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1. A highly conserved protein of unknown function in Sinorhizobium meliloti affects sRNA regulation similar to Hfq

Author:
Pandey, Shree P.; Minesinger, Brenda K.; Kumar, Janesh; Walker, Graham C.
Source:
Nucleic acids research 2011 v.39 no.11 pp. 4691-4708
ISSN:
0305-1048
Subject:
Ensifer meliloti; bacteria; genes; messenger RNA; mutants; phenotype; phosphates; proteins
Abstract:
... The SMc01113/YbeY protein, belonging to the UPF0054 family, is highly conserved in nearly every bacterium. However, the function of these proteins still remains elusive. Our results show that SMc01113/YbeY proteins share structural similarities with the MID domain of the Argonaute (AGO) proteins, and might similarly bind to a small-RNA (sRNA) seed, making a special interaction with the phosphate o ...
DOI:
10.1093/nar/gkr060
PubMed:
21325267
PubMed Central:
PMC3113577

2. Comparative whole genome sequencing reveals phenotypic tRNA gene duplication in spontaneous Schizosaccharomyces pombe La mutants

Author:
Iben, James R.; Epstein, Jonathan A.; Bayfield, Mark A.; Bruinsma, Monique W.; Hasson, Samuel; Bacikova, Dagmar; Ahmad, Daniel; Rockwell, Denise; Kittler, Ellen L.W.; Zapp, Maria L.; Maraia, Richard J.
Source:
Nucleic acids research 2011 v.39 no.11 pp. 4728-4742
ISSN:
0305-1048
Subject:
Schizosaccharomyces pombe; gene duplication; genes; mitochondria; mitochondrial DNA; mutants; phenotype; sequence analysis; single nucleotide polymorphism; transfer RNA
Abstract:
... We used a genetic screen based on tRNA-mediated suppression (TMS) in a Schizosaccharomyces pombe La protein (Sla1p) mutant. Suppressor pre-tRNASerUCA-C47:6U with a debilitating substitution in its variable arm fails to produce tRNA in a sla1-rrm mutant deficient for RNA chaperone-like activity. The parent strain and spontaneous mutant were analyzed using Solexa sequencing. One synonymous single-nu ...
DOI:
10.1093/nar/gkr066
PubMed:
21317186
PubMed Central:
PMC3113579

3. Genome-wide chromatin occupancy analysis reveals a role for ASH2 in transcriptional pausing

Author:
Pérez-Lluch, Sílvia; Blanco, Enrique; Carbonell, Albert; Raha, Debasish; Snyder, Michael; Serras, Florenci; Corominas, Montserrat
Source:
Nucleic acids research 2011 v.39 no.11 pp. 4628-4639
ISSN:
0305-1048
Subject:
DNA-directed RNA polymerase; Drosophila; gene expression regulation; genes; histones; imaginal discs; lysine; mutants; mutation; nucleic acids; nucleosomes; phosphorylation; precipitin tests; serine; transcription (genetics)
Abstract:
... An important mechanism for gene regulation involves chromatin changes via histone modification. One such modification is histone H3 lysine 4 trimethylation (H3K4me3), which requires histone methyltranferase complexes (HMT) containing the trithorax-group (trxG) protein ASH2. Mutations in ash2 cause a variety of pattern formation defects in the Drosophila wing. We have identified genome-wide binding ...
DOI:
10.1093/nar/gkq1322
PubMed:
21310711
PubMed Central:
PMC3113561

4. The BCL2 gene is regulated by a special AT-rich sequence binding protein 1-mediated long range chromosomal interaction between the promoter and the distal element located within the 3'-UTR

Author:
Gong, Feiran; Sun, Luan; Wang, Zongdan; Shi, Junfeng; Li, Wei; Wang, Sumeng; Han, Xiao; Sun, Yujie
Source:
Nucleic acids research 2011 v.39 no.11 pp. 4640-4652
ISSN:
0305-1048
Subject:
3' untranslated regions; apoptosis; binding proteins; binding sites; caspase-6; chromatin; epigenetics; gene overexpression; genes; mutants; precipitin tests; transcription (genetics)
Abstract:
... The 279-bp major breakpoint region (mbr) within the 3'-untranslated region (3'-UTR) of the BCL2 gene is a binding site of special AT-rich sequence binding protein 1 (SATB1) that is well known to participate in the long-range regulation of gene transcription. Our previous studies have revealed that the mbr could regulate BCL2 transcription over a 200-kb distance and this regulatory function was clo ...
DOI:
10.1093/nar/gkr023
PubMed:
21310710
PubMed Central:
PMC3113567