Bentzinger C F, Wang Y X, Rudnicki M A. 2012. Building muscle: Molecular regulation of myogenesis. Cold Spring Harbor Perspectives in Biology, 4, a008342

Berti F, Nogueira J M, Wohrle S, Sobreira D R, Hawrot K, Dietrich S. 2015. Time course and side-by-side analysis of mesodermal, pre-myogenic, myogenic and differentiated cell markers in the chicken model for skeletal muscle formation. Journal of Anatomy, 227, 361–382.

Bryson-Richardson R J, Currie P D. 2008. The genetics of vertebrate myogenesis. Nature Review in Genetics, 9, 632–646.

Buckingham M, Rigby P W. 2014. Gene regulatory networks and transcriptional mechanisms that control myogenesis. Developmental Cell, 28, 225–238.

Cardoso-Moreira M, Halbert J, Valloton D, Velten B, Chen C, Shao Y, Liechti A, Ascencao K, Rummel C, Ovchinnikova S, Mazin P V, Xenarios I, Harshman K, Mort M, Cooper D N, Sandi C, Soares M J, Ferreira P G, Afonso S, Carneiro M, et al. 2019. Gene expression across mammalian organ development. Nature, 571, 505–509.

Chandra T, Ewels P A, Schoenfelder S, Furlan-Magaril M, Wingett S W, Kirschner K, Thuret J Y, Andrews S, Fraser P, Reik W. 2015. Global reorganization of the nuclear landscape in senescent cells. Cell Reports, 10, 471–483.

Chen G, Wang Y, Garate M, Zhou J, Li G. 2010. The tumor suppressor ING3 is degraded by SCF(Skp2)-mediated ubiquitin-proteasome system. Oncogene, 29, 1498–1508.

Chen L, Li J, Yuan R, Wang Y, Zhang J, Lin Y, Wang L, Zhu X, Zhu W, Bai J, Kong F, Zeng B, Lu L, Ma J, Long K, Jin L, Huang Z, Huo J, Gu Y, Wang D, Mo D, et al. 2022. Dynamic 3D genome reorganization during development and metabolic stress of the porcine liver. Cell Discovery, 8, 56.

Chen W, Lv Y T, Zhang H X, Ruan D, Wang S, Lin Y C. 2013. Developmental specificity in skeletal muscle of late-term avian embryos and its potential manipulation. Poultry Science, 92, 2754–2764.

Chin R M, Fu X, Pai M Y, Vergnes L, Hwang H, Deng G, Diep S, Lomenick B, Meli V S, Monsalve G C, Hu E, Whelan S A, Wang J X, Jung G, Solis G M, Fazlollahi F, Kaweeteerawat C, Quach A, Nili M, Krall A S, et al. 2014. The metabolite alpha-ketoglutarate extends lifespan by inhibiting ATP synthase and TOR. Nature, 510, 397–401.

Chung C Y T, Lo P H Y, Lee K K H. 2020. Babam2 regulates cell cycle progression and pluripotency in mouse embryonic stem cells as revealed by induced DNA damage. Biomedicines, 8, 397.

Coppe J P, Desprez P Y, Krtolica A, Campisi J. 2010. The senescence-associated secretory phenotype: The dark side of tumor suppression. Annual Review of Pathology, 5, 99–118.

Courtois-Cox S, Jones S L, Cichowski K. 2008. Many roads lead to oncogene-induced senescence. Oncogene, 27, 2801–2809.

Crane E, Bian Q, McCord R P, Lajoie B R, Wheeler B S, Ralston E J, Uzawa S, Dekker J, Meyer B J. 2015. Condensin-driven remodelling of X chromosome topology during dosage compensation. Nature, 523, 240–244.

Criscione S W, Teo Y V, Neretti N. 2016. The chromatin landscape of cellular senescence. Trends in Genetics: TIG, 32, 751–761.

David V, Martin A, Hedge A M, Rowe P S. 2009. Matrix extracellular phosphoglycoprotein (MEPE) is a new bone renal hormone and vascularization modulator. Endocrinology, 150, 4012–4023.

Deschamps J, Duboule D. 2017. Embryonic timing, axial stem cells, chromatin dynamics, and the Hox clock. Genes & Development, 31, 1406–1416.

Dethlefsen M M, Halling J F, Moller H D, Plomgaard P, Regenberg B, Ringholm S, Pilegaard H. 2018. Regulation of apoptosis and autophagy in mouse and human skeletal muscle with aging and lifelong exercise training. Experimental Gerontology, 111, 141–153.

Dittmer J. 2003. The biology of the Ets1 proto-oncogene. Molecular Cancer, 2, 29.

Dixon J R, Jung I, Selvaraj S, Shen Y, Antosiewicz-Bourget J E, Lee A Y, Ye Z, Kim A, Rajagopal N, Xie W, Diao Y, Liang J, Zhao H, Lobanenkov V V, Ecker J R, Thomson J A, Ren B. 2015. Chromatin architecture reorganization during stem cell differentiation. Nature, 518, 331–336.

Dixon J R, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu J S, Ren B. 2012. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature, 485, 376–380.

Doi T, Puri P, Bannigan J, Thompson J. 2012. Eya1 and Eya2 gene expression is down-regulated during somitic myogenesis in the cadmium-induced omphalocele chick model. Journal of Pediatric Surgery, 47, 1123–1127.

Durand N C, Shamim M S, Machol I, Rao S S, Huntley M H, Lander E S, Aiden E L. 2016. Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments. Cell Systems, 3, 95–98.

Esteves de Lima J, Bou Akar R, Mansour M, Rocancourt D, Buckingham M, Relaix F. 2021. M-Cadherin Is a PAX3 target during myotome patterning. Frontiers in Cell Developmental Biology, 9, 652652.

Fishman V, Battulin N, Nuriddinov M, Maslova A, Zlotina A, Strunov A, Chervyakova D, Korablev A, Serov O, Krasikova A. 2019. 3D organization of chicken genome demonstrates evolutionary conservation of topologically associated domains and highlights unique architecture of erythrocytes’ chromatin. Nucleic Acids Research, 47, 648–665.

Flyamer I M, Gassler J, Imakaev M, Brandão H B, Ulianov S V, Abdennur N, Razin S V, Mirny L A, Tachibana-Konwalski K. 2017. Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition. Nature, 544, 110–114.

Ghosh S, Chan C K. 2016. Analysis of RNA-seq data using TopHat and Cufflinks. Methods in Molecular Biology, 1374, 339–361.

Grifone R, Demignon J, Giordani J, Niro C, Souil E, Bertin F, Laclef C, Xu P X, Maire P. 2007. Eya1 and Eya2 proteins are required for hypaxial somitic myogenesis in the mouse embryo. Developmental Biology, 302, 602–616.

Grove B K, Cerny L, Perriard J C, Eppenberger H M. 1985. Myomesin and M-protein: Expression of two M-band proteins in pectoral muscle and heart during development. The Journal of Cell Biology, 101, 1413–1421.

Gupta A, Place M, Goldstein S, Sarkar D, Zhou S, Potamousis K, Kim J, Flanagan C, Li Y, Newton M A, Callander N S, Hematti P, Bresnick E H, Ma J, Asimakopoulos F, Schwartz D C. 2015. Single-molecule analysis reveals widespread structural variation in multiple myeloma. Proceedings of the National Academy of Sciences of the United States of America, 112, 7689–7694.

Knížetová H, Hyánek J, Hyánková L, Bělíček P. 1995. Comparative study of growth curves in poultry. Genetics Selection Evolution, 27, 365–375.

Hammoud S S, Low D H P, Yi C, Carrell D T, Guccione E, Cairns B R. 2014. Chromatin and transcription transitions of mammalian adult germline stem cells and spermatogenesis. Cell Stem Cell, 15, 239–253.

Heinz S, Benner C, Spann N, Bertolino E, Lin Y C, Laslo P, Cheng J X, Murre C, Singh H, Glass C K. 2010. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Molecular Cell, 38, 576–589.

van Hengel J, Calore M, Bauce B, Dazzo E, Mazzotti E, De Bortoli M, Lorenzon A, Li Mura I E, Beffagna G, Rigato I, Vleeschouwers M, Tyberghein K, Hulpiau P, van Hamme E, Zaglia T, Corrado D, Basso C, Thiene G, Daliento L, Nava A, et al. 2013. Mutations in the area composita protein alphaT-catenin are associated with arrhythmogenic right ventricular cardiomyopathy. European Heart Journal, 34, 201–210.

Hernandez S F, Vahidi N A, Park S, Weitzel R P, Tisdale J, Rueda B R, Wolff E F. 2015. Characterization of extracellular DDX4- or Ddx4-positive ovarian cells. Nature Medcine, 21, 1114–1116.

Huang Q, Li F, Liu X, Li W, Shi W, Liu F F, O’Sullivan B, He Z, Peng Y, Tan A C, Zhou L, Shen J, Han G, Wang X J, Thorburn J, Thorburn A, Jimeno A, Raben D, Bedford J S, Li C Y. 2011. Caspase 3-mediated stimulation of tumor cell repopulation during cancer radiotherapy. Nature Medcine, 17, 860–866.

Hug C B, Vaquerizas J M. 2018. The birth of the 3D genome during early embryonic development. Trends in Genetics, 34, 903–914.

Imakaev M, Fudenberg G, McCord R P, Naumova N, Goloborodko A, Lajoie B R, Dekker J, Mirny L A. 2012. Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nature Methods, 9, 999–1003.

Ishihara T, Ikeda K, Sato S, Yajima H, Kawakami K. 2008. Differential expression of Eya1 and Eya2 during chick early embryonic development. Gene Expression Patterns, 8, 357–367.

Janssens B, Mohapatra B, Vatta M, Goossens S, Vanpoucke G, Kools P, Montoye T, van Hengel J, Bowles N E, van Roy F, Towbin J A. 2003. Assessment of the CTNNA3 gene encoding human alpha T-catenin regarding its involvement in dilated cardiomyopathy. Human Genetics, 112, 227–236.

Jejurikar S S, Henkelman E A, Cederna P S, Marcelo C L, Urbanchek M G, Kuzon Jr W M. 2006. Aging increases the susceptibility of skeletal muscle derived satellite cells to apoptosis. Experimental Gerontology, 41, 828–836.

Jin L, Wang D, Zhang J, Liu P, Wang Y, Lin Y, Liu C, Han Z, Long K, Li D, Jiang Y, Li G, Zhang Y, Bai J, Li X, Li J, Lu L, Kong F, Wang X, Li H, et al. 2023. Dynamic chromatin architecture of the porcine adipose tissues with weight gain and loss. Nature Communications, 14, 3457.

Kalmes A, Daum G, Clowes A W. 2001. EGFR transactivation in the regulation of SMC function. Annals of the New York Academy of Sciences, 947, 42–54.

Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg S L. 2013. TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biology, 14, R36.

Knight P A, Ruiz D. 2012. A fast algorithm for matrix balancing. IMA Journal of Numerical Analysis, 33, 1029–1047.

Kocamis H, McFarland D C, Killefer J. 2001. Temporal expression of growth factor genes during myogenesis of satellite cells derived from the biceps femoris and pectoralis major muscles of the chicken. Journal of Cellular Physiology, 186, 146–152.

Kong S, Zhang Y. 2019. Deciphering Hi-C: From 3D genome to function. Cell Biology and Toxicology, 35, 15–32.

Kragesteen B K, Spielmann M, Paliou C, Heinrich V, Schopflin R, Esposito A, Annunziatella C, Bianco S, Chiariello A M, Jerkovic I, Harabula I, Guckelberger P, Pechstein M, Wittler L, Chan W L, Franke M, Lupianez D G, Kraft K, Timmermann B, Vingron M, et al. 2018. Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis. Nature Genetics, 50, 1463–1473.

Krijger P H, Di Stefano B, de Wit E, Limone F, van Oevelen C, de Laat W, Graf T. 2016. Cell-of-origin-specific 3D genome structure acquired during somatic cell reprogramming. Cell Stem Cell, 18, 597–610.

Lamber E P, Guicheney P, Pinotsis N. 2022. The role of the M-band myomesin proteins in muscle integrity and cardiac disease. Journal of Biomedical Science, 29, 18.

Langmead B, Salzberg S L. 2012. Fast gapped-read alignment with Bowtie 2. Nature Methods, 9, 357–359.

Li C, Liu F, Liu S, Pan H, Du H, Huang J, Xie Y, Li Y, Zhao R, Wei Y. 2020. Elevated myocardial SORBS2 and the underlying implications in left ventricular noncompaction cardiomyopathy. eBioMedicine, 53, 102695.

Li D, He M, Tang Q, Tian S, Zhang J, Li Y, Wang D, Jin L, Ning C, Zhu W, Hu S, Long K, Ma J, Liu J, Zhang Z, Li M. 2022a. Comparative 3D genome architecture in vertebrates. BMC Biology, 20, 99.

Li D, Li Y, Li M, Che T, Tian S, Chen B, Zhou X, Zhang G, Gaur U, Luo M, Tian K, He M, He S, Xu Z, Jin L, Tang Q, Dai Y, Xu H, Hu Y, Zhao X, et al. 2019. Population genomics identifies patterns of genetic diversity and selection in chicken. BMC Genomics, 20, 263.

Li D, Ning C, Zhang J, Wang Y, Tang Q, Kui H, Wang T, He M, Jin L, Li J, Lin Y, Zeng B, Yin H, Zhao X, Zhang Y, Xu H, Zhu Q, Li M. 2022b. Dynamic transcriptome and chromatin architecture in granulosa cells during chicken folliculogenesis. Nature Communications, 13, 131.

Li H, Cybulsky M I, Gimbrone Jr M A, Libby P. 1993. Inducible expression of vascular cell adhesion molecule-1 by vascular smooth muscle cells in vitro and within rabbit atheroma. The American Journal of Pathology, 143, 1551–1559.

Li H, Durbin R. 2010. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics, 26, 589–595.

Liang F, Wang B, Geng J, You G, Fa J, Zhang M, Sun H, Chen H, Fu Q, Zhang X, Zhang Z. 2021. SORBS2 is a genetic factor contributing to cardiac malformation of 4q deletion syndrome patients. eLife, 10, e67481.

Lieberman-Aiden E, van Berkum N L, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie B R, Sabo P J, Dorschner M O, Sandstrom R, Bernstein B, Bender M A, Groudine M, Gnirke A, Stamatoyannopoulos J, Mirny L A, Lander E S, Dekker J. 2009. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science, 326, 289–293.

Liesenfeld M, Mosig S, Funke H, Jansen L, Runnebaum I B, Durst M, Backsch C. 2013. SORBS2 and TLR3 induce premature senescence in primary human fibroblasts and keratinocytes. BMC Cancer, 13, 507.

Lindsly S, Chen C, Liu S, Ronquist S, Dilworth S, Perlman M, Rajapakse I. 2021. 4DNvestigator: Time series genomic data analysis toolbox. Nucleus, 12, 58–64.

Ljt K, Rh V D W, Ketting R F, De W E. 2018. Systemic loss and gain of chromatin architecture throughout zebrafish development. Cell Reports, 24, 1–10.

Lombardo S D, Mazzon E, Basile M S, Campo G, Corsico F, Presti M, Bramanti P, Mangano K, Petralia M C, Nicoletti F, Fagone P. 2019. Modulation of tetraspanin 32 (TSPAN32) expression in T cell-mediated immune responses and in multiple sclerosis. International Journal of Molecular Sciences, 20, 4323.

Love M I, Huber W, Anders S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 15, 550.

Lu H, Ju D D, Yang G D, Zhu L Y, Yang X M, Li J, Song W W, Wang J H, Zhang C C, Zhang Z G, Zhang R. 2019. Targeting cancer stem cell signature gene SMOC-2 overcomes chemoresistance and inhibits cell proliferation of endometrial carcinoma. eBioMedicine, 40, 276–289.

Luo W, Lin Z, Chen J, Chen G, Zhang S, Liu M, Li H, He D, Liang S, Luo Q, Zhang D, Nie Q, Zhang X. 2021. TMEM182 interacts with integrin beta 1 and regulates myoblast differentiation and muscle regeneration. Journal of Cachexia, Sarcopenia and Muscle, 12, 1704–1723.

Lupianez D G, Kraft K, Heinrich V, Krawitz P, Brancati F, Klopocki E, Horn D, Kayserili H, Opitz J M, Laxova R, Santos-Simarro F, Gilbert-Dussardier B, Wittler L, Borschiwer M, Haas S A, Osterwalder M, Franke M, Timmermann B, Hecht J, Spielmann M, et al. 2015. Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions. Cell, 161, 1012–1025.

MacPhillamy C, Pitchford W S, Alinejad-Rokny H, Low W Y. 2021. Opportunity to improve livestock traits using 3D genomics. Animal Genetics, 52, 785–798.

Magli A, Baik J, Pota P, Cordero C O, Kwak I Y, Garry D J, Love P E, Dynlacht B D, Perlingeiro R C R. 2019. Pax3 cooperates with Ldb1 to direct local chromosome architecture during myogenic lineage specification. Nature Communications, 10, 2316.

Maharjan P, Beitia A, Weil J, Suesuttajit N, Hilton K, Caldas J, Umberson C, Martinez D, Kong B, Owens C M, Coon C. 2021. Woody breast myopathy broiler show age-dependent adaptive differential gene expression in pectoralis major and altered in-vivo triglyceride kinetics in adipogenic tissues. Poultry Science, 100, 101092.

Malik L, Patro R. 2019. Rich chromatin structure prediction from Hi-C data. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 16, 1448–1458.

Martone J, Mariani D, Desideri F, Ballarino M. 2019. Non-coding RNAs shaping muscle. Frontiers in Cell and Developmental Biology, 7, 394.

Matharu N, Ahituv N. 2015. Minor loops in major folds: Enhancer-promoter looping, chromatin restructuring, and their association with transcriptional regulation and disease. PLoS Genetics, 11, e1005640.

Mele M, Ferreira P G, Reverter F, DeLuca D S, Monlong J, Sammeth M, Young T R, Goldmann J M, Pervouchine D D, Sullivan T J, Johnson R, Segre A V, Djebali S, Niarchou A, Consortium G T, Wright F A, Lappalainen T, Calvo M, Getz G, Dermitzakis E T, et al. 2015. Human genomics. The human transcriptome across tissues and individuals. Science, 348, 660–665.

Molina-Privado I, Jimenez P R, Montes-Moreno S, Chiodo Y, Rodriguez-Martinez M, Sanchez-Verde L, Iglesias T, Piris M A, Campanero M R. 2012. E2F4 plays a key role in Burkitt lymphoma tumorigenesis. Leukemia, 26, 2277–2285.

Neems D S, Garza-Gongora A G, Smith E D, Kosak S T. 2016. Topologically associated domains enriched for lineage-specific genes reveal expression-dependent nuclear topologies during myogenesis. Proceedings of the National Academy of Sciences of the United States of America, 113, E1691–E1700.

Newman A B, Kupelian V, Visser M, Simonsick E M, Goodpaster B H, Kritchevsky S B, Tylavsky F A, Rubin S M, Harris T B, Ofhealth, Behalf O. 2006. Strength, but not muscle mass, is associated with mortality in the health, aging and body composition study cohort. The Journals of Gerontology Series A (Biological Sciences and Medical Sciences), 61, 72–77.

Nkabyo Y S, Go Y M, Ziegler T R, Jones D P. 2005. Extracellular cysteine/cystine redox regulates the p44/p42 MAPK pathway by metalloproteinase-dependent epidermal growth factor receptor signaling. American Journal of Physiology Gastrointestinal and Liver Physiology, 289, G70–G78.

Noordermeer D, Leleu M, Schorderet P, Joye E, Chabaud F, Duboule D. 2014. Temporal dynamics and developmental memory of 3D chromatin architecture at Hox gene loci. eLife, 3, e02557.

Nora E P, Lajoie B R, Schulz E G, Giorgetti L, Okamoto I, Servant N, Piolot T, van Berkum N L, Meisig J, Sedat J, Gribnau J, Barillot E, Bluthgen N, Dekker J, Heard E. 2012. Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature, 485, 381–385.

Nueda M J, Tarazona S, Conesa A. 2014. Next maSigPro: Updating maSigPro bioconductor package for RNA-seq time series. Bioinformatics, 30, 2598–2602.

Paliou C, Guckelberger P, Schopflin R, Heinrich V, Esposito A, Chiariello A M, Bianco S, Annunziatella C, Helmuth J, Haas S, Jerkovic I, Brieske N, Wittler L, Timmermann B, Nicodemi M, Vingron M, Mundlos S, Andrey G. 2019. Preformed chromatin topology assists transcriptional robustness of Shh during limb development. Proceedings of the National Academy of Sciences of the United States of America, 116, 12390–12399.

Pan W, Zhang N, Liu W, Liu J, Zhou L, Liu Y, Yang M. 2018. The long noncoding RNA GAS8-AS1 suppresses hepatocarcinogenesis by epigenetically activating the tumor suppressor GAS8. The Journal of Biological Chemistry, 293, 17154–17165.

Parker M H, Seale P, Rudnicki M A. 2003. Looking back to the embryo: Defining transcriptional networks in adult myogenesis. Nature Reviews Genetics, 4, 497–507.

Paulsen J, Liyakat Ali T M, Nekrasov M, Delbarre E, Baudement M O, Kurscheid S, Tremethick D, Collas P. 2019. Long-range interactions between topologically associating domains shape the four-dimensional genome during differentiation. Nature Genetics, 51, 835–843.

Pertea M, Pertea G M, Antonescu C M, Chang T C, Mendell J T, Salzberg S L. 2015. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nature Biotechnology, 33, 290–295.

Prenzel N, Fischer O M, Streit S, Hart S, Ullrich A. 2001. The epidermal growth factor receptor family as a central element for cellular signal transduction and diversification. Endocrine Related Cancer, 8, 11–31.

Quiat D, Voelker K A, Pei J, Grishin N V, Grange R W, Bassel-Duby R, Olson E N. 2011. Concerted regulation of myofiber-specific gene expression and muscle performance by the transcriptional repressor Sox6. Proceedings of the National Academy of Sciences of the United States of America, 108, 10196–10201.

Rao S S, Huntley M H, Durand N C, Stamenova E K, Bochkov I D, Robinson J T, Sanborn A L, Machol I, Omer A D, Lander E S, Aiden E L. 2014. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell, 159, 1665–1680.

Rieber L, Mahony S. 2017. miniMDS: 3D structural inference from high-resolution Hi-C data. Bioinformatics, 33, i261-i266.

Robin J D, Jacome Burbano M S, Peng H, Croce O, Thomas J L, Laberthonniere C, Renault V, Lototska L, Pousse M, Tessier F, Bauwens S, Leong W, Sacconi S, Schaeffer L, Magdinier F, Ye J, Gilson E. 2020. Mitochondrial function in skeletal myofibers is controlled by a TRF2-SIRT3 axis over lifetime. Aging Cell, 19, e13097.

Rosa-Garrido M, Chapski D J, Schmitt A D, Kimball T H, Karbassi E, Monte E, Balderas E, Pellegrini M, Shih T T, Soehalim E, Liem D, Ping P, Galjart N J, Ren S, Wang Y, Ren B, Vondriska T M. 2017. High-resolution mapping of chromatin conformation in cardiac myocytes reveals structural remodeling of the epigenome in heart failure. Circulation, 136, 1613–1625.

Rowley M J, Nichols M H, Lyu X, Ando-Kuri M, Rivera I S M, Hermetz K, Wang P, Ruan Y, Corces V G. 2017. Evolutionarily conserved principlespredict 3D chromatin organization. Molecular Cell, 67, 837–852.e7.

Ruis P, Van Ly D, Borel V, Kafer G R, McCarthy A, Howell S, Blassberg R, Snijders A P, Briscoe J, Niakan K K, Marzec P, Cesare A J, Boulton S J. 2021. TRF2-independent chromosome end protection during pluripotency. Nature, 589, 103–109.

Salama R, Sadaie M, Hoare M, Narita M. 2014. Cellular senescence and its effector programs. Genes & Development, 28, 99–114.

Sanders S J, Campbell A J, Cottrell J R, Moller R S, Wagner F F, Auldridge A L, Bernier R A, Catterall W A, Chung W K, Empfield J R, George Jr A L, Hipp J F, Khwaja O, Kiskinis E, Lal D, Malhotra D, Millichap J J, Otis T S, Petrou S, Pitt G, et al. 2018. Progress in understanding and treating SCN2A-mediated disorders. Trends in Neuroscience, 41, 442–456.

Sati S, Bonev B, Szabo Q, Jost D, Bensadoun P, Serra F, Loubiere V, Papadopoulos G L, Rivera-Mulia J C, Fritsch L, Bouret P, Castillo D, Gelpi J L, Orozco M, Vaillant C, Pellestor F, Bantignies F, Marti-Renom M A, Gilbert D M, Lemaitre J M, et al. 2020. 4D Genome rewiring during oncogene-induced and replicative senescence. Molecular Cell, 78, 522–538. e9.

Schrauwen I, Valgaeren H, Tomas-Roca L, Sommen M, Altunoglu U, Wesdorp M, Beyens M, Fransen E, Nasir A, Vandeweyer G, Schepers A, Rahmoun M, van Beusekom E, Huentelman M J, Offeciers E, Dhooghe I, Huber A, Van de Heyning P, Zanetti D, De Leenheer E M R, et al. 2019. Variants affecting diverse domains of MEPE are associated with two distinct bone disorders, a craniofacial bone defect and otosclerosis. Genetics in Medcine, 21, 1199–1208.

Sousa-Victor P, Garcia-Prat L, Munoz-Canoves P. 2022. Control of satellite cell function in muscle regeneration and its disruption in ageing. Nature Reviews. Molecular Cell Biology, 23, 204–226.

Stanic B, Katsuyama M, Miller Jr F J. 2010. An oxidized extracellular oxidation-reduction state increases Nox1 expression and proliferation in vascular smooth muscle cells via epidermal growth factor receptor activation. Arteriosclerosis, Thrombosis, and Vascular Biology, 30, 2234–2241.

Su Y, Wang T, Wu N, Li D, Fan X, Xu Z, Mishra S K, Yang M. 2019. Alpha-ketoglutarate extends Drosophila lifespan by inhibiting mTOR and activating AMPK. Aging, 11, 4183–4197.

Surakka I, Fritsche L G, Zhou W, Backman J, Kosmicki J A, Lu H, Brumpton B, Nielsen J B, Gabrielsen M E, Skogholt A H, Wolford B, Graham S E, Chen Y E, Lee S, Kang H M, Langhammer A, Forsmo S, Asvold B O, Styrkarsdottir U, Holm H, Gudbjartsson D, et al. 2020. MEPE loss-of-function variant associates with decreased bone mineral density and increased fracture risk. Nature Communications, 11, 4093.

Syafruddin S E, Mohtar M A, Wan Mohamad Nazarie W F, Low T Y. 2020. Two sides of the same coin: The roles of KLF6 in physiology and pathophysiology. Biomolecules, 10, 1378.

Symmons O, Pan L, Remeseiro S, Aktas T, Klein F, Huber W, Spitz F. 2016. The Shh topological domain facilitates the action of remote enhancers by reducing the effects of genomic distances. Developmental Cell, 39, 529–543.

Taglietti V, Maroli G, Cermenati S, Monteverde S, Ferrante A, Rossi G, Cossu G, Beltrame M, Messina G. 2016. Nfix induces a switch in Sox6 transcriptional activity to regulate MyHC-I expression in fetal muscle. Cell Reports, 17, 2354–2366.

Tiscia G L, Margaglione M. 2018. Human fibrinogen: Molecular and genetic aspects of congenital disorders. International Journal of Molecular Sciences, 19, 1597.

Whyte W A, Orlando D A, Hnisz D, Abraham B J, Lin C Y, Kagey M H, Rahl P B, Lee T I, Young R A. 2013. Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell, 153, 307–319.

Williams T M, Lisanti M P. 2004. The caveolin proteins. Genome Biology, 5, 214.

Xu P X, Cheng J, Epstein J A, Maas R L. 1997. Mouse Eya genes are expressed during limb tendon development and encode a transcriptional activation function. Proceedings of the National Academy of Sciences of the United States of America, 94, 11974–11979.

Xu Z, Che T, Li F, Tian K, Zhu Q, Mishra S K, Dai Y, Li M, Li D. 2018. The temporal expression patterns of brain transcriptome during chicken development and ageing. BMC Genomics, 19, 917.

Yang T, Zhang F, Yardimci G G, Song F, Hardison R C, Noble W S, Yue F, Li Q. 2017. HiCRep: Assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient. Genome Research, 27, 1939–1949.

Yau M S, Kuipers A L, Price R, Nicolas A, Tajuddin S M, Handelman S K, Arbeeva L, Chesi A, Hsu Y H, Liu C T, Karasik D, Zemel B S, Grant S F, Jordan J M, Jackson R D, Evans M K, Harris T B, Zmuda J M, Kiel D P. 2021. A meta-analysis of the transferability of bone mineral density genetic loci associations from European to African ancestry populations. Journal of Bone and Mineral Research, 36, 469–479.

Yuan R, Zhang J, Wang Y, Zhu X, Hu S, Zeng J, Liang F, Tang Q, Chen Y, Chen L, Zhu W, Li M, Mo D. 2021. Reorganization of chromatin architecture during prenatal development of porcine skeletal muscle. DNA Research, 28, 1–11.

Zhan Y, Mariani L, Barozzi I, Schulz E G, Bluthgen N, Stadler M, Tiana G, Giorgetti L. 2017. Reciprocal insulation analysis of Hi-C data shows that TADs represent a functionally but not structurally privileged scale in the hierarchical folding of chromosomes. Genome Research, 27, 479–490.

Zhang Y, Liu T, Meyer C A, Eeckhoute J, Johnson D S, Bernstein B E, Nusbaum C, Myers R M, Brown M, Li W, Liu X S. 2008. Model-based analysis of ChIP-seq (MACS). Genome Biology, 9, R137.

Zheng H, Xie W. 2019. The role of 3D genome organization in development and cell differentiation. Nature Reviews. Molecular Cell Biology, 20, 53tt50.

Zhou Y, Zhou B, Pache L, Chang M, Khodabakhshi A H, Tanaseichuk O, Benner C, Chanda S K. 2019. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nature Communications, 10, 1523.

Zhu B, Rippe C, Holmberg J, Zeng S, Perisic L, Albinsson S, Hedin U, Uvelius B, Swärd K. 2018. Nexilin/NEXN controls actin polymerization in smooth muscle and is regulated by myocardin family coactivators and YAP. Scientific Reports, 8, 13025.