Nucleotide sequences of two soybean U1 snRNA genes

Nucleic Acids Research

Volume 16 Number 9 1988 Nucleotide sequences of two soybean Ul snRNA genes Vicky L.van Santen, William Swain' and Richard A.Spritz

Laboratory of Genetics, 445 Henry Mall, University of Wisconsin, Madison, WI 53706 and 1Agracetus, 8520 University Green, Middleton, WI 53562, USA Submitted February 4, 1988 Accession nos X06809 and X06810

Southern blot analyses show that the soybean genome contains many Ul snRNA genes, both in tandem arrays and as isolated genes. We have cloned and sequenced two soybean Ul snRNA genes, Ula and Ulb, which represent distinct multicopy tandem repeat elements. Sequence analysis of the first 46 nt of soybean embryo protoplast Ul snRNA by primer extension shows that sequences corresponding to Ula and Ulb are present in approximately equal proportions. Soybean Ula and Ulb snRNA sequences, shown aligned to maximize homolgy, are both very similar to common bean Ul snRNA (1). Plus signs indicate sequences common to all three genes; dots indicate bases identical between the two soybean genes. The predicted secondary structure and sequences of the single-stranded 5' end, loops (indicated by Roman numerals in brackets), and Sm binding site are virtually identical to those of other Ul snRNAs (1). The 5' flanking regions of the two soybean Ul snRNA genes exhibit 71% homology, mostly concentrated in blocks of identity. A "TATAAA" sequence occurs 3126 bases 5' to both genes. Blocks of sequences shared by common bean Ul and soybean Ula and Ul b snRNA genes (indicated by + in the figure) occur as far as 228 bases 5' to the Ul snRNA gene. One shared sequence (TCCCACATCG, underlined in figure) also occurs 5' to several Arabidopsis thaliana U2 snRNA genes and is required for their expression (2). However, we have been unable to detect transcription of the cloned soybean Ula and Ulb genes when introduced into soybean embryo or tobacco leaf protoplasts. ULla

ATACCCGATTCATTATTAGTTGATG-GAAATTAAACCTATATAATCTTGATTCCACTGGTAGTATAATAACAA--AMCACATCTTCTA ---------

U lb

TTTTGAACACTCAAT;CA TtATTGGTTGAAATTAAACCTATA--ATCTTGATTCCACTTOTAGTAACTGATTCTGGAACGCAAATTCTTCCGACGTTA

.

.. . ................... ..... ................ .

Ula

---GTATAOTTCCACTTGATTOTAOTCTTOTTTAAACCATCTTAT ------------cGTAGcCTTTGAAGTAcTcTOCcCAAA-AAATcCcAcATcGAA

U lb

GATGTATAGTTCCACTTAGACACACATCAAGTCAGAACTATTTTACTGTACGTAOCCTTGOTACTCTTTACATCAA

Ula Ulb

C I I 4 5' terminus CAGASTTTGTCAGAGTAGAAaGOAGOATGACCTATAAATTAAGASTOTTATCACATTOCAACTATCTTACCTGaACOGGaTCAATOGATOATCAAGAAGG +.-++4++ 4.++ . 4+ .. .+.. +++.+. . +++ +.... . +...+.* -++++++++++++++++++++++++++++++++*+++++ AAGASTTTGCTAGAGTAACAAAGAGAATACACTATuAACTOAGACGTOTAACCCATTOCAACATACTTACCTGGACOGGGGTCAATOGATGATCAATAAGO

Uia

m II I III)] I Ss TCCATGGCCTAaGOAAGTAACCTCCATTOCACTOAGGAaaOOTGCCTTTCTAAGGTCTOTCCAAGTGACAGAGCCTACOTCATAATTTOTOGTAGTOGaG

Ulb

TCCATGGCCTAGGGAAGTAACCTCCATTocACTTAGaAGaaGTaCTTTCCTAAGGTCTGCCCAAGTaaCAGAGCCTACGTCATAATTTaTToGAaTaGaG

Ula

....t.. [IV) 3' t-rinus OCCTOCOTCOCOCGGCCCCTTTCAATACAGCTTATCGATTCTATCTTTATAGGTAATACATGATTTGATGSTTT

Vib

OCTTGCGTTCGCGCAGCCCCTTCCAATTTTAT -T-------TTTCAAGTTTTTTATTTGAGGAGTTAGATAGGCATGTTTCCTGTTTTGTTGCTTAAAGT

Ula

TCTATTTCTATTGAAATOAAAATATATATCATAACTCACGCCGTCTCTCCOTTGTTGGTTTAA .. ...... .564 ATCCOTTTGATT?GGTTTAATOATOTGAOCCTAAGATAGCTT

++++++++......

.

. ..

.

. 4+4 +

. +..........+.......... . .

44

.++ .......... ....... ....

....

Ulb

7.4+4+4+4+4..+ ... .

44*

..

...

4

100

200

300

++++++++++++++++++++++++ 400

----

TTTTACTCACTGOCAC

......

500

.....

REFERENCES 1. van Santen,V.L. and Spritz,R.A. (1987) Proc. Natl. Acad. Sci. USA 84, 9094-9098. 2. Vankan,P. and Filipowicz,W. (1988) EMBO J. 7, in press.

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