic technique and specialized applications. John Wiley & Sons Inc, Hoboken, NJ, USA

Book  Google Scholar 

Fudenberg G, Imakaev M, Lu C et al (2016) Formation of chromosomal domains by loop extrusion. Cell Rep 15:2038–2049. https://doi.org/10.1016/j.celrep.2016.04.085

Article  PubMed  PubMed Central  Google Scholar 

Gaginskaya E, Kulikova T, Krasikova A (2009) Avian lampbrush chromosomes: a powerful tool for exploration of genome expression. Cytogenet Genome Res 124:251–267. https://doi.org/10.1159/000218130

Article  PubMed  Google Scholar 

Galkina S, Deryusheva S, Fillon V et al (2006) FISH on avian lampbrush chromosomes produces higher resolution gene mapping. Genetica 128:241–251. https://doi.org/10.1007/s10709-005-5776-7

Article  PubMed  Google Scholar 

Gall JG, Callan HG (1962) H3 uridine incorporation in lampbrush chromosomes. Proc Natl Acad Sci 48:562–570. https://doi.org/10.1073/pnas.48.4.562

Article  PubMed  PubMed Central  Google Scholar 

Gardner EJ, Nizami ZF, Talbot CC Jr, Gall JG (2012) Stable intronic sequence RNA (sisRNA), a new class of noncoding RNA from the oocyte nucleus of Xenopus tropicalis. Genes Dev 15;26(22):2550–9. https://doi.org/10.1101/gad.202184.112

Gibcus JH, Dekker J (2013) The hierarchy of the 3D genome. Mol Cell 49:773–782. https://doi.org/10.1016/j.molcel.2013.02.011

Article  PubMed  PubMed Central  Google Scholar 

Giorgetti L, Heard E (2016) Closing the loop: 3C versus DNA FISH. Genome Biol 17:215. https://doi.org/10.1186/s13059-016-1081-2

Article  PubMed  PubMed Central  Google Scholar 

Goetze S, Mateos-Langerak J, van Driel R (2007) Three-dimensional genome organization in interphase and its relation to genome function. Semin Cell Dev Biol 18:707–714. https://doi.org/10.1016/j.semcdb.2007.08.007

Article  PubMed  Google Scholar 

Griffin DK, Robertson LBW, Tempest HG, Skinner BM (2007) The evolution of the avian genome as revealed by comparative molecular cytogenetics. Cytogenet Genome Res 117:64–77. https://doi.org/10.1159/000103166

Article  PubMed  Google Scholar 

Hartley SE, Callan HG (1978) RNA transcription on the giant lateral loops of the lampbrush chromosomes of the American newt Notophthalmus viridescens. J Cell Sci 34:279–288. https://doi.org/10.1242/jcs.34.1.279

Article  PubMed  Google Scholar 

Heng HHQ, Tsui L-C (1993) Modes of DAPI banding and simultaneous in situ hybridization. Chromosoma 102:325–332. https://doi.org/10.1007/BF00661275

Article  PubMed  Google Scholar 

Holwerda S, Laat W de (2012) Chromatin loops, gene positioning, and gene expression. Front Gene 3. https://doi.org/10.3389/fgene.2012.00217

Hori T, Suzuki Y, Solovei I et al (1996) Characterization of DNA sequences constituting the terminal heterochromatin of the chicken Z chromosome. Chromosome Res 4:411–426. https://doi.org/10.1007/BF02265048

Article  PubMed  Google Scholar 

Hutchison N (1987) Lampbrush chromosomes of the chicken, Gallus domesticus. J Cell Biol 105:1493–1500. https://doi.org/10.1083/jcb.105.4.1493

Article  PubMed  Google Scholar 

Iannuccelli E, Mompart F, Gellin J et al (2010) NEMO: a tool for analyzing gene and chromosome territory distributions from 3D-FISH experiments. Bioinformatics 26:696–697. https://doi.org/10.1093/bioinformatics/btq013

Article  PubMed  Google Scholar 

Kaufmann R, Cremer C, Gall JG (2012) Superresolution imaging of transcription units on newt lampbrush chromosomes. Chromosome Res 20:1009–1015. https://doi.org/10.1007/s10577-012-9306-z

Article  PubMed  PubMed Central  Google Scholar 

Keinath MC, Davidian A, Timoshevskiy V, Timoshevskaya N, Gall JG (2021) Characterization of axolotl lampbrush chromosomes by fluorescence in situ hybridization and immunostaining. Exp Cell Res 401:112523. https://doi.org/10.1016/j.yexcr.2021.112523

Article  PubMed  PubMed Central  Google Scholar 

Knoll JHM, Lichter P (2005) In situ hybridization to metaphase chromosomes and interphase nuclei. Current Protocols in Human Genetics 45. https://doi.org/10.1002/0471142905.hg0403s45

Kolesnikova TD, Goncharov FP, Zhimulev IF (2018) Similarity in replication timing