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::General Information
ID U0001
Creation Date 30 July 1997
Updating Date 23 September 2009
Standard Name Histone 3'UTR stem-loop structure (HSL3)
UTRSite Pattern
r1={au,ua,gc,cg,gu,ug}
0...1 mmmm p1=ggyyy u hhuh a r1~p1 mm 0...3
Random Expectation 0.0 hits/kb
::Taxonomy
UTR Region 3'
Taxon Range Eukaryota
::Description
Description

Metazoan histone 3'-UTR mRNAs, lacking a polyA tail, contain a highly conserved stem-loop structure with a six base stem and a four base loop (HSL3). This stem-loop structure plays a different role in the nucleus and in the cytoplasm. In the nucleus, it is involved in pre-mRNA processing and nucleocytoplasmic transport, whereas in the cytoplasm it enhances translation efficiency and regulates histone mRNA stability. The trans-acting factor which interacts with the 3'-UTR hairpin structure of histone mRNAs is a 31 kDa stem-loop binding protein in mammals (SLBP) present both in nuclei and polyribosomes. In mammals in addition to SLBP, which also stimulate translation, histone mRNA processing involves additional factors including: i) the U7 snRNP, which binds a purine-rich element 10-20 nt downstream of the stem-loop sequence (Histone Downstream Element, HDE);  ii) a 3'->5' exonuclease 3'hExo, which can bind the 3' side of HSL3 both alone and simultaneously with SLBP; and iii) ZFP100 a 100kDa zinc-finger protein recognizing the complex between HSL3 and SLBP (Dominski et al., 2007).

In all histone mRNAs analyzed so far no G has been observed in the four base loop. In all metazoan except C. elegans , there are two invariant urydines in the first and third base of the loop. In C.elegans the first base of the loop is C. Either 5' and 3' flanking sequences are necessary for high affinity binding of SLBP. The 5' flanking sequence consensus is CCAAA and the 3' flanking sequence consensus is ACCCA or ACCA with cleavage occuring after the A. The histone 3'-UTR hairpin structure is peculiar in that the bases of the stem are conserved unlike most functional hairpin motifs where conserved bases are found in single stranded loop regions only. The sequence of the stem and flanking sequences are critical for binding of the SLBP.

Image
::Features
Feature Key HSL3
::Database Cross-references
Link
RFAM: RF00032
::Transcript(s) / Gene(s)
UTR(s)
Description Species Link Ref.
3'UTR in Mus musculus histone 2, H2aa1 (Hist2h2aa1), mRNA Mus musculus UTRef: 3MMUR026879 [U1]
Transcript(s)
Description Species Link Ref.
Mus musculus histone cluster 2, H2aa1 (Hist2h2aa1), mRNA Mus musculus RefSeq: NM_013549 [T1]
Gene(s)
Description Species Link Ref.
histone cluster 2, H2aa1 Mus musculus EntrezGene: 15267 [G1]
::Protein(s)
Binding Protein(s)
Description Species Link Ref.
Stem loop (histone) binding protein Homo sapiens RefSeq: NP_006518 [B1]
three prime histone mRNA exonuclease 1 Homo sapiens RefSeq: NP_699163 [B2]
Interactor(s) of Binding Protein(s)
Description Species Link Ref.
zinc finger protein 473 [ZPF100] Homo sapiens RefSeq: NP_056243 [P1]
::References
ID [1]
Authors Williams A.S. and Marzluff W.F.
Title The sequence of the stem and flanking sequences at the 3'end of histone mRNA are critical determinants for the binding of the stemm-loop binding protein
Citation Nucleic Acid Research vol.23 n.4
Year 1995
ID [2]
Authors Dominski Z, Marzluff WF.
Title Formation of the 3' end of histone mRNA: getting closer to the end.
Citation Gene 2007 Jul 15; 396(2): 373-90
Year 2007
ID [U1]
Authors Williams A.S. and Marzluff W.F.
Title The sequence of the stem and flanking sequences at the 3'end of histone mRNA are critical determinants for the binding of the stemm-loop binding protein
Citation Nucleic Acid Research vol.23 n.4
Year 1995
ID [T1]
Authors Williams A.S. and Marzluff W.F.
Title The sequence of the stem and flanking sequences at the 3'end of histone mRNA are critical determinants for the binding of the stemm-loop binding protein
Citation Nucleic Acid Research vol.23 n.4
Year 1995
ID [G1]
Authors Williams A.S. and Marzluff W.F.
Title The sequence of the stem and flanking sequences at the 3'end of histone mRNA are critical determinants for the binding of the stemm-loop binding protein
Citation Nucleic Acid Research vol.23 n.4
Year 1995
ID [B1]
Authors Martin F, Schaller A, Eglite S, Schümperli D, Müller B.
Title The gene for histone RNA hairpin binding protein is located on human chromosome 4 and encodes a novel type of RNA binding protein.
Citation EMBO J. 1997 Feb 17; 16(4): 769-78
Year 1997
ID [B2]
Authors Dominski Z, Yang XC, Kaygun H, Dadlez M, Marzluff WF.
Title A 3' exonuclease that specifically interacts with the 3' end of histone mRNA.
Citation Mol. Cell 2003 Aug; 12(2): 295-305
Year 2003
ID [P1]
Authors Dominski Z, Marzluff WF.
Title Formation of the 3' end of histone mRNA: getting closer to the end.
Citation Gene 2007 Jul 15; 396(2): 373-90
Year 2007