Hi-C sequencing unravels dynamic three-dimensional chromatin interactions in muntjac lineage: insights from chromosome fusions in Fea’s muntjac genome
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P. Duengkae | Worapong Singchat | N. Muangmai | K. Srikulnath | S. F. Ahmad | Thitipong Panthum | Maryam Jehangir | Pakpoom Aramsirirujiwet | Thanyapat Thong | Artem Lisachov | Kyudong Han | Akihiko Koga
[1] D. Conrad,et al. TAD evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function , 2023, Nature communications.
[2] H. A. Lawson,et al. Transposable elements in mammalian chromatin organization , 2023, Nature Reviews Genetics.
[3] Heather K. Schmidt,et al. Widespread contribution of transposable elements to the rewiring of mammalian 3D genomes , 2023, Nature Communications.
[4] D. G. Lupiáñez,et al. Evolution of 3D chromatin organization at different scales. , 2023, Current opinion in genetics & development.
[5] D. Cooper,et al. Large-Scale Chromosomal Changes Lead to Genome-Level Expression Alterations, Environmental Adaptation, and Speciation in the Gayal (Bos frontalis) , 2023, Molecular biology and evolution.
[6] T. J. Robinson,et al. Principles of 3D chromosome folding and evolutionary genome reshuffling in mammals. , 2022, Cell reports.
[7] Yuan Wang,et al. Morphological, Phaneroptic, Habitat and Population Description of Three Muntjac Species in a Tibetan Nature Reserve , 2022, Animals : an open access journal from MDPI.
[8] S. Schaeffer,et al. The relevance of chromatin architecture to genome rearrangements in Drosophila , 2022, Philosophical Transactions of the Royal Society B.
[9] Zhihua Zhang,et al. Comparative 3D genome architecture in vertebrates , 2022, BMC biology.
[10] M. Bush,et al. Early to mid-Holocene human activity exerted gradual influences on Amazonian forest vegetation , 2022, Philosophical Transactions of the Royal Society B.
[11] H. Lewin,et al. Conservation of chromatin conformation in carnivores , 2022, Proceedings of the National Academy of Sciences of the United States of America.
[12] Wen Wang,et al. Molecular mechanisms and topological consequences of drastic chromosomal rearrangements of muntjac deer , 2021, Nature Communications.
[13] D. Griffin,et al. Remnant of Unrelated Amniote Sex Chromosomal Linkage Sharing on the Same Chromosome in House Gecko Lizards, Providing a Better Understanding of the Ancestral Super-Sex Chromosome , 2021, Cells.
[14] Jonas Paulsen,et al. TAD cliques predict key features of chromatin organization , 2021, BMC Genomics.
[15] D. Reinberg,et al. A molecular toolkit for superorganisms. , 2021, Trends in genetics : TIG.
[16] Yu-Hao Deng. Perovskite decomposition and missing crystal planes in HRTEM , 2021, Nature.
[17] R. Aiese Cigliano,et al. The impact of chromosomal fusions on 3D genome folding and recombination in the germ line , 2021, Nature Communications.
[18] E. Greene,et al. DNA Repair Pathway Choices in CRISPR-Cas9-Mediated Genome Editing. , 2021, Trends in genetics : TIG.
[19] Zhou Zhou,et al. Mrc1-Dependent Chromatin Compaction Represses DNA Double-Stranded Break Repair by Homologous Recombination Upon Replication Stress , 2021, Frontiers in Cell and Developmental Biology.
[20] J. Duarte,et al. Satellite DNA in Neotropical Deer Species , 2021, Genes.
[21] Y. Gilad,et al. A TAD Skeptic: Is 3D Genome Topology Conserved? , 2020, Trends in genetics : TIG.
[22] Jilin Zhang,et al. A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals , 2020, bioRxiv.
[23] Jonas Paulsen,et al. TAD cliques predict key features of chromatin organization , 2020, bioRxiv.
[24] D. Rokhsar,et al. Analysis of muntjac deer genome and chromatin architecture reveals rapid karyotype evolution , 2020, Communications biology.
[25] Worapong Singchat,et al. Consequence of Paradigm Shift with Repeat Landscapes in Reptiles: Powerful Facilitators of Chromosomal Rearrangements for Diversity and Evolution (Running Title: Genomic Impact of Repeats on Chromosomal Dynamics in Reptiles) , 2020, Genes.
[26] T. Derrien,et al. Multi-species annotation of transcriptome and chromatin structure in domesticated animals , 2019, BMC Biology.
[27] A. Heck,et al. High-Throughput Assessment of Kinome-wide Activation States , 2019, Cell systems.
[28] R. Aiese Cigliano,et al. Three-Dimensional Genomic Structure and Cohesin Occupancy Correlate with Transcriptional Activity during Spermatogenesis , 2019, Cell reports.
[29] P. Sung,et al. The RecQ helicase Sgs1 drives ATP-dependent disruption of Rad51 filaments , 2019, Nucleic acids research.
[30] M. Nuriddinov,et al. 3D organization of chicken genome demonstrates evolutionary conservation of topologically associated domains and highlights unique architecture of erythrocytes’ chromatin , 2018, Nucleic acids research.
[31] V. Corces,et al. Organizational principles of 3D genome architecture , 2018, Nature Reviews Genetics.
[32] Ilya M. Flyamer,et al. Quantitative differences in TAD border strength underly the TAD hierarchy in Drosophila chromosomes , 2018, Journal of Cellular Biochemistry.
[33] J. Rinn,et al. Interchromosomal interactions: A genomic love story of kissing chromosomes , 2018, The Journal of cell biology.
[34] R. O’Neill,et al. Epigenetic maintenance of topological domains in the highly rearranged gibbon genome , 2018, Genome research.
[35] Aristotelis Tsirigos,et al. Stratification of TAD boundaries reveals preferential insulation of super-enhancers by strong boundaries , 2018, Nature Communications.
[36] Nuno A. Fonseca,et al. Two independent modes of chromatin organization revealed by cohesin removal , 2017, Nature.
[37] B. Lenhard,et al. Topologically associating domains are ancient features that coincide with Metazoan clusters of extreme noncoding conservation , 2017, Nature Communications.
[38] Sudhir Kumar,et al. TimeTree: A Resource for Timelines, Timetrees, and Divergence Times. , 2017, Molecular biology and evolution.
[39] J. Gómez-Skarmeta,et al. Topologically associated domains: a successful scaffold for the evolution of gene regulation in animals , 2017, Wiley interdisciplinary reviews. Developmental biology.
[40] Kin Chung Lam,et al. High-resolution TADs reveal DNA sequences underlying genome organization in flies , 2017, Nature Communications.
[41] Roger D. Kornberg,et al. Stable Chromosome Condensation Revealed by Chromosome Conformation Capture , 2015, Cell.
[42] J. Dekker,et al. Structural and functional diversity of Topologically Associating Domains , 2015, FEBS letters.
[43] T. Misteli,et al. Long-Range Chromatin Interactions. , 2015, Cold Spring Harbor perspectives in biology.
[44] Wei-Hien Cheong,et al. ClicO FS: an interactive web-based service of Circos , 2015, Bioinform..
[45] K. Hansen,et al. Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data , 2015, Genome Biology.
[46] Giacomo Cavalli,et al. The Role of Chromosome Domains in Shaping the Functional Genome , 2015, Cell.
[47] D. Odom,et al. Comparative Hi-C Reveals that CTCF Underlies Evolution of Chromosomal Domain Architecture , 2015, Cell reports.
[48] Noam Kaplan,et al. The Hitchhiker's guide to Hi-C analysis: practical guidelines. , 2015, Methods.
[49] Neva C. Durand,et al. A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping , 2014, Cell.
[50] Maitreya J. Dunham,et al. Species-Level Deconvolution of Metagenome Assemblies with Hi-C–Based Contact Probability Maps , 2014, G3: Genes, Genomes, Genetics.
[51] Edith Heard,et al. Segmental folding of chromosomes: A basis for structural and regulatory chromosomal neighborhoods? , 2013, BioEssays : news and reviews in molecular, cellular and developmental biology.
[52] Daniel Ruiz,et al. A Fast Algorithm for Matrix Balancing , 2013, Web Information Retrieval and Linear Algebra Algorithms.
[53] J. Dekker,et al. The hierarchy of the 3D genome. , 2013, Molecular cell.
[54] L. Mirny,et al. Iterative Correction of Hi-C Data Reveals Hallmarks of Chromosome Organization , 2012, Nature Methods.
[55] Jesse R. Dixon,et al. Topological Domains in Mammalian Genomes Identified by Analysis of Chromatin Interactions , 2012, Nature.
[56] Steven L Salzberg,et al. Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.
[57] Hideaki Sugawara,et al. The Sequence Read Archive , 2010, Nucleic Acids Res..
[58] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[59] E. Green,et al. Comparative sequence analyses reveal sites of ancestral chromosomal fusions in the Indian muntjac genome , 2008, Genome Biology.
[60] A. Miele,et al. Long-range chromosomal interactions and gene regulation. , 2008, Molecular bioSystems.
[61] Fengtang Yang,et al. Neo-sex chromosomes in the black muntjac recapitulate incipient evolution of mammalian sex chromosomes , 2008, Genome Biology.
[62] T. Glover,et al. Chromosome fragile sites. , 2007, Annual review of genetics.
[63] M. Ferguson-Smith,et al. Mammalian karyotype evolution , 2007, Nature Reviews Genetics.
[64] J. Wang,et al. Tandem chromosome fusions in karyotypic evolution of Muntiacus: evidence from M. feae and M. gongshanensis , 2006, Chromosome Research.
[65] Fengtang Yang,et al. High-density comparative BAC mapping in the black muntjac (Muntiacus crinifrons): molecular cytogenetic dissection of the origin of MCR 1p+4 in the X1X2Y1Y2Y3 sex chromosome system. , 2006, Genomics.
[66] E. Eichler,et al. Chromosome evolution in eukaryotes: a multi-kingdom perspective. , 2005, Trends in genetics : TIG.
[67] J. Chi,et al. Defining the orientation of the tandem fusions that occurred during the evolution of Indian muntjac chromosomes by BAC mapping , 2005, Chromosoma.
[68] R. O’Neill,et al. Centromere dynamics and chromosome evolution in marsupials. , 2004, The Journal of heredity.
[69] H. Scherthan,et al. Characterization of ancestral chromosome fusion points in the Indian muntjac deer , 2004, Chromosoma.
[70] Stephen J O'Brien,et al. Evolution of mammalian genome organization inferred from comparative gene mapping , 2001, Genome Biology.
[71] H. Lan,et al. Rapid and parallel chromosomal number reductions in muntjac deer inferred from mitochondrial DNA phylogeny. , 2000, Molecular biology and evolution.
[72] P. Slijepcevic. Telomeres and mechanisms of Robertsonian fusion , 1998, Chromosoma.
[73] D. Hill,et al. Use of the Indian muntjac idiogram to align conserved chromosomal segments in sheep and human genomes by chromosome painting. , 1997, Genomics.
[74] J. Wienberg,et al. A reappraisal of the tandem fusion theory of karyotype evolution in the Indian muntjac using chromosome painting , 1997, Chromosome Research.
[75] Fengtang Yang,et al. Comparative chromosome painting in mammals: human and the Indian muntjac (Muntiacus muntjak vaginalis). , 1997, Genomics.
[76] N. Carter,et al. A comparative study of karyotypes of muntjacs by chromosome painting , 1995, Chromosoma.
[77] D C Ward,et al. Origin of human chromosome 2: an ancestral telomere-telomere fusion. , 1991, Proceedings of the National Academy of Sciences of the United States of America.
[78] C. Lin,et al. New evidence for tandem chromosome fusions in the karyotypic evolution of Asian muntjacs , 1991, Chromosoma.
[79] Shi Li-ming,et al. A New Karyotype of Muntjac (Muntiacus sp.) From Gongshan County in China , 1988 .
[80] R. Moyzis,et al. Fragile sites, telomeric DNA sequences, B chromosomes, and DNA content in raccoon dogs, Nyctereutes procyonoides, with comparative notes on foxes, coyote, wolf, and raccoon. , 1988, Cytogenetics and cell genetics.
[81] B. Mcclintock,et al. The significance of responses of the genome to challenge. , 1984, Science.
[82] N. Atkin,et al. Muntjac chromosomes: A new karyotype forMuntiacus muntjak , 1972, Experientia.
[83] K. Benirschke,et al. Indian Momtjac, Muntiacus muntiak: A Deer with a Low Diploid Chromosome Number , 1970, Science.
[84] K. Benirschke,et al. Chromosome studies in some deer, the springbok, and the pronghorn, with notes on placentation in deer. , 1967, Cytologia.
[85] T. Mackay,et al. Charting the genotype–phenotype map: lessons from the Drosophila melanogaster Genetic Reference Panel , 2018, Wiley interdisciplinary reviews. Developmental biology.
[86] R Core Team,et al. R: A language and environment for statistical computing. , 2014 .
[87] R. Housley,et al. Chromosome , 2011, Encyclopedia of Cryptography and Security.
[88] C. Cremer. NUCLEAR ARCHITECTURE AND GENE REGULATION IN MAMMALIAN CELLS , 2001 .
[89] C. Lottaz,et al. BIOINFORMATICS APPLICATIONS NOTE , 2001 .
[90] C. Lin,et al. Interstitial localization of telomeric DNA sequences in the Indian muntjac chromosomes: further evidence for tandem chromosome fusions in the karyotypic evolution of the Asian muntjacs. , 1993, Cytogenetics and cell genetics.
[91] H. Kada,et al. Confirmation of the Chromosomal Constitution of Fea's Muntjac, Muntiacus feae , 1987 .
[92] H. Kada,et al. The chromosomes of Muntiacus feae. , 1983, Cytogenetics and cell genetics.
[93] S. Liming,et al. Comparative cytogenetic studies on the red muntjac, Chinese muntjac, and their F1 hybrids. , 1980, Cytogenetics and cell genetics.
[94] D. Kubai,et al. Chromosome structure. , 1970, Annual review of genetics.
[95] I. Amit,et al. Supporting Online Material Materials and Methods Som Text Comprehensive Mapping of Long-range Interactions Reveals Folding Principles of the Human Genome , 2022 .