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Basic chromosome definitions and staining techniques

Year 2025, Volume: 11 Issue: 3, 268 - 283, 30.08.2025

Abstract

The essential molecules that preserve genetic information, control expression, and guarantee accurate and complete transfer are chromosomes. Any disruption in any of these stages will also be reflected in the organism. Therefore, understanding the "normal" of chromosomes—such as normal packing or normal separation—is crucial for identifying the root causes of disorders.
From a health sciences perspective, identifying the relationship between chromosomes and disorders is the first step toward diagnoses, advanced research for numerous diseases, and even treatment recommendations. While more complicated, quick, and accurate methods have emerged due to methodological developments, traditional chromosomal approaches continue to be the most important and innovative in many labs.
In the context of all mentioned above, this review gives a general overview of the packaging and classification of eukaryotic chromosomes as well as the grouping of human chromosomes. It also presents the basic concepts underlying the G, C, Q, R, and T banding and NOR staining techniques and discusses their consequences for human chromosomes.

References

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  • Witty MJH. Pollen Development, Membranes and Features of the Nucleus in Tradescantia and related genera: A Translation of Wilhelm Hofmeister’s 1848 Paper ‘Ueber die Entwicklung des Pollens.’.15:75-86.
  • Liehr T. Molecular Cytogenetics in the Era of Chromosomics and Cytogenomic Approaches. 2021;12.
  • Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P. Chromosomal DNA and its packaging in the chromatin fiber. Molecular Biology of the Cell 4th edition: Garland Science; 2002.
  • Allison LA. Fundumental molecular biology. Ankara: Palme; 2014.
  • Doğan A, Kumbıçak Z. Cytogenetic studies on some spider species belonging to the family Lycosidae (araneae) distributed in Göreme National Park [Master thesis]. Nevşehir Nevşehir Hacı Bektaş Veli University; 2014.
  • Therman E, Susman M. Human chromosomes: structure, behavior, and effects: Springer Science & Business Media; 2012.
  • Miller OJ, Therman E, Miller OJ, Therman EJHC. The chemistry and packaging of chromosomes. 2001:61-77.
  • Li Y, Agrawal V, Virk RKA, Roth E, Li WS, Eshein A, et al. Analysis of three-dimensional chromatin packing domains by chromatin scanning transmission electron microscopy (ChromSTEM). Scientific Reports. 2022;12(1):12198.
  • Fyodorov DV, Zhou B-R, Skoultchi AI, Bai Y. Emerging roles of linker histones in regulating chromatin structure and function. Nature Reviews Molecular Cell Biology. 2018;19(3):192-206.
  • Saygun S. Comparison of chromosome structures of various flatfish (Pisces, Pleuronectiformes) living in the Black Sea [Master thesis]. Samsun: Ondokuz Mayıs University; 2005.
  • Karyology definition 2024 [Available from: https://www.genome.gov/genetics-glossary/Karyotype.
  • Nadler CF, editor Chromosomal evolution in rodents. Comparative Mammalian Cytogenetics: An International Conference at Dartmouth Medical School Hanover, New Hampshire, July 29—August 2, 1968; 1969: Springer.
  • Madian N, Jayanthi K, Somasundaram D, Suresh SJM. Identifying centromere position of human chromosome images using contour and shape based analysis. 2019;144:243-59.
  • Schweizer D, Ehrendorfer FJPS, Evolution. Giemsa banded karyotypes, systematics, and evolution in Anacyclus (Asteraceae-Anthemideae). 1976;126:107-48.
  • Asadi-Corom F, Mirzaie-Nodoushan H, Calagari MJPGR. Comparative karyological features of several populations of Populus euphratica Oliv., grown under different environmental conditions in Iran. 2024:1-7.
  • Syafriani E, Somala MUA, Triani NJNS, Proceedings T. Biotechnology for Beginner Student. 2021:10-6.
  • Krietenstein N, Abraham S, Venev SV, Abdennur N, Gibcus J, Hsieh T-HS, et al. Ultrastructural details of mammalian chromosome architecture. 2020;78(3):554-65. e7.
  • Nicodemi M, Pombo AJCoicb. Models of chromosome structure. 2014;28:90-5.
  • Macgregor HCJCr. Chromomeres revisited. 2012;20:911-24.
  • Das D. Essential practical handbook of cell biology & genetics, biometry & microbiology: A laboratory manual: Academic Publishers; 2017.
  • Paulson JR, Hudson DF, Cisneros-Soberanis F, Earnshaw WC, editors. Mitotic chromosomes. Seminars in cell & developmental biology; 2021: Elsevier.
  • Navarro AP, Cheeseman IM, editors. Kinetochore assembly throughout the cell cycle. Seminars in cell & developmental biology; 2021: Elsevier.
  • Schleif R. Genetics and molecular biology: The Johns Hopkins University Press; 2023.
  • Chakravarti D, LaBella KA, DePinho RAJC. Telomeres: history, health, and hallmarks of aging. 2021;184(2):306-22.
  • Berns MW, Cheng WKJECR. Are chromosome secondary constrictions nucleolar organizers?: A re-examination using a laser microbeam. 1971;69(1):185-92.
  • Hasterok R, Borowska-Zuchowska N, Robaszkiewicz EJIJoMS. Cytomolecular Organisation of the Nuclear Genome. MDPI; 2022. p. 13028.
  • Thakur J, Packiaraj J, Henikoff S. Sequence, chromatin and evolution of satellite DNA. International journal of molecular sciences. 2021;22(9):4309.
  • O. J. Miller, Therman E. Human Chromosomes: Springer Science & Business Media.; 2011.
  • Emiroğlu Ü. Chromosomes: Basic concepts and mechanisms. Izmir: Ege University Publications 2017.
  • Kumar S, Kiso A, Kithan NAJC-c, molecular strategies for analysing heredity material. IntechOpen L. Chromosome banding and mechanism of chromosome aberrations. 2021:45-60.
  • Sharma A. Chromosome techniques: CRC Press; 2020.
  • Montazerinezhad S, Emamjomeh A, Hajieghrari BJMBR. Chromosomal abnormality, laboratory techniques, tools and databases in molecular Cytogenetics. 2020;47(11):9055-73.
  • Bickmore WA, editor Karyotype Analysis and Chromosome Banding2001.
  • Milani DAQ, Tadi P. Genetics, Chromosome Abnormalities. StatPearls [Internet]: StatPearls Publishing; 2023.
  • Deepthi B, Prayaga AK, Rukmangadha NJJoC. Comparison of modified ultrafast giemsa stain with the standard may grunwald giemsa stain in FNAC of various organs. 2022;39(4):174-9.
  • Dutta U. Essentials of Cytogenetic and Molecular Cytogenetic Laboratory Testing: Cambridge Scholars Publishing; 2022.
  • Huisinga K, Brower-Toland B, Elgin S. The contradictory definitions of heterochromatin: Transcription and silencing. Chromosoma. 2006;115:110-22.
  • Moore CM, Best RG. Chromosome Preparation and Banding. eLS.
  • Stockert JC, Blázquez-Castro A, Horobin RWJFAoD, Chromatin. Identifying different types of chromatin using Giemsa staining. 2014:25-38.
  • Pederson TJCSHpib. The nucleolus. 2011;3(3):a000638.
  • McKay RJC. The mechanism of G and C banding in mammalian metaphase chromosomes. 1973;44(1):1-14.
  • Shaffer LG, McGowan-Jordan J, Schmid M. ISCN 2013: an international system for human cytogenetic nomenclature (2013): Karger Medical and Scientific Publishers; 2013.
  • Arsham MS, Barch MJ, Lawce HJ. The AGT cytogenetics laboratory manual: John Wiley & Sons; 2017.
  • Zhu JJ, Qi H, Cai LR, Wen XH, Zeng W, Tang GD, et al. C-banding and AgNOR-staining were still effective complementary methods to indentify chromosomal heteromorphisms and some structural abnormalities in prenatal diagnosis. 2019;12:1-11.
  • Trere DJM. AgNOR staining and quantification. 2000;31(2):127-31.
  • Rahman N, Rahman M, Zaman SU. Diagnostic Utility of Modified Method of AgNOR Staining in the Evaluation of Benign and Malignant Effusions. European Journal of Medical and Health Sciences. 2024;6(5):160-9.
  • Nabil A, Sarra F. Q-Banding 2017 [1-3]. Available from: https://faculty.ksu.edu.sa/sites/default/files/q-banding_amor_2017.pdf.
  • Comings DE, Kovacs BW, Avelino E, Harris DCJC. Mechanisms of chromosome banding: V. Quinacrine banding. 1975;50:111-45.
  • Van der Ploeg MJEjohE. Cytochemical nucleic acid research during the twentieth century. 2000;44(1):7.
  • Wyandt HE, Wilson GN, Tonk VS. Human chromosome variation: heteromorphism, polymorphism and pathogenesis: Springer; 2017.
  • Chai H, Li P. Banding cytogenetics. Cytogenetics and molecular cytogenetics: CRC Press; 2022. p. 7-26.
  • Chauhan A. Principle and Techniques of Chromosome Banding: A Primitive Method for Chromosome Analysis. Essentials of Basic and Applied Sciences: Crdeep journals; 2022.
  • Miller OJ, Therman E. Human chromosomes. 4 ed. New York, USA: Springer 2011.

Year 2025, Volume: 11 Issue: 3, 268 - 283, 30.08.2025

Abstract

References

  • Heng J, Heng HH. Karyotype coding: The creation and maintenance of system information for complexity and biodiversity. Biosystems. 2021;208:104476.
  • Witty MJH. Pollen Development, Membranes and Features of the Nucleus in Tradescantia and related genera: A Translation of Wilhelm Hofmeister’s 1848 Paper ‘Ueber die Entwicklung des Pollens.’.15:75-86.
  • Liehr T. Molecular Cytogenetics in the Era of Chromosomics and Cytogenomic Approaches. 2021;12.
  • Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P. Chromosomal DNA and its packaging in the chromatin fiber. Molecular Biology of the Cell 4th edition: Garland Science; 2002.
  • Allison LA. Fundumental molecular biology. Ankara: Palme; 2014.
  • Doğan A, Kumbıçak Z. Cytogenetic studies on some spider species belonging to the family Lycosidae (araneae) distributed in Göreme National Park [Master thesis]. Nevşehir Nevşehir Hacı Bektaş Veli University; 2014.
  • Therman E, Susman M. Human chromosomes: structure, behavior, and effects: Springer Science & Business Media; 2012.
  • Miller OJ, Therman E, Miller OJ, Therman EJHC. The chemistry and packaging of chromosomes. 2001:61-77.
  • Li Y, Agrawal V, Virk RKA, Roth E, Li WS, Eshein A, et al. Analysis of three-dimensional chromatin packing domains by chromatin scanning transmission electron microscopy (ChromSTEM). Scientific Reports. 2022;12(1):12198.
  • Fyodorov DV, Zhou B-R, Skoultchi AI, Bai Y. Emerging roles of linker histones in regulating chromatin structure and function. Nature Reviews Molecular Cell Biology. 2018;19(3):192-206.
  • Saygun S. Comparison of chromosome structures of various flatfish (Pisces, Pleuronectiformes) living in the Black Sea [Master thesis]. Samsun: Ondokuz Mayıs University; 2005.
  • Karyology definition 2024 [Available from: https://www.genome.gov/genetics-glossary/Karyotype.
  • Nadler CF, editor Chromosomal evolution in rodents. Comparative Mammalian Cytogenetics: An International Conference at Dartmouth Medical School Hanover, New Hampshire, July 29—August 2, 1968; 1969: Springer.
  • Madian N, Jayanthi K, Somasundaram D, Suresh SJM. Identifying centromere position of human chromosome images using contour and shape based analysis. 2019;144:243-59.
  • Schweizer D, Ehrendorfer FJPS, Evolution. Giemsa banded karyotypes, systematics, and evolution in Anacyclus (Asteraceae-Anthemideae). 1976;126:107-48.
  • Asadi-Corom F, Mirzaie-Nodoushan H, Calagari MJPGR. Comparative karyological features of several populations of Populus euphratica Oliv., grown under different environmental conditions in Iran. 2024:1-7.
  • Syafriani E, Somala MUA, Triani NJNS, Proceedings T. Biotechnology for Beginner Student. 2021:10-6.
  • Krietenstein N, Abraham S, Venev SV, Abdennur N, Gibcus J, Hsieh T-HS, et al. Ultrastructural details of mammalian chromosome architecture. 2020;78(3):554-65. e7.
  • Nicodemi M, Pombo AJCoicb. Models of chromosome structure. 2014;28:90-5.
  • Macgregor HCJCr. Chromomeres revisited. 2012;20:911-24.
  • Das D. Essential practical handbook of cell biology & genetics, biometry & microbiology: A laboratory manual: Academic Publishers; 2017.
  • Paulson JR, Hudson DF, Cisneros-Soberanis F, Earnshaw WC, editors. Mitotic chromosomes. Seminars in cell & developmental biology; 2021: Elsevier.
  • Navarro AP, Cheeseman IM, editors. Kinetochore assembly throughout the cell cycle. Seminars in cell & developmental biology; 2021: Elsevier.
  • Schleif R. Genetics and molecular biology: The Johns Hopkins University Press; 2023.
  • Chakravarti D, LaBella KA, DePinho RAJC. Telomeres: history, health, and hallmarks of aging. 2021;184(2):306-22.
  • Berns MW, Cheng WKJECR. Are chromosome secondary constrictions nucleolar organizers?: A re-examination using a laser microbeam. 1971;69(1):185-92.
  • Hasterok R, Borowska-Zuchowska N, Robaszkiewicz EJIJoMS. Cytomolecular Organisation of the Nuclear Genome. MDPI; 2022. p. 13028.
  • Thakur J, Packiaraj J, Henikoff S. Sequence, chromatin and evolution of satellite DNA. International journal of molecular sciences. 2021;22(9):4309.
  • O. J. Miller, Therman E. Human Chromosomes: Springer Science & Business Media.; 2011.
  • Emiroğlu Ü. Chromosomes: Basic concepts and mechanisms. Izmir: Ege University Publications 2017.
  • Kumar S, Kiso A, Kithan NAJC-c, molecular strategies for analysing heredity material. IntechOpen L. Chromosome banding and mechanism of chromosome aberrations. 2021:45-60.
  • Sharma A. Chromosome techniques: CRC Press; 2020.
  • Montazerinezhad S, Emamjomeh A, Hajieghrari BJMBR. Chromosomal abnormality, laboratory techniques, tools and databases in molecular Cytogenetics. 2020;47(11):9055-73.
  • Bickmore WA, editor Karyotype Analysis and Chromosome Banding2001.
  • Milani DAQ, Tadi P. Genetics, Chromosome Abnormalities. StatPearls [Internet]: StatPearls Publishing; 2023.
  • Deepthi B, Prayaga AK, Rukmangadha NJJoC. Comparison of modified ultrafast giemsa stain with the standard may grunwald giemsa stain in FNAC of various organs. 2022;39(4):174-9.
  • Dutta U. Essentials of Cytogenetic and Molecular Cytogenetic Laboratory Testing: Cambridge Scholars Publishing; 2022.
  • Huisinga K, Brower-Toland B, Elgin S. The contradictory definitions of heterochromatin: Transcription and silencing. Chromosoma. 2006;115:110-22.
  • Moore CM, Best RG. Chromosome Preparation and Banding. eLS.
  • Stockert JC, Blázquez-Castro A, Horobin RWJFAoD, Chromatin. Identifying different types of chromatin using Giemsa staining. 2014:25-38.
  • Pederson TJCSHpib. The nucleolus. 2011;3(3):a000638.
  • McKay RJC. The mechanism of G and C banding in mammalian metaphase chromosomes. 1973;44(1):1-14.
  • Shaffer LG, McGowan-Jordan J, Schmid M. ISCN 2013: an international system for human cytogenetic nomenclature (2013): Karger Medical and Scientific Publishers; 2013.
  • Arsham MS, Barch MJ, Lawce HJ. The AGT cytogenetics laboratory manual: John Wiley & Sons; 2017.
  • Zhu JJ, Qi H, Cai LR, Wen XH, Zeng W, Tang GD, et al. C-banding and AgNOR-staining were still effective complementary methods to indentify chromosomal heteromorphisms and some structural abnormalities in prenatal diagnosis. 2019;12:1-11.
  • Trere DJM. AgNOR staining and quantification. 2000;31(2):127-31.
  • Rahman N, Rahman M, Zaman SU. Diagnostic Utility of Modified Method of AgNOR Staining in the Evaluation of Benign and Malignant Effusions. European Journal of Medical and Health Sciences. 2024;6(5):160-9.
  • Nabil A, Sarra F. Q-Banding 2017 [1-3]. Available from: https://faculty.ksu.edu.sa/sites/default/files/q-banding_amor_2017.pdf.
  • Comings DE, Kovacs BW, Avelino E, Harris DCJC. Mechanisms of chromosome banding: V. Quinacrine banding. 1975;50:111-45.
  • Van der Ploeg MJEjohE. Cytochemical nucleic acid research during the twentieth century. 2000;44(1):7.
  • Wyandt HE, Wilson GN, Tonk VS. Human chromosome variation: heteromorphism, polymorphism and pathogenesis: Springer; 2017.
  • Chai H, Li P. Banding cytogenetics. Cytogenetics and molecular cytogenetics: CRC Press; 2022. p. 7-26.
  • Chauhan A. Principle and Techniques of Chromosome Banding: A Primitive Method for Chromosome Analysis. Essentials of Basic and Applied Sciences: Crdeep journals; 2022.
  • Miller OJ, Therman E. Human chromosomes. 4 ed. New York, USA: Springer 2011.
There are 54 citations in total.

Details

Primary Language English
Subjects Dental Therapeutics, Pharmacology and Toxicology, Medical Genetics (Excl. Cancer Genetics)
Journal Section Review
Authors

Nihan Küçük Yılmaz 0000-0002-9205-1467

Ceren Börçek Kasurka 0000-0002-5772-9463

Yasemin Esin Aydın 0009-0000-5967-6783

Aleyna Kaya 0009-0000-8448-8338

Publication Date August 30, 2025
Submission Date December 18, 2024
Acceptance Date January 12, 2025
Published in Issue Year 2025 Volume: 11 Issue: 3

Cite

Vancouver Küçük Yılmaz N, Börçek Kasurka C, Aydın YE, Kaya A. Basic chromosome definitions and staining techniques. Mid Blac Sea J Health Sci. 2025;11(3):268-83.

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