Heterogeneous ribonucleoprotein particle

Heterogeneous nuclear ribonucleoproteins (hnRNPs) are complexes of RNA and protein present in the cell nucleus during gene transcription and subsequent post-transcriptional modification of the newly synthesized RNA (pre-mRNA). The presence of the proteins bound to a pre-mRNA molecule serves as a signal that the pre-mRNA is not yet fully processed and therefore not ready for export to the cytoplasm. ^[1] Since most mature RNA is exported from the nucleus relatively quickly, most RNA-binding protein in the nucleus exist as heterogeneous ribonucleoprotein particles. After splicing has occurred, the proteins remain bound to spliced introns and target them for degradation.

hnRNPs are also integral to the 40S subunit of the ribosome and therefore important for the translation of mRNA in the cytoplasm. ^[2] However, hnRNPs also have their own nuclear localization sequences (NLS) and are therefore found mainly in the nucleus. Though it is known that a few hnRNPs shuttle between the cytoplasm and nucleus, immunofluorescence microscopy with hnRNP-specific antibodies shows nucleoplasmic localization of these proteins with little staining in the nucleolus or cytoplasm. ^[3] This is likely because of its major role in binding to newly transcribed RNAs. High-resolution immunoelectron microscopy has shown that hnRNPs localize predominantly to the border regions of chromatin, where it has access to these nascent RNAs. ^[4]

The proteins involved in the hnRNP complexes are collectively known as heterogeneous ribonucleoproteins. They include protein K and polypyrimidine tract-binding protein (PTB), which is regulated by phosphorylation catalyzed by protein kinase A and is responsible for suppressing RNA splicing at a particular exon by blocking access of the spliceosome to the polypyrimidine tract. ^{[5] : 326} hnRNPs are also responsible for strengthening and inhibiting splice sites by making such sites more or less accessible to the spliceosome. ^[6] Cooperative interactions between attached hnRNPs may encourage certain splicing combinations while inhibiting others. ^[7]

Role in cell cycle and DNA damage

hnRNPs affect several aspects of the cell cycle by recruiting, splicing, and co-regulating certain cell cycle control proteins. Much of hnRNPs' importance to cell cycle control is evidenced by its role as an oncogene, in which a loss of its functions results in various common cancers. Often, misregulation by hnRNPs is due to splicing errors, but some hnRNPs are also responsible for recruiting and guiding the proteins themselves, rather than just addressing nascent RNAs.

BRCA1

hnRNP C is a key regulator of the BRCA1 and BRCA2 genes. In response to ionizing radiation, hnRNP C partially localizes to the site of DNA damage, and when depleted, S-phase progression of the cell is impaired. ^[8] Additionally, BRCA1 and BRCA2 levels fall when hnRNP C is lost. BRCA1 and BRCA2 are crucial tumor-suppressor genes which are strongly implicated in breast cancers when mutated. BRCA1 in particular causes G2/M cell cycle arrest in response to DNA damage via the CHEK1 signaling cascade. ^[9] hnRNP C is important for the proper expression of other tumor suppressor genes including RAD51 and BRIP1 as well. Through these genes, hnRNP is necessary to induce cell-cycle arrest in response to DNA damage by ionizing radiation. ^[7]

HER2

HER2 is overexpressed in 20-30% of breast cancers and is commonly associated with poor prognosis. It is therefore an oncogene whose differently spliced variants have been shown to have different functions. Knocking down hnRNP H1 was shown to increase the amount of an oncogenic variant Δ16HER2. ^[10] HER2 is an upstream regulator of cyclin D1 and p27, and its overexpression leads to the deregulation of the G1/S checkpoint. ^[11]

p53

hnRNPs also play a role in DNA damage response in coordination with p53. hnRNP K is rapidly induced after DNA damage by ionizing radiation. It cooperates with p53 to induce the activation of p53 target genes, thus activating cell-cycle checkpoints. ^[12] p53 itself is an important tumor-suppressor gene sometimes known by the epithet “the guardian of the genome.” hnRNP K’s close association with p53 demonstrates its importance in DNA damage control.

p53 regulates a large group of RNAs that are not translated into protein, called large intergenic noncoding RNAs (lincRNAs). p53 suppression of genes is often carried out by a number of these lincRNAs, which in turn have been shown to act though hnRNP K. Through physical interactions with these molecules, hnRNP K is targeted to genes and transmits p53 regulation, thus acting as a key repressor within the p53-dependent transcriptional pathway. ^{[13] [14]}

Functions

hnRNP serves a variety of processes in the cell, some of which include:

1. Preventing the folding of pre-mRNA into secondary structures that may inhibit its interactions with other proteins.
2. Possible association with the splicing apparatus.
3. Transport of mRNA out of the nucleus.

The association of a pre-mRNA molecule with a hnRNP particle prevents formation of short secondary structures dependent on base pairing of complementary regions, thereby making the pre-mRNA accessible for interactions with other proteins.

CD44 Regulation

hnRNP has been shown to regulate CD44, a cell-surface glycoprotein, through splicing mechanisms. CD44 is involved in cell-cell interactions and has roles in cell adhesion and migration. Splicing of CD44 and the functions of the resulting isoforms are different in breast cancer cells, and when knocked down, hnRNP reduced both cell viability and invasiveness. ^[15]

Telomeres

Several hnRNPs interact with telomeres, which protect the ends of chromosomes from deterioration and are often associated with cell longevity. hnRNP D associates with the G-rich repeat region of the telomeres, possibly stabilizing the region from secondary structures which would inhibit telomere replication. ^[16]

hnRNP has also been shown to interact with telomerase, the protein responsible for elongating telomeres and prevent their degradation. hnRNPs C1 and C2 associate with the RNA component of telomerase, which improves its ability to access the telomere. ^{[17] [18] [19]}

Examples

Human genes encoding heterogeneous nuclear ribonucleoproteins include:

• HNRNPA0, HNRNPA1, HNRNPA1L1, HNRNPA1L2, HNRNPA3, HNRNPA2B1
• HNRNPAB
• HNRNPB1
• HNRNPC, HNRNPCL1
• HNRNPD (AUF1), HNRPDL
• HNRNPF
• HNRNPG (RBMX)
• HNRNPH1, HNRNPH2, HNRNPH3
• HNRNPI (PTB)
• HNRNPK
• HNRNPL, HNRPLL
• HNRNPM
• HNRNPP2 (FUS/TLS)
• HNRNPR
• HNRNPQ (SYNCRIP)
• HNRNPU, HNRNPUL1, HNRNPUL2, HNRNPUL3
• FMR1 ^[20]

See also

• Messenger RNP: complex between mRNA and protein(s) present in nucleus

References

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2. Beyer, Ann L.; Christensen, Mark E.; Walker, Barbara W.; LeStourgeon, Wallace M. (1977). "Identification and characterization of the packaging proteins of core 40S hnRNP particles". Cell. 11 (1): 127–138. doi:10.1016/0092-8674(77)90323-3. PMID   872217. S2CID   41245800.
3. Dreyfuss, Gideon; Matunis, Michael J.; Pinol-Roma, Serafin; Burd, Christopher G. (1993-06-01). "hnRNP Proteins and the Biogenesis of mRNA". Annual Review of Biochemistry. 62 (1): 289–321. doi:10.1146/annurev.bi.62.070193.001445. ISSN   0066-4154. PMID   8352591.
4. Fakan, S.; Leser, G.; Martin, T. E. (January 1984). "Ultrastructural distribution of nuclear ribonucleoproteins as visualized by immunocytochemistry on thin sections". The Journal of Cell Biology. 98 (1): 358–363. doi:10.1083/jcb.98.1.358. ISSN   0021-9525. PMC   2113018 . PMID   6231300.
5. Matsudaira PT, Lodish HF, Berk A, Kaiser C, Krieger M, Scott MP, Bretscher A, Ploegh H (2008). Molecular cell biology. San Francisco: W.H. Freeman. ISBN   978-0-7167-7601-7.
6. Matlin, Arianne J.; Clark, Francis; Smith, Christopher W. J. (2005). "Understanding alternative splicing: towards a cellular code". Nature Reviews Molecular Cell Biology. 6 (5): 386–398. doi:10.1038/nrm1645. ISSN   1471-0080. PMID   15956978. S2CID   14883495.
7. Martinez-Contreras, Rebeca; Cloutier, Philippe; Shkreta, Lulzim; Fisette, Jean-François; Revil, Timothée; Chabot, Benoit (2007). "HNRNP Proteins and Splicing Control" . Alternative Splicing in the Postgenomic Era. Advances in Experimental Medicine and Biology. Vol. 623. pp.  123–147. doi:10.1007/978-0-387-77374-2_8. ISBN   978-0-387-77373-5. ISSN   0065-2598. PMID   18380344.
8. Anantha, Rachel W.; Alcivar, Allen L.; Ma, Jianglin; Cai, Hong; Simhadri, Srilatha; Ule, Jernej; König, Julian; Xia, Bing (2013-04-09). "Requirement of Heterogeneous Nuclear Ribonucleoprotein C for BRCA Gene Expression and Homologous Recombination". PLOS ONE. 8 (4): e61368. Bibcode:2013PLoSO...861368A. doi: 10.1371/journal.pone.0061368 . ISSN   1932-6203. PMC   3621867 . PMID   23585894.
9. Yoshida, Kiyotsugu; Miki, Yoshio (November 2004). "Role of BRCA1 and BRCA2 as regulators of DNA repair, transcription, and cell cycle in response to DNA damage". Cancer Science. 95 (11): 866–871. doi:10.1111/j.1349-7006.2004.tb02195.x. ISSN   1347-9032. PMC   11159131 . PMID   15546503. S2CID   24297965.
10. Gautrey, Hannah; Jackson, Claire; Dittrich, Anna-Lena; Browell, David; Lennard, Thomas; Tyson-Capper, Alison (2015-10-03). "SRSF3 and hnRNP H1 regulate a splicing hotspot of HER2 in breast cancer cells". RNA Biology. 12 (10): 1139–1151. doi:10.1080/15476286.2015.1076610. ISSN   1547-6286. PMC   4829299 . PMID   26367347.
11. Moasser, M M (2007). "The oncogene HER2: its signaling and transforming functions and its role in human cancer pathogenesis". Oncogene. 26 (45): 6469–6487. doi:10.1038/sj.onc.1210477. ISSN   1476-5594. PMC   3021475 . PMID   17471238.
12. Moumen, Abdeladim; Masterson, Philip; O'Connor, Mark J.; Jackson, Stephen P. (2005). "hnRNP K: An HDM2 Target and Transcriptional Coactivator of p53 in Response to DNA Damage". Cell. 123 (6): 1065–1078. doi: 10.1016/j.cell.2005.09.032 . PMID   16360036. S2CID   16756766. (Retracted, see doi:10.1016/j.cell.2024.10.008, PMID   39389056 . If this is an intentional citation to a retracted paper, please replace {{ retracted |...}} with {{ retracted |...|intentional=yes}}.)
13. Huarte, Maite; Guttman, Mitchell; Feldser, David; Garber, Manuel; Koziol, Magdalena J.; Kenzelmann-Broz, Daniela; Khalil, Ahmad M.; Zuk, Or; Amit, Ido (2010). "A Large Intergenic Noncoding RNA Induced by p53 Mediates Global Gene Repression in the p53 Response". Cell. 142 (3): 409–419. doi:10.1016/j.cell.2010.06.040. PMC   2956184 . PMID   20673990.
14. Sun, Xinghui; Ali, Mohamed Sham Shihabudeen Haider; Moran, Matthew (2017-09-01). "The role of interactions of long non-coding RNAs and heterogeneous nuclear ribonucleoproteins in regulating cellular functions". Biochemical Journal. 474 (17): 2925–2935. doi:10.1042/bcj20170280. ISSN   0264-6021. PMC   5553131 . PMID   28801479.
15. Loh, Tiing Jen; Moon, Heegyum; Cho, Sunghee; Jang, Hana; Liu, Yong Chao; Tai, Hongmei; Jung, Da-Woon; Williams, Darren R.; Kim, Hey-Ran (September 2015). "CD44 alternative splicing and hnRNP A1 expression are associated with the metastasis of breast cancer". Oncology Reports. 34 (3): 1231–1238. doi: 10.3892/or.2015.4110 . ISSN   1791-2431. PMID   26151392.
16. Eversole, A.; Maizels, N. (August 2000). "In vitro properties of the conserved mammalian protein hnRNP D suggest a role in telomere maintenance". Molecular and Cellular Biology. 20 (15): 5425–5432. doi:10.1128/mcb.20.15.5425-5432.2000. ISSN   0270-7306. PMC   85994 . PMID   10891483.
17. Ford, L. P.; Suh, J. M.; Wright, W. E.; Shay, J. W. (December 2000). "Heterogeneous nuclear ribonucleoproteins C1 and C2 associate with the RNA component of human telomerase". Molecular and Cellular Biology. 20 (23): 9084–9091. doi:10.1128/mcb.20.23.9084-9091.2000. ISSN   0270-7306. PMC   86561 . PMID   11074006.
18. Ford, Lance P.; Wright, Woodring E.; Shay, Jerry W. (2002-01-21). "A model for heterogeneous nuclear ribonucleoproteins in telomere and telomerase regulation". Oncogene. 21 (4): 580–583. doi:10.1038/sj.onc.1205086. ISSN   0950-9232. PMID   11850782.
19. Görlach, M.; Burd, C. G.; Dreyfuss, G. (1994-09-16). "The determinants of RNA-binding specificity of the heterogeneous nuclear ribonucleoprotein C proteins". The Journal of Biological Chemistry. 269 (37): 23074–23078. doi: 10.1016/S0021-9258(17)31621-6 . ISSN   0021-9258. PMID   8083209.
20. Dityatev, Alexander; El-Husseini, Alaa (2006-11-24). Molecular Mechanisms of Synaptogenesis. Springer. ISBN   9780387325620.

Further reading

• Xie J, Lee JA, Kress TL, Mowry KL, Black DL (July 2003). "Protein kinase A phosphorylation modulates transport of the polypyrimidine tract-binding protein". Proc. Natl. Acad. Sci. U.S.A. 100 (15): 8776–81. Bibcode:2003PNAS..100.8776X. doi: 10.1073/pnas.1432696100 . PMC   166389 . PMID   12851456.
• Geuens T, Delphine B, Timmerman V (August 2016). "The hnRNP Family: Insights into Their Role in Health and Disease". Human Genetics. 135 (8): 851–67. doi:10.1007/s00439-016-1683-5. PMC   4947485 . PMID   27215579.
• Takimoto M, Tomonaga T, Matunis M, et al. (August 1993). "Specific binding of heterogeneous ribonucleoprotein particle protein K to the human c-myc promoter, in vitro". J. Biol. Chem. 268 (24): 18249–58. doi: 10.1016/S0021-9258(17)46837-2 . hdl: 2115/72478 . PMID   8349701.
• Watson, James D. (2004). Molecular biology of the gene. San Francisco: Pearson/Benjamin Cummings. pp. ch. 9 and 10. ISBN   978-0-8053-4635-0.