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Chromosomal fragile site

{{short description|Cytogenetic feature}}

File:FragileX.png gene in Fragile X syndrome. FMR1 co-localizes with a rare fragile site, visible here as a gap on the long arms of the X chromosome.]]

A chromosomal fragile site is a specific heritable point on a chromosome that tends to form a gap or constriction and may tend to break Sutherland, GR and Hecht, F: Fragile Sites on Human Chromosomes. New York and Oxford: Oxford University Press, 280 pages (1985). when the cell is exposed to partial replication stress.{{Citation | title = The molecular basis of common and rare fragile sites | year = 2005 | journal = Cancer Letters | pages = 13–26 | volume = 232 | issue = 1 | pmid = 16236432 | last1 = Schwartz | first1 = M. | last2 = Zlotorynski | first2 = E. | last3 = Kerem | first3 = B. | doi=10.1016/j.canlet.2005.07.039 }} Based on their frequency, fragile sites are classified as "common" or "rare".{{Citation | title = Human chromosome fragility | year = 2008 | pages = 3–16 | volume = 1779 | issue = 1 | pmid = 18078840 | last1 = Lukusa | first1 = T. | last2 = Fryns | first2 = J.P. | journal = Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms | doi=10.1016/j.bbagrm.2007.10.005}} To date, more than 120 fragile sites have been identified in the human genome.{{Citation | title = Chromosome fragile sites | year = 2007 | journal = Annual Review of Genetics | pages = 169–192 | volume = 41 | pmid = 17608616 | last1 = Durkin | first1 = S.G. | last2 = Glover | first2 = T.W. | doi=10.1146/annurev.genet.41.042007.165900}}

Common fragile sites are considered part of normal chromosome structure and are present in all (or nearly all) individuals in a population. Under normal conditions, most common fragile sites are not prone to spontaneous breaks. Common fragile sites are of interest in cancer studies because they are frequently affected in cancer and they can be found in healthy individuals. Sites FRA3B (harboring the FHIT gene) and FRA16D (harboring the WWOX gene) are two well known examples and have been a major focus of research.

Rare fragile sites are found in less than 5% of the population, and are often composed of two- or three-nucleotide repeats. They are often susceptible to spontaneous breakage during replication, frequently affecting neighboring genes. Clinically, the most important rare fragile site is FRAXA in the FMR1 gene, which is associated with the fragile X syndrome, the most common cause of hereditary intellectual disability.

For a database of fragile sites in human chromosomes, see {{Citation | title = HumCFS: a database of fragile sites in human chromosomes | year = 2019 | journal = BMC Genomics | volume = 9 | last1 = Kumar | first1 = R. | last2 = Nagpal | first2 = G. | last3 = Kumar | first3 = V. | last4 = Usmani | first4 = S.S. | last5 = Agrawal | first5 = P. | last6 = Raghava | first6 = G. | issue = Suppl 9 | page = 985 | doi=10.1186/s12864-018-5330-5 | pmid = 30999860 | pmc = 7402404 | doi-access = free }}

Rare fragile sites

=Classification=

Rare fragile sites (RFSs) are classified into two sub-groups based on the compounds that elicit breakage: folate-sensitive groups (for examples, see {{cite journal|last1=Sutherland|first1=GR |authorlink1=Grant Robert Sutherland |author2=Jacky, PB |author3=Baker, E |author4= Manuel, A |title=Heritable fragile sites on human chromosomes. X. New folate-sensitive fragile sites: 6p23, 9p21, 9q32, and 11q23.|journal=American Journal of Human Genetics|date=May 1983|volume=35|issue=3|pages=432–7|pmid=6859039|pmc=1685660}}), and nonfolate-sensitive groups, which are induced by bromodeoxyuridine (BrdU) or distamycin A,{{cite journal|last1=Sutherland|first1=GR |authorlink1=Grant Robert Sutherland |author2=Baker, E |author3=Seshadri, RS |title=Heritable fragile sites on human chromosomes. V. A new class of fragile site requiring BrdU for expression.|journal=American Journal of Human Genetics|date=Jul 1980|volume=32|issue=4|pages=542–8|pmid=7395866|pmc=1686118}} an antibiotic that preferentially binds to AT-pairs of DNA.{{cite journal|last=Luck|first=G|author2=Zimmer, C |author3=Reinert, KE |author4= Arcamone, F |title=Specific interactions of distamycin A and its analogs with (A-T) rich and (G-C) rich duplex regions of DNA and deoxypolynucleotides.|journal=Nucleic Acids Research|date=Aug 1977|volume=4|issue=8|pages=2655–70|pmid=561949|doi=10.1093/nar/4.8.2655 |pmc=342599}} The folate-sensitive group is characterized by an expansion of CGG repeats,{{cite journal |last1=Balakumaran |first1=BS |last2=Freudenreich |first2=CH |author-link2=Catherine Freudenreich |last3=Zakian |first3=VA |date=Jan 1, 2000 |title=CGG/CCG repeats exhibit orientation-dependent instability and orientation-independent fragility in Saccharomyces cerevisiae. |journal=Human Molecular Genetics |volume=9 |issue=1 |pages=93–100 |doi=10.1093/hmg/9.1.93 |pmid=10587583 |doi-access=free}} while the nonfolate-sensitive group contains many AT-rich minisatellite repeats.{{cite journal|last=Yu|first=S|author2=Mangelsdorf, M |author3=Hewett, D |author4=Hobson, L |author5=Baker, E |author6=Eyre, HJ |author7=Lapsys, N |author8=Le Paslier, D |author9=Doggett, NA |author10=Sutherland, GR |authorlink10=Grant Robert Sutherland |author11=Richards, RI |title=Human chromosomal fragile site FRA16B is an amplified AT-rich minisatellite repeat.|journal=Cell|date=Feb 7, 1997|volume=88|issue=3|pages=367–74|pmid=9039263|doi=10.1016/S0092-8674(00)81875-9|doi-access=free}}

=Mechanisms of instability=

The CGG and AT-rich repeats characteristic of RFSs can form hairpins{{cite journal|last=Gacy|first=AM|author2=Goellner, G |author3=Juranić, N |author4=Macura, S |author5= McMurray, CT |title=Trinucleotide repeats that expand in human disease form hairpin structures in vitro.|journal=Cell|date=May 19, 1995|volume=81|issue=4|pages=533–40|pmid=7758107|doi=10.1016/0092-8674(95)90074-8|doi-access=free}} and other non-B DNA structures that block replication forks and can result in breakage.{{cite journal|last=Wells|first=RD|title=Molecular basis of genetic instability of triplet repeats.|journal=The Journal of Biological Chemistry|date=Feb 9, 1996|volume=271|issue=6|pages=2875–8|pmid=8621672|doi=10.1074/jbc.271.6.2875|doi-access=free}}{{cite journal|last=Zhang|first=Haihua|author2=Freudenreich, Catherine H.|title=An AT-Rich Sequence in Human Common Fragile Site FRA16D Causes Fork Stalling and Chromosome Breakage in S. cerevisiae|journal=Molecular Cell|volume=27|issue=3|pages=367–379|doi=10.1016/j.molcel.2007.06.012|pmid=17679088|pmc=2144737|year=2007}}{{cite journal|last=Aguilera|first=A|author2=Gómez-González, B|title=Genome instability: a mechanistic view of its causes and consequences.|journal=Nature Reviews Genetics|date=Mar 2008|volume=9|issue=3|pages=204–17|pmid=18227811|doi=10.1038/nrg2268|s2cid=14024154}} DNA polymerase has been shown to pause at CTG and CGG triplet repeat sequences, which can result in continual expansion via slippage.{{cite journal|last=Ohshima|first=K.|title=Pausing of DNA Synthesis in Vitro at Specific Loci in CTG and CGG Triplet Repeats from Human Hereditary Disease Genes|journal=Journal of Biological Chemistry|date=10 November 1995|volume=270|issue=45|pages=27014–27021|doi=10.1074/jbc.270.45.27014|pmid=7592950|doi-access=free}}

Common fragile sites

=Classification=

Unlike RFSs, common fragile sites (CFSs) are not the result of nucleotide repeat expansion mutations. They are a part of the normal human genome and are typically stable when not under replicative stress.{{cite journal|last=Smith|first=DI|author2=Huang, H |author3=Wang, L |title=Common fragile sites and cancer (review).|journal=International Journal of Oncology|date=Jan 1998|volume=12|issue=1|pages=187–96|pmid=9454904|doi=10.3892/ijo.12.1.187}} The majority of breakages at CFSs are induced by low doses of the antibiotic aphidicolin (APH).{{cite journal|last=Glover|first=TW|author2=Berger, C |author3=Coyle, J |author4= Echo, B |title=DNA polymerase alpha inhibition by aphidicolin induces gaps and breaks at common fragile sites in human chromosomes.|journal=Human Genetics|year=1984|volume=67|issue=2|pages=136–42|pmid=6430783|doi=10.1007/bf00272988|s2cid=9241289}} Co-treatment with low concentrations of the topoisomerase I inhibitor, camptothecin (CPT), reduces APH-induced breakage.{{cite journal|last=Arlt|first=MF|author2=Glover, TW|title=Inhibition of topoisomerase I prevents chromosome breakage at common fragile sites.|journal=DNA Repair|date=Jun 4, 2010|volume=9|issue=6|pages=678–89|pmid=20413351|doi=10.1016/j.dnarep.2010.03.005|pmc=2896008}} CFS regions are highly conserved in mouse{{cite journal|last=Shiraishi|first=T|author2=Druck, T |author3=Mimori, K |author4=Flomenberg, J |author5=Berk, L |author6=Alder, H |author7=Miller, W |author8=Huebner, K |author9= Croce, CM |title=Sequence conservation at human and mouse orthologous common fragile regions, FRA3B/FHIT and Fra14A2/Fhit.|journal=Proceedings of the National Academy of Sciences of the United States of America|date=May 8, 2001|volume=98|issue=10|pages=5722–7|pmid=11320209|doi=10.1073/pnas.091095898|pmc=33280|bibcode=2001PNAS...98.5722S|doi-access=free}}{{cite journal|last=Krummel|first=KA|author2=Denison, SR |author3=Calhoun, E |author4=Phillips, LA |author5= Smith, DI |title=The common fragile site FRA16D and its associated gene WWOX are highly conserved in the mouse at Fra8E1.|journal=Genes, Chromosomes & Cancer|date=Jun 2002|volume=34|issue=2|pages=154–67|pmid=11979549|doi=10.1002/gcc.10047|s2cid=42821144|doi-access=free}} and other species, including primates, cat, dog, pig, horse, cow, Indian mole rat, and yeast (for review, see ). While CFSs could be a result of higher-order chromosome structure, the conservation throughout species could also indicate that they may have some conserved biological purpose.{{cite journal|last=Schmid|first=M|author2=Ott, G |author3=Haaf, T |author4= Scheres, JM |title=Evolutionary conservation of fragile sites induced by 5-azacytidine and 5-azadeoxycytidine in man, gorilla, and chimpanzee.|journal=Human Genetics|year=1985|volume=71|issue=4|pages=342–50|pmid=4077049|doi=10.1007/bf00388461|s2cid=7765805}}

=Mechanisms of instability=

The instability of CFSs is proposed to stem from late replication: CFSs are likely to initiate proper replication but slow to complete it, introducing breaks from unreplicated regions of DNA. Late-replication may be a result of formation of non-B DNA structures like hairpins and toroids that stall the replication fork in AT rich regions, analogous to the proposed mechanism of rare fragile site instability.{{cite journal|last=Zlotorynski|first=E|author2=Rahat, A |author3=Skaug, J |author4=Ben-Porat, N |author5=Ozeri, E |author6=Hershberg, R |author7=Levi, A |author8=Scherer, SW |author9=Margalit, H |author10= Kerem, B |title=Molecular basis for expression of common and rare fragile sites.|journal=Molecular and Cellular Biology|date=Oct 2003|volume=23|issue=20|pages=7143–51|pmid=14517285|pmc=230307|doi=10.1128/mcb.23.20.7143-7151.2003}} Ataxia-telengiectasia and Rad3 Related (ATR) checkpoint kinase is required for maintaining stability of CFS under both stressed and normal replicating conditions.{{cite journal|last=Casper|first=Anne M.|author2=Nghiem, Paul |author3=Arlt, Martin F. |author4= Glover, Thomas W. |title=ATR Regulates Fragile Site Stability|journal=Cell|date=1 December 2002|volume=111|issue=6|pages=779–789|doi=10.1016/S0092-8674(02)01113-3|pmid=12526805|doi-access=free}} Breakage is reduced after treatment with CPT (camptothecin) (without APH), signifying that CPT also has a necessary role in stabilizing CFSs.

Clinical relevance

Fragile sites are associated with numerous disorders and diseases, both heritable and not. The FRAXA site is perhaps most famous for its role in Fragile X syndrome, but fragile sites are clinically implicated in many other important diseases, such as cancer.

FRA3B and FRA16D lie within the large tumor-suppressor genes, FHIT{{cite journal|last=Zanesi|first=N|author2=Fidanza, V |author3=Fong, LY |author4=Mancini, R |author5=Druck, T |author6=Valtieri, M |author7=Rüdiger, T |author8=McCue, PA |author9=Croce, CM |author10= Huebner, K |title=The tumor spectrum in FHIT-deficient mice.|journal=Proceedings of the National Academy of Sciences of the United States of America|date=Aug 28, 2001|volume=98|issue=18|pages=10250–5|pmid=11517343|doi=10.1073/pnas.191345898|pmc=56947|bibcode=2001PNAS...9810250Z|doi-access=free}} and WWOX,{{cite journal|last=Aqeilan|first=RI |author2=Trapasso, F |author3=Hussain, S |author4=Costinean, S |author5=Marshall, D |author6=Pekarsky, Y |author7=Hagan, JP |author8=Zanesi, N |author9=Kaou, M |author10=Stein, GS |author11=Lian, JB |author12=Croce, CM|title=Targeted deletion of Wwox reveals a tumor suppressor function.|journal=Proceedings of the National Academy of Sciences of the United States of America|date=Mar 6, 2007|volume=104|issue=10|pages=3949–54|pmid=17360458|doi=10.1073/pnas.0609783104|pmc=1820689|bibcode=2007PNAS..104.3949A |doi-access=free }} respectively. High frequency of deletions at breakpoints within these fragile sites has been associated with many cancers, including breast, lung, and gastric cancers (for review, see )

MicroRNA genes, which are preferentially involved in chromosomal alterations, are frequently located at fragile sites.{{cite journal|last=Calin|first=GA |author2=Sevignani, C |author3=Dumitru, CD |author4=Hyslop, T |author5=Noch, E |author6=Yendamuri, S |author7=Shimizu, M |author8=Rattan, S |author9=Bullrich, F |author10=Negrini, M |author11=Croce, CM|title=Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers.|journal=Proceedings of the National Academy of Sciences of the United States of America|date=Mar 2, 2004|volume=101|issue=9|pages=2999–3004|pmid=14973191|doi=10.1073/pnas.0307323101|pmc=365734|bibcode=2004PNAS..101.2999C |doi-access=free }} Chromosomal alterations may lead to deregulation of microRNA, which could be of diagnostic and prognostic significance for cancers.{{cite journal|last=Calin|first=GA|author2=Croce, CM|title=Chromosomal rearrangements and microRNAs: a new cancer link with clinical implications.|journal=The Journal of Clinical Investigation|date=Aug 2007|volume=117|issue=8|pages=2059–66|pmid=17671640|doi=10.1172/JCI32577|pmc=1934569}}

Additionally, the Hepatitis B virus (HBV){{cite journal|last=Jiang|first=S |author2=Yang, Z |author3=Li, W |author4=Li, X |author5=Wang, Y |author6=Zhang, J |author7=Xu, C |author8=Chen, PJ |author8-link=Chen Pei-jer |author9=Hou, J |author10=McCrae, MA |author11=Chen, X |author12=Zhuang, H |author13=Lu, F|title=Re-evaluation of the carcinogenic significance of hepatitis B virus integration in hepatocarcinogenesis.|journal=PLOS ONE|year=2012|volume=7|issue=9|pages=e40363|pmid=22962577|doi=10.1371/journal.pone.0040363|pmc=3433482|bibcode=2012PLoSO...740363J |doi-access=free }} and HPV-16 virus, the strain of human papilloma virus most likely to produce cancer, appear to integrate preferentially in or around fragile sites, and it has been proposed that this is crucial to the development of tumors.{{cite journal|last=Thorland|first=EC|author2=Myers, SL |author3=Gostout, BS |author4= Smith, DI |title=Common fragile sites are preferential targets for HPV16 integrations in cervical tumors.|journal=Oncogene|date=Feb 27, 2003|volume=22|issue=8|pages=1225–37|pmid=12606949|doi=10.1038/sj.onc.1206170|doi-access=free}}{{cite journal|last=Wilke|first=CM|author2=Hall, BK |author3=Hoge, A |author4=Paradee, W |author5=Smith, DI |author6= Glover, TW |title=FRA3B extends over a broad region and contains a spontaneous HPV16 integration site: direct evidence for the coincidence of viral integration sites and fragile sites.|journal=Human Molecular Genetics|date=Feb 1996|volume=5|issue=2|pages=187–95|pmid=8824874|doi=10.1093/hmg/5.2.187|doi-access=free}}

Fragile sites have also been implicated in a variety of syndromes (for a review, see {{cite journal|last=Debacker|first=K|author2=Kooy, RF|title=Fragile sites and human disease.|journal=Human Molecular Genetics|date=Oct 15, 2007|volume=16 Spec No. 2|pages=R150-8|pmid=17567780|doi=10.1093/hmg/ddm136|doi-access=free}}). For example, breakage at or near the FRA11b locus has been implicated in Jacobsen syndrome, which is characterized by loss of part of the long arm of chromosome 11 accompanied by mild mental retardation.{{cite journal|last=Jones|first=C|author2=Penny, L |author3=Mattina, T |author4=Yu, S |author5=Baker, E |author6=Voullaire, L |author7=Langdon, WY |author8=Sutherland, GR |authorlink8=Grant Robert Sutherland |author9=Richards, RI |author10= Tunnacliffe, A |title=Association of a chromosome deletion syndrome with a fragile site within the proto-oncogene CBL2.|journal=Nature|date=Jul 13, 1995|volume=376|issue=6536|pages=145–9|pmid=7603564|doi=10.1038/376145a0|bibcode=1995Natur.376..145J|s2cid=4229039}} The FRAXE site is associated in the development of a form of mental retardation without any distinctive phenotypic features. Seckel syndrome, a genetic disease characterized by low levels of ATR, results in increased instability of chromosomes at fragile sites.{{cite journal|last=Casper|first=AM|author2=Durkin, SG |author3=Arlt, MF |author4= Glover, TW |title=Chromosomal instability at common fragile sites in Seckel syndrome.|journal=American Journal of Human Genetics|date=Oct 2004|volume=75|issue=4|pages=654–60|pmid=15309689|doi=10.1086/422701 |pmc=1182052}}

Fragile sites and affected genes

{{div col|colwidth=30em}}

  • FRA1A
  • FRA1B (DAB1 gene)
  • FRA1C
  • FRA1D
  • FRA1E (DPYD gene)
  • FRA1F
  • FRA1G
  • FRA1H
  • FRA1I
  • FRA1J
  • FRA1K
  • FRA1L
  • FRA1M
  • FRA2A
  • FRA2B
  • FRA2C
  • FRA2D
  • FRA2E
  • FRA2F (LRP1B gene)
  • FRA2G
  • FRA2H
  • FRA2I
  • FRA2J
  • FRA2K
  • FRA2L
  • FRA3A
  • FRA3B (FHIT gene)
  • FRA3C (NAALADL2 gene{{Cite journal|last1=Li|first1=Yilong|last2=Roberts|first2=Nicola D.|last3=Wala|first3=Jeremiah A.|last4=Shapira|first4=Ofer|last5=Schumacher|first5=Steven E.|last6=Kumar|first6=Kiran|last7=Khurana|first7=Ekta|last8=Waszak|first8=Sebastian|last9=Korbel|first9=Jan O.|last10=Haber|first10=James E.|last11=Imielinski|first11=Marcin|date=February 2020|title=Patterns of somatic structural variation in human cancer genomes|journal=Nature|volume=578|issue=7793|pages=112–121|doi=10.1038/s41586-019-1913-9|issn=1476-4687|pmc=7025897|pmid=32025012|bibcode=2020Natur.578..112L }}{{Cite journal|last1=Simpson|first1=Benjamin S.|last2=Pye|first2=Hayley|last3=Whitaker|first3=Hayley C.|date=2021-05-12|title=The oncological relevance of fragile sites in cancer|journal=Communications Biology|volume=4|issue=1|pages=567|doi=10.1038/s42003-021-02020-5|issn=2399-3642|pmc=8115686|pmid=33980983}})
  • FRA3D
  • FRA4A
  • FRA4B
  • FRA4C
  • FRA4D
  • FRA4E
  • FRA4F (GRID2 gene)
  • FRA5A
  • FRA5B
  • FRA5C
  • FRA5D
  • FRA5E
  • FRA5F
  • FRA5G
  • FRA5H (PDE4D gene)
  • FRA6A
  • FRA6B
  • FRA6C
  • FRA6D
  • FRA6E (PARK2 gene)
  • FRA6F
  • FRA6G
  • FRA6H
  • FRA7A
  • FRA7B
  • FRA7C
  • FRA7D
  • FRA7E
  • FRA7F
  • FRA7G
  • FRA7H
  • FRA7I (CNTNAP2 gene)
  • FRA7J
  • FRA7K (IMMP2L gene)
  • FRA8A
  • FRA8B
  • FRA8C
  • FRA8D
  • FRA8E
  • FRA8F
  • FRA9A
  • FRA9B
  • FRA9C
  • FRA9D
  • FRA9E
  • FRA9F
  • FRA9G
  • FRA10A
  • FRA10B
  • FRA10C
  • FRA10D (CTNNA3 gene)
  • FRA10E
  • FRA10F
  • FRA10G
  • FRA11A
  • FRA11B
  • FRA11C
  • FRA11D
  • FRA11E
  • FRA112F (DLG2 gene)
  • FRA11G
  • FRA11H
  • FRA11I
  • FRA12A
  • FRA12B
  • FRA12C
  • FRA12D
  • FRA12E
  • FRA13A (NBEA gene)
  • FRA13B
  • FRA13C
  • FRA13D
  • FRA13E
  • FRA14B (GPHN gene{{cite journal |last1=Zheglo |first1=Diana |last2=Brueckner |first2=Lena M. |last3=Sepman |first3=Olga |last4=Wecht |first4=Elisa M. |last5=Kuligina |first5=Ekaterina |last6=Suspitsin |first6=Evgenij |last7=Imyanitov |first7=Evgenij |last8=Savelyeva |first8=Larissa |title=The FRA14B common fragile site maps to a region prone to somatic and germline rearrangements within the large GPHN gene |journal=Genes, Chromosomes and Cancer |date=May 2019 |volume=58 |issue=5 |pages=284–294 |doi=10.1002/gcc.22706 |pmid=30411419 |doi-access= }})
  • FRA14C
  • FRA15A (RORA gene)
  • FRA16A
  • FRA16B
  • FRA16C
  • FRA16D (WWOX gene)
  • FRA16E
  • FRA17A
  • FRA17B
  • FRA18A
  • FRA18B
  • FRA18C
  • FRA19A
  • FRA19B
  • FRA20A
  • FRA20B
  • FRA22A
  • FRA22B
  • FRAXB
  • FRAXC (IL1RAPL1/DMD genes)
  • FRAXD
  • FRAXA
  • FRAXE
  • FRAXF

{{Div col end}}

References

{{Reflist}}

{{DEFAULTSORT:Fragile Sites}}

Category:Cytogenetics