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pY RNA1-s2: a highly retina-enriched small RNA that selectively binds to Matrin 3 (Matr3).

Yamazaki F, Kim HH, Lau P, Hwang CK, Iuvone PM, Klein D, Clokie SJ - PLoS ONE (2014)

Bottom Line: In contrast, pY RNA1-s1 does not bind these proteins.Hypothetically, pY RNA1-S2 might act to modulate cellular function through this molecular mechanism.The retinal enrichment of pY RNA1-s2 provides reason to suspect that the pY RNA1-s2/Matr3 interaction could play a role in vision.

View Article: PubMed Central - PubMed

Affiliation: Section on Neuroendocrinology, Program in Developmental Endocrinology and Genetics, The Eunice Shriver Kennedy National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America.

ABSTRACT
The purpose of this study was to expand our knowledge of small RNAs, which are known to function within protein complexes to modulate the transcriptional output of the cell. Here we describe two previously unrecognized, small RNAs, termed pY RNA1-s1 and pY RNA1-s2 (processed Y RNA1-stem -1 and -2), thereby expanding the list of known small RNAs. pY RNA1-s1 and pY RNA1-s2 were discovered by RNA sequencing and found to be 20-fold more abundant in the retina than in 14 other rat tissues. Retinal expression of pY RNAs is highly conserved, including expression in the human retina, and occurs in all retinal cell layers. Mass spectrometric analysis of pY RNA1-S2 binding proteins in retina indicates that pY RNA1-s2 selectively binds the nuclear matrix protein Matrin 3 (Matr3) and to a lesser degree to hnrpul1 (heterogeneous nuclear ribonucleoprotein U-like protein). In contrast, pY RNA1-s1 does not bind these proteins. Accordingly, the molecular mechanism of action of pY RNA1-s2 is likely be through an action involving Matr3; this 95 kDa protein has two RNA recognition motifs (RRMs) and is implicated in transcription and RNA-editing. The high affinity binding of pY RNA1-s2 to Matr3 is strongly dependent on the sequence of the RNA and both RRMs of Matr3. Related studies also indicate that elements outside of the RRM region contribute to binding specificity and that phosphorylation enhances pY RNA-s2/Matr3 binding. These observations are of significance because they reveal that a previously unrecognized small RNA, pY RNA1-s2, binds selectively to Matr3. Hypothetically, pY RNA1-S2 might act to modulate cellular function through this molecular mechanism. The retinal enrichment of pY RNA1-s2 provides reason to suspect that the pY RNA1-s2/Matr3 interaction could play a role in vision.

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Tissue specific expression of pY RNA1-s2.Northern blotting of RNA extracted from the indicated tissue obtained during the Day (ZT 7) and Night (ZT 19). Tissues from three rats were pooled and RNA was extracted as described in “Materials and Methods”. Equal amounts (1 µg) of total RNA were separated on 15% TBE-Urea polyacrylamide gels, transferred and chemically cross-linked to the membrane, followed by probing with an LNA™-probe, designed against pY RNA1-s2. For further details see “Materials and Methods”. The upper panel; full-length Y RNA; middle panel, pY RNA1-s2; lower panel, U6 as loading control. This analysis was repeated two more times with similar results.
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pone-0088217-g002: Tissue specific expression of pY RNA1-s2.Northern blotting of RNA extracted from the indicated tissue obtained during the Day (ZT 7) and Night (ZT 19). Tissues from three rats were pooled and RNA was extracted as described in “Materials and Methods”. Equal amounts (1 µg) of total RNA were separated on 15% TBE-Urea polyacrylamide gels, transferred and chemically cross-linked to the membrane, followed by probing with an LNA™-probe, designed against pY RNA1-s2. For further details see “Materials and Methods”. The upper panel; full-length Y RNA; middle panel, pY RNA1-s2; lower panel, U6 as loading control. This analysis was repeated two more times with similar results.

Mentions: The relative abundance of pY RNA1-s2 was determined using Northern blot analysis of fourteen neuronal and peripheral rat tissues (Figure 2). The LNA probe used for this purpose specifically recognizes the sequence of pY RNA1-s2 and the full length Y RNA1 parent. The abundance of full length Y RNA1 was relatively similar among the 14 tissues examined, in contrast to the processed form: pY RNA1-s2, which was >20 times more abundant in retina (Figure 2). Significant night/day difference in the abundance of pY RNA1-s2 abundance was not observed.


pY RNA1-s2: a highly retina-enriched small RNA that selectively binds to Matrin 3 (Matr3).

Yamazaki F, Kim HH, Lau P, Hwang CK, Iuvone PM, Klein D, Clokie SJ - PLoS ONE (2014)

Tissue specific expression of pY RNA1-s2.Northern blotting of RNA extracted from the indicated tissue obtained during the Day (ZT 7) and Night (ZT 19). Tissues from three rats were pooled and RNA was extracted as described in “Materials and Methods”. Equal amounts (1 µg) of total RNA were separated on 15% TBE-Urea polyacrylamide gels, transferred and chemically cross-linked to the membrane, followed by probing with an LNA™-probe, designed against pY RNA1-s2. For further details see “Materials and Methods”. The upper panel; full-length Y RNA; middle panel, pY RNA1-s2; lower panel, U6 as loading control. This analysis was repeated two more times with similar results.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3928194&req=5

pone-0088217-g002: Tissue specific expression of pY RNA1-s2.Northern blotting of RNA extracted from the indicated tissue obtained during the Day (ZT 7) and Night (ZT 19). Tissues from three rats were pooled and RNA was extracted as described in “Materials and Methods”. Equal amounts (1 µg) of total RNA were separated on 15% TBE-Urea polyacrylamide gels, transferred and chemically cross-linked to the membrane, followed by probing with an LNA™-probe, designed against pY RNA1-s2. For further details see “Materials and Methods”. The upper panel; full-length Y RNA; middle panel, pY RNA1-s2; lower panel, U6 as loading control. This analysis was repeated two more times with similar results.
Mentions: The relative abundance of pY RNA1-s2 was determined using Northern blot analysis of fourteen neuronal and peripheral rat tissues (Figure 2). The LNA probe used for this purpose specifically recognizes the sequence of pY RNA1-s2 and the full length Y RNA1 parent. The abundance of full length Y RNA1 was relatively similar among the 14 tissues examined, in contrast to the processed form: pY RNA1-s2, which was >20 times more abundant in retina (Figure 2). Significant night/day difference in the abundance of pY RNA1-s2 abundance was not observed.

Bottom Line: In contrast, pY RNA1-s1 does not bind these proteins.Hypothetically, pY RNA1-S2 might act to modulate cellular function through this molecular mechanism.The retinal enrichment of pY RNA1-s2 provides reason to suspect that the pY RNA1-s2/Matr3 interaction could play a role in vision.

View Article: PubMed Central - PubMed

Affiliation: Section on Neuroendocrinology, Program in Developmental Endocrinology and Genetics, The Eunice Shriver Kennedy National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America.

ABSTRACT
The purpose of this study was to expand our knowledge of small RNAs, which are known to function within protein complexes to modulate the transcriptional output of the cell. Here we describe two previously unrecognized, small RNAs, termed pY RNA1-s1 and pY RNA1-s2 (processed Y RNA1-stem -1 and -2), thereby expanding the list of known small RNAs. pY RNA1-s1 and pY RNA1-s2 were discovered by RNA sequencing and found to be 20-fold more abundant in the retina than in 14 other rat tissues. Retinal expression of pY RNAs is highly conserved, including expression in the human retina, and occurs in all retinal cell layers. Mass spectrometric analysis of pY RNA1-S2 binding proteins in retina indicates that pY RNA1-s2 selectively binds the nuclear matrix protein Matrin 3 (Matr3) and to a lesser degree to hnrpul1 (heterogeneous nuclear ribonucleoprotein U-like protein). In contrast, pY RNA1-s1 does not bind these proteins. Accordingly, the molecular mechanism of action of pY RNA1-s2 is likely be through an action involving Matr3; this 95 kDa protein has two RNA recognition motifs (RRMs) and is implicated in transcription and RNA-editing. The high affinity binding of pY RNA1-s2 to Matr3 is strongly dependent on the sequence of the RNA and both RRMs of Matr3. Related studies also indicate that elements outside of the RRM region contribute to binding specificity and that phosphorylation enhances pY RNA-s2/Matr3 binding. These observations are of significance because they reveal that a previously unrecognized small RNA, pY RNA1-s2, binds selectively to Matr3. Hypothetically, pY RNA1-S2 might act to modulate cellular function through this molecular mechanism. The retinal enrichment of pY RNA1-s2 provides reason to suspect that the pY RNA1-s2/Matr3 interaction could play a role in vision.

Show MeSH