scholarly journals Intron 7 conserved sequence elements regulate the splicing of the SMN genes

2009 ◽  
Vol 126 (6) ◽  
pp. 833-841 ◽  
Author(s):  
Jordan T. Gladman ◽  
Dawn S. Chandler
Keyword(s):  
Conserved Sequence ◽  
Sequence Elements

scholarly journals Olfactory expression of trace amine-associated receptors requires cooperative cis-acting enhancers

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ami Shah ◽  
Madison Ratkowski ◽  
Alessandro Rosa ◽  
Paul Feinstein ◽  
Thomas Bozza
Keyword(s):  
Gene Expression ◽  
Large Family ◽  
Sequence Motifs ◽  
Specific Expression ◽  
Cis Acting ◽  
Conserved Sequence ◽  
Trace Amine ◽  
Sequence Elements ◽  
Cell Type Specific Expression ◽  
Cell Type Specific

AbstractOlfactory sensory neurons express a large family of odorant receptors (ORs) and a small family of trace amine-associated receptors (TAARs). While both families are subject to so-called singular expression (expression of one allele of one gene), the mechanisms underlying TAAR gene choice remain obscure. Here, we report the identification of two conserved sequence elements in the mouse TAAR cluster (T-elements) that are required for TAAR gene expression. We observed that cell-type-specific expression of a TAAR-derived transgene required either T-element. Moreover, deleting either element reduced or abolished expression of a subset of TAAR genes, while deleting both elements abolished olfactory expression of all TAARs in cis with the mutation. The T-elements exhibit several features of known OR enhancers but also contain highly conserved, unique sequence motifs. Our data demonstrate that TAAR gene expression requires two cooperative cis-acting enhancers and suggest that ORs and TAARs share similar mechanisms of singular expression.

scholarly journals Ultraconserved Non-coding DNA Within Diptera and Hymenoptera

2020 ◽  
Vol 10 (9) ◽  
pp. 3015-3024 ◽  
Author(s):  
Thomas Brody ◽  
Amarendra Yavatkar ◽  
Alexander Kuzin ◽  
Ward F Odenwald
Keyword(s):  
Genomic Sequence ◽  
Mosquito Species ◽  
Phylogenetic Footprinting ◽  
Reference Sequence ◽  
Phylogenetic Groups ◽  
Developmental Genes ◽  
Coding Sequences ◽  
Conserved Sequence ◽  
Sequence Elements ◽  
And Function

Abstract This study has taken advantage of the availability of the assembled genomic sequence of flies, mosquitos, ants and bees to explore the presence of ultraconserved sequence elements in these phylogenetic groups. We compared non-coding sequences found within and flanking Drosophila developmental genes to homologous sequences in Ceratitis capitata and Musca domestica. Many of the conserved sequence blocks (CSBs) that constitute Drosophila cis-regulatory DNA, recognized by EvoPrinter alignment protocols, are also conserved in Ceratitis and Musca. Also conserved is the position but not necessarily the orientation of many of these ultraconserved CSBs (uCSBs) with respect to flanking genes. Using the mosquito EvoPrint algorithm, we have also identified uCSBs shared among distantly related mosquito species. Side by side comparison of bee and ant EvoPrints of selected developmental genes identify uCSBs shared between these two Hymenoptera, as well as less conserved CSBs in either one or the other taxon but not in both. Analysis of uCSBs in these dipterans and Hymenoptera will lead to a greater understanding of their evolutionary origin and function of their conserved non-coding sequences and aid in discovery of core elements of enhancers. This study applies the phylogenetic footprinting program EvoPrinter to detection of ultraconserved non-coding sequence elements in Diptera, including flies and mosquitos, and Hymenoptera, including ants and bees. EvoPrinter outputs an interspecies comparison as a single sequence in terms of the input reference sequence. Ultraconserved sequences flanking known developmental genes were detected in Ceratitis and Musca when compared with Drosophila species, in Aedes and Culex when compared with Anopheles, and between ants and bees. Our methods are useful in detecting and understanding the core evolutionarily hardened sequences required for gene regulation.

scholarly journals Different Mechanisms for Pseudouridine Formation in Yeast 5S and 5.8S rRNAs

2008 ◽  
Vol 28 (10) ◽  
pp. 3089-3100 ◽  
Author(s):  
Wayne A. Decatur ◽  
Murray N. Schnare
Keyword(s):  
Large Subunit ◽  
Consensus Sequence ◽  
5S Rrna ◽  
Stem Loop ◽  
Conserved Sequence ◽  
5.8S Rrna ◽  
Sequence Elements ◽  
The Individual ◽  
A Site ◽  
Large Subunit Rrna

ABSTRACT The selection of sites for pseudouridylation in eukaryotic cytoplasmic rRNA occurs by the base pairing of the rRNA with specific guide sequences within the RNA components of box H/ACA small nucleolar ribonucleoproteins (snoRNPs). Forty-four of the 46 pseudouridines (Ψs) in the cytoplasmic rRNA of Saccharomyces cerevisiae have been assigned to guide snoRNAs. Here, we examine the mechanism of Ψ formation in 5S and 5.8S rRNA in which the unassigned Ψs occur. We show that while the formation of the Ψ in 5.8S rRNA is associated with snoRNP activity, the pseudouridylation of 5S rRNA is not. The position of the Ψ in 5.8S rRNA is guided by snoRNA snR43 by using conserved sequence elements that also function to guide pseudouridylation elsewhere in the large-subunit rRNA; an internal stem-loop that is not part of typical yeast snoRNAs also is conserved in snR43. The multisubstrate synthase Pus7 catalyzes the formation of the Ψ in 5S rRNA at a site that conforms to the 7-nucleotide consensus sequence present in other substrates of Pus7. The different mechanisms involved in 5S and 5.8S rRNA pseudouridylation, as well as the multiple specificities of the individual trans factors concerned, suggest possible roles in linking ribosome production to other processes, such as splicing and tRNA synthesis.

scholarly journals Alphavirus RNA Genome Repair and Evolution: Molecular Characterization of Infectious Sindbis Virus Isolates Lacking a Known Conserved Motif at the 3′ End of the Genome

2000 ◽  
Vol 74 (20) ◽  
pp. 9776-9785 ◽  
Author(s):  
Jyothi George ◽  
Ramaswamy Raju
Keyword(s):  
Sindbis Virus ◽  
Repeat Sequence ◽  
Genome Replication ◽  
Sequence Element ◽  
Conserved Sequence ◽  
Long Term Stability ◽  
Nontranslated Region ◽  
Viral Promoters ◽  
Sequence Elements

ABSTRACT The 3′ nontranslated region of the genomes of Sindbis virus (SIN) and other alphaviruses carries several repeat sequence elements (RSEs) as well as a 19-nucleotide (nt) conserved sequence element (3′CSE). The 3′CSE and the adjoining poly(A) tail of the SIN genome are thought to act as viral promoters for negative-sense RNA synthesis and genome replication. Eight different SIN isolates that carry altered 3′CSEs were studied in detail to evaluate the role of the 3′CSE in genome replication. The salient findings of this study as it applies to SIN infection of BHK cells are as follows: i) the classical 19-nt 3′CSE of the SIN genome is not essential for genome replication, long-term stability, or packaging; ii) compensatory amino acid or nucleotide changes within the SIN genomes are not required to counteract base changes in the 3′ terminal motifs of the SIN genome; iii) the 5′ 1-kb regions of all SIN genomes, regardless of the differences in 3′ terminal motifs, do not undergo any base changes even after 18 passages; iv) although extensive addition of AU-rich motifs occurs in the SIN genomes carrying defective 3′CSE, these are not essential for genome viability or function; and v) the newly added AU-rich motifs are composed predominantly of RSEs. These findings are consistent with the idea that the 3′ terminal AU-rich motifs of the SIN genomes do not bind directly to the viral polymerase and that cellular proteins with broad AU-rich binding specificity may mediate this interaction. In addition to the classical 3′CSE, other RNA motifs located elsewhere in the SIN genome must play a major role in template selection by the SIN RNA polymerase.

scholarly journals Two evolutionarily conserved sequence elements for Peg3/Usp29 transcription

2008 ◽  
Vol 9 (1) ◽  
pp. 108 ◽  
Author(s):  
Jeong Do Kim ◽  
Sungryul Yu ◽  
Jung Ha Choo ◽  
Joomyeong Kim
Keyword(s):  
Conserved Sequence ◽  
Evolutionarily Conserved ◽  
Sequence Elements

Each of the conserved sequence elements flanking the cleavage site of mammalian histone pre-mRNAs has a distinct role in the 3'-end processing reaction

1989 ◽  
Vol 9 (7) ◽  
pp. 3105-3108
Author(s):  
K L Mowry ◽  
R Oh ◽  
J A Steitz
Keyword(s):  
Small Nuclear Rna ◽  
Hairpin Loop ◽  
Apparent Contrast ◽  
Conserved Sequence ◽  
Histone 3 ◽  
Nuclear Rna ◽  
Sequence Elements ◽  
Loop Element ◽  
Processing Site

To study the substrate requirements for the histone 3'-end processing reaction of mammalian histone pre-mRNAs, we created a set of mutations in the sequences flanking the processing site of a mouse H3 gene. We found that deletion of the downstream purine-rich element hypothesized to interact with U7 small nuclear RNA abolishes in vitro 3'-end processing. Somewhat surprisingly, however, mutations in the hairpin loop element which destabilize or destroy the secondary structure reduce but do not abolish 3'-end processing. This is in apparent contrast to results obtained for the sea urchin system, where both sequence elements appear to be absolutely required for 3'-end formation.

Promoter sequences required for transcription of Xenopus laevis histone genes in injected frog oocyte nuclei

1988 ◽  
Vol 8 (9) ◽  
pp. 3676-3682
Author(s):  
L M Heindl ◽  
T S Weil ◽  
M Perry
Keyword(s):  
Histone Gene ◽  
Base Pairs ◽  
Promoter Sequences ◽  
Conserved Sequence ◽  
General Transcription Factors ◽  
Histone Gene Expression ◽  
Genes Encoding ◽  
Sequence Elements ◽  
Frog Oocyte ◽  
Common Sequence

Amphibian oogenesis is accompanied by the accumulation of histone mRNA and proteins in the absence of ongoing DNA replication. To begin an analysis of the mechanisms by which histone gene expression is regulated during frog oogenesis and embryogenesis, we used oocyte injection to examine the upstream sequences required for transcription of genes encoding each of the five histone classes. We found that sequences necessary for maximal levels of transcription are located 100 to 200 base pairs upstream of the corresponding start sites. In this region, each promoter examined contains conserved sequence elements, several of which seem to be histone gene class specific, in addition to other, more common sequence elements believed to be used by general transcription factors.

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