Non-coding deletions identify Maenli lncRNA as a limb-specific En1 regulator.
Animals
Cell Line
Chromatin
/ genetics
Disease Models, Animal
Extremities
Female
Homeodomain Proteins
/ genetics
Humans
Limb Deformities, Congenital
/ genetics
Mice
Mice, Transgenic
RNA, Long Noncoding
/ genetics
Sequence Deletion
/ genetics
Transcription, Genetic
Transcriptional Activation
/ genetics
Journal
Nature
ISSN: 1476-4687
Titre abrégé: Nature
Pays: England
ID NLM: 0410462
Informations de publication
Date de publication:
04 2021
04 2021
Historique:
received:
05
10
2019
accepted:
07
01
2021
pubmed:
12
2
2021
medline:
10
4
2021
entrez:
11
2
2021
Statut:
ppublish
Résumé
Long non-coding RNAs (lncRNAs) can be important components in gene-regulatory networks
Identifiants
pubmed: 33568816
doi: 10.1038/s41586-021-03208-9
pii: 10.1038/s41586-021-03208-9
doi:
Substances chimiques
Chromatin
0
EN1 protein, human
0
Homeodomain Proteins
0
RNA, Long Noncoding
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
93-98Subventions
Organisme : Wellcome Trust
ID : 206475/Z/17/Z
Pays : United Kingdom
Références
Kopp, F. & Mendell, J. T. Functional classification and experimental dissection of long noncoding RNAs. Cell 172, 393–407 (2018).
pubmed: 29373828
pmcid: 5978744
Hon, C. C. et al. An atlas of human long non-coding RNAs with accurate 5′ ends. Nature 543, 199–204 (2017).
pubmed: 28241135
pmcid: 6857182
Engreitz, J. M. et al. Local regulation of gene expression by lncRNA promoters, transcription and splicing. Nature 539, 452–455 (2016).
pubmed: 27783602
pmcid: 6853796
Loomis, C. A. et al. The mouse Engrailed-1 gene and ventral limb patterning. Nature 382, 360–363 (1996).
pubmed: 8684466
Wurst, W., Auerbach, A. B. & Joyner, A. L. Multiple developmental defects in Engrailed-1 mutant mice: an early mid-hindbrain deletion and patterning defects in forelimbs and sternum. Development 120, 2065–2075 (1994).
pubmed: 7925010
Franke, M. et al. Formation of new chromatin domains determines pathogenicity of genomic duplications. Nature 538, 265–269 (2016).
pubmed: 27706140
Kragesteen, B. K. et al. Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis. Nat. Genet. 50, 1463–1473 (2018).
pubmed: 30262816
Huettl, R. E. et al. Engrailed 1 mediates correct formation of limb innervation through two distinct mechanisms. PLoS ONE 10, e0118505 (2015).
pubmed: 25710467
pmcid: 4340014
Andrey, G. et al. Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding. Genome Res. 27, 223–233 (2017).
doi: 10.1101/gr.213066.116
pubmed: 27923844
pmcid: 5287228
Xiang, J. F. et al. Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus. Cell Res. 24, 513–531 (2014).
pubmed: 24662484
pmcid: 4011346
Cho, S. W. et al. Promoter of lncRNA gene PVT1 Is a tumor-suppressor DNA boundary element. Cell 173, 1398–1412 (2018).
pubmed: 29731168
pmcid: 5984165
Isoda, T. et al. Non-coding transcription instructs chromatin folding and compartmentalization to dictate enhancer-promoter communication and T cell fate. Cell 171, 103–119 (2017).
pubmed: 28938112
pmcid: 5621651
Vian, L. et al. The energetics and physiological impact of cohesin extrusion. Cell 175, 292–294 (2018).
pubmed: 30241609
pmcid: 6251724
Kraft, K. et al. Serial genomic inversions induce tissue-specific architectural stripes, gene misexpression and congenital malformations. Nat. Cell Biol. 21, 305–310 (2019).
pubmed: 30742094
Wang, K. C. et al. A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 472, 120–124 (2011).
pubmed: 21423168
pmcid: 3670758
Gutschner, T. & Diederichs, S. The hallmarks of cancer: a long non-coding RNA point of view. RNA Biol. 9, 703–719 (2012).
pubmed: 22664915
pmcid: 3495743
Ishii, N. et al. Identification of a novel non-coding RNA, MIAT, that confers risk of myocardial infarction. J. Hum. Genet. 51, 1087–1099 (2006).
pubmed: 17066261
Broadbent, H. M. et al. Susceptibility to coronary artery disease and diabetes is encoded by distinct, tightly linked SNPs in the ANRIL locus on chromosome 9p. Hum. Mol. Genet. 17, 806–814 (2008).
pubmed: 18048406
Cabianca, D. S. et al. A long ncRNA links copy number variation to a polycomb/trithorax epigenetic switch in FSHD muscular dystrophy. Cell 149, 819–831 (2012).
pubmed: 22541069
pmcid: 3350859
van Dijk, M. et al. HELLP babies link a novel lincRNA to the trophoblast cell cycle. J. Clin. Invest. 122, 4003–4011 (2012).
pubmed: 23093777
pmcid: 3484460
Maass, P. G. et al. A misplaced lncRNA causes brachydactyly in humans. J. Clin. Invest. 122, 3990–4002 (2012).
pubmed: 23093776
pmcid: 3485082
Castellanos-Rubio, A. et al. A long noncoding RNA associated with susceptibility to celiac disease. Science 352, 91–95 (2016).
pubmed: 27034373
pmcid: 4994711
Royer-Bertrand, B. et al. Mutations in the heat-shock protein A9 (HSPA9) gene cause the EVEN-PLUS syndrome of congenital malformations and skeletal dysplasia. Sci. Rep. 5, 17154 (2015).
pubmed: 26598328
pmcid: 4657157
Van der Auwera, G. A. et al. From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Curr. Protoc. Bioinformatics. 43, 11.10.1–11.10.33 (2013).
Karczewski, K. J. et al. The ExAC browser: displaying reference data information from over 60 000 exomes. Nucleic Acids Res. 45 (D1), D840–D845 (2017).
pubmed: 27899611
Lek, M. et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature 536, 285–291 (2016).
pubmed: 27535533
pmcid: 5018207
Auton, A. et al. A global reference for human genetic variation. Nature 526, 68–74 (2015).
pubmed: 26432245
Naslavsky, M. S. et al. Exomic variants of an elderly cohort of Brazilians in the ABraOM database. Hum. Mutat. 38, 751–763 (2017).
pubmed: 28332257
Kraft, K. et al. Deletions, inversions, duplications: engineering of structural variants using CRISPR/Cas in mice. Cell Rep. 10, 833–839 (2015).
pubmed: 25660031
George, S. H. et al. Developmental and adult phenotyping directly from mutant embryonic stem cells. Proc. Natl Acad. Sci. USA 104, 4455–4460 (2007).
pubmed: 17360545
pmcid: 1838622
Artus, J. & Hadjantonakis, A. K. Generation of chimeras by aggregation of embryonic stem cells with diploid or tetraploid mouse embryos. Methods Mol. Biol. 693, 37–56 (2011).
pubmed: 21080273
Liska, F. et al. Impairment of Sox9 expression in limb buds of rats homozygous for hypodactyly mutation. Folia Biol. 56, 58–65 (2010).
Wingett, S. et al. HiCUP: pipeline for mapping and processing Hi-C data. F1000Res. 4, 1310 (2015).
pubmed: 26835000
pmcid: 4706059
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
doi: 10.1038/nmeth.1923
pubmed: 22388286
pmcid: 3322381
Durand, N. C. et al. Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments. Cell Syst. 3, 95–98 (2016).
pubmed: 27467249
pmcid: 5846465
Rao, S. S. et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665–1680 (2014).
pubmed: 25497547
pmcid: 5635824
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
pubmed: 23104886
Lupiáñez, D. G. et al. Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions. Cell 161, 1012–1025 (2015).
pubmed: 25959774
pmcid: 4791538
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
pubmed: 25516281
pmcid: 4302049
Wolock, S. L., Lopez, R. & Klein, A. M. Scrublet: computational identification of cell doublets in single-cell transcriptomic data. Cell Syst. 8, 281–291 (2019).
pubmed: 30954476
pmcid: 6625319
Hafemeister, C. & Satija, R. Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression. Genome Biol. 20, 296 (2019).
pubmed: 31870423
pmcid: 6927181
Butler, A., Hoffman, P., Smibert, P., Papalexi, E. & Satija, R. Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat. Biotechnol. 36, 411–420 (2018).
pubmed: 29608179
pmcid: 6700744
Ibrahim, D. M. et al. Distinct global shifts in genomic binding profiles of limb malformation-associated HOXD13 mutations. Genome Res. 23, 2091–2102 (2013).
pubmed: 23995701
pmcid: 3847778
Lee, T. I., Johnstone, S. E. & Young, R. A. Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat. Protoc. 1, 729–748 (2006).
pubmed: 17406303
pmcid: 3004291
Paliou, C. et al. Preformed chromatin topology assists transcriptional robustness of Shh during limb development. Proc. Natl Acad. Sci. USA 116, 12390–12399 (2019).
pubmed: 31147463
pmcid: 6589666
Ramírez, F. et al. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 44 (W1), W160–W165 (2016).
pubmed: 27079975
pmcid: 4987876
Vogel, M. J., Peric-Hupkes, D. & van Steensel, B. Detection of in vivo protein-DNA interactions using DamID in mammalian cells. Nat. Protoc. 2, 1467–1478 (2007).
pubmed: 17545983
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
pubmed: 19451168
pmcid: 2705234
Gagnon, K. T., Li, L., Janowski, B. A. & Corey, D. R. Analysis of nuclear RNA interference in human cells by subcellular fractionation and Argonaute loading. Nat. Protoc. 9, 2045–2060 (2014).
pubmed: 25079428
pmcid: 4251768
Grote, P. et al. The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall development in the mouse. Dev. Cell 24, 206–214 (2013).
pubmed: 23369715
pmcid: 4149175
Livak, K. J. & Schmittgen, T. D. Analysis of relative gene expression data using real-time quantitative PCR and the 2
pubmed: 11846609