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Aspegren, A., Hinas, A., Larsson, P., Larsson, A., Soderbom, F., (2004) ' Novel non-coding RNAs in Dictyostelium discoideum and their expression during development. ' Nucleic Acids Res 32 4646-56

 

Abstract:The quest for non-coding RNAs (ncRNAs) in the last few years has revealed a surprisingly large number of small RNAs belonging to previously known as well as entirely novel classes. Computational and experimental approaches have uncovered new ncRNAs in all kingdoms of life. In this work, we used a shotgun cloning approach to construct full-length cDNA libraries of small RNAs from the eukaryotic model organism Dictyostelium discoideum. Interestingly, two entirely novel classes of RNAs were identified of which one is developmentally regulated. The RNAs within each class share conserved 5'- and 3'-termini that can potentially form stem structures. RNAs of both classes show predominantly cytoplasmic localization. In addition, based on conserved structure and/or sequence motifs, several of the identified ncRNAs could be divided into classes known from other organisms, e.g. 18 small nucleolar RNA candidates (17 box C/D, of which a few are developmentally regulated, and one box H/ACA). Two ncRNAs showed a high degree of similarity to the small nuclear U2 RNA and signal recognition particle RNA (SRP RNA), respectively. Furthermore, the majority of the regions upstream of the sequences encoding the isolated RNAs share conserved motifs that may constitute new promoter elements.
Status:	epublish	Type:	Journal article	Source:	PUBMED	PubMed ID:	15333696

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	Genes addressed in this paper
	r21	r22	r23A	r23B	r23C	r24A	r24B	r25
Topics in this paper
RNA Levels and Processing	X	X	X	X	X	X	X	X
Non-mammalian Gene Related
DNA/RNA Sequence Features	X	X	X	X	X	X	X	X
Cellular Location	X	X	X	X	X	X	X	X
Substrates/Ligands/Cofactors
Synonym
Function/Process

	Genes addressed in this paper
	r26	r28	r29	r30	r31	r32	r33	r34
Topics in this paper
RNA Levels and Processing	X	X	X	X	X	X	X	X
Non-mammalian Gene Related
DNA/RNA Sequence Features	X	X	X	X	X	X	X	X
Cellular Location	X	X	X	X	X	X	X	X
Substrates/Ligands/Cofactors
Synonym
Function/Process

	Genes addressed in this paper
	r35	r36	r41	r42	r43	r44	r45	r46
Topics in this paper
RNA Levels and Processing	X	X
Non-mammalian Gene Related			X	X	X	X	X	X
DNA/RNA Sequence Features	X	X	X	X	X	X	X	X
Cellular Location	X	X
Substrates/Ligands/Cofactors
Synonym
Function/Process

	Genes addressed in this paper
	r47	r48	r49	r50	r51	r52	r53	r54
Topics in this paper
RNA Levels and Processing
Non-mammalian Gene Related	X	X	X	X	X	X	X	X
DNA/RNA Sequence Features	X	X	X	X	X	X	X	X
Cellular Location
Substrates/Ligands/Cofactors
Synonym
Function/Process

	Genes addressed in this paper
	r55	r56	r57	r58	r59	r60	r61	r62
Topics in this paper
RNA Levels and Processing
Non-mammalian Gene Related	X	X	X	X	X	X	X	X
DNA/RNA Sequence Features	X	X	X	X	X	X	X	X
Cellular Location
Substrates/Ligands/Cofactors
Synonym
Function/Process

	Genes addressed in this paper
	rnu2a	rnu2b	rnu2c	sno1	sno10	sno11a	sno11b	sno12
Topics in this paper
RNA Levels and Processing	X	X	X	X	X	X	X	X
Non-mammalian Gene Related
DNA/RNA Sequence Features				X	X	X	X	X
Cellular Location	X	X	X
Substrates/Ligands/Cofactors				X
Synonym	X	X	X	X	X	X	X	X
Function/Process				X

	Genes addressed in this paper
	sno13	sno14	sno15	sno16	sno17	sno18	sno2	sno3
Topics in this paper
RNA Levels and Processing	X	X	X	X	X	X	X	X
Non-mammalian Gene Related
DNA/RNA Sequence Features	X	X	X	X	X	X	X	X
Cellular Location
Substrates/Ligands/Cofactors
Synonym	X	X	X	X	X	X	X	X
Function/Process

	Genes addressed in this paper
	sno4	sno5	sno6	sno7	sno8	sno9	srpA	srpB
Topics in this paper
RNA Levels and Processing	X	X	X	X	X	X	X	X
Non-mammalian Gene Related
DNA/RNA Sequence Features	X	X	X	X	X	X	X	X
Cellular Location
Substrates/Ligands/Cofactors
Synonym	X	X	X	X	X	X	X	X
Function/Process