Ere, a Family of Short Interspersed Elements in the Genomes of Odd-Toed Ungulates (Perissodactyla).

Short Interspersed Elements (SINEs) are eukaryotic retrotransposons transcribed by RNA polymerase III (pol III). Many mammalian SINEs (T SINEs) contain a polyadenylation signal (AATAAA), a pol III transcription terminator, and an A-rich tail in their 3'-end. The RNAs of such SINEs have the capacity for AAUAAA-dependent polyadenylation, which is unique to pol III-generated transcripts.

SINEs as Potential Expression Cassettes: Impact of Deletions and Insertions on Polyadenylation and Lifetime of B2 and Ves SINE Transcripts Generated by RNA Polymerase III.

Short Interspersed Elements (SINEs) are common in the genomes of most multicellular organisms. They are transcribed by RNA polymerase III from an internal promoter comprising boxes A and B. As transcripts of certain SINEs from mammalian genomes can be polyadenylated, such transcripts should contain the AATAAA sequence as well as those called β- and τ-signals.

Nucleotide Context Can Modulate Promoter Strength in Genes Transcribed by RNA Polymerase III.

The small nuclear RNAs 4.5SH and 4.5SI were characterized only in mouse-like rodents; their genes originate from 7SL RNA and tRNA, respectively.

Tail Wags Dog's SINE: Retropositional Mechanisms of Can SINE Depend on Its A-Tail Structure.

SINEs, non-autonomous short retrotransposons, are widespread in mammalian genomes. Their transcripts are generated by RNA polymerase III (pol III). Transcripts of certain SINEs can be polyadenylated, which requires polyadenylation and pol III termination signals in their sequences.

Analysis of SINE Families B2, Dip, and Ves with Special Reference to Polyadenylation Signals and Transcription Terminators.

Short Interspersed Elements (SINEs) are eukaryotic non-autonomous retrotransposons transcribed by RNA polymerase III (pol III). The 3'-terminus of many mammalian SINEs has a polyadenylation signal (AATAAA), pol III transcription terminator, and A-rich tail. The RNAs of such SINEs can be polyadenylated, which is unique for pol III transcripts.

Identification of nucleotide sequences and some proteins involved in polyadenylation of RNA transcribed by Pol III from SINEs.

We have previously reported that not only transcripts of RNA polymerase II (pol II), but also one type of RNA transcribed by RNA polymerase III (pol III), undergo AAUAAA-dependent polyadenylation. Such an unusual feature is inherent in Short Interspersed Elements (SINEs) from genomes of certain mammals. For polyadenylation of its transcript, SINE should contain, besides an AATAAA hexamer and a transcription terminator, two specific regions: β, located downstream of box B of a promoter, and τ, preceding AATAAA.

TATA-Like Boxes in RNA Polymerase III Promoters: Requirements for Nucleotide Sequences.

tRNA and some other non-coding RNA genes are transcribed by RNA polymerase III (pol III), due to the presence of intragenic promoter, consisting of boxes A and B spaced by 30-40 bp. Such pol III promoters, called type 2, are also intrinsic to Short Interspersed Elements (SINEs). The contribution of 5'-flanking sequences to the transcription efficiency of genes containing type 2 promoters is still studied insufficiently.

Influence of 5'-flanking sequence on 4.5SI RNA gene transcription by RNA polymerase III.

Short nuclear 4.5SI RNA can be found in three related rodent families. Its function remains unknown.

Heat shock increases lifetime of a small RNA and induces its accumulation in cells.

4.5SH and 4.5SI RNA are two abundant small non-coding RNAs specific for several related rodent families including Muridae.

Polyadenylation of RNA transcribed from mammalian SINEs by RNA polymerase III: Complex requirements for nucleotide sequences.

It is generally accepted that only transcripts synthesized by RNA polymerase II (e.g., mRNA) were subject to AAUAAA-dependent polyadenylation.

A 5'-3' terminal stem in small non-coding RNAs extends their lifetime.

4.5SI and 4.5SH are two non-coding RNAs about 100nt long, synthesized by RNA polymerase III in cells of various rodents including mice, rats, and hamsters.

SINEBase: a database and tool for SINE analysis.

SINEBase (http://sines.eimb.ru) integrates the revisited body of knowledge about short interspersed elements (SINEs).

Complementarity of end regions increases the lifetime of small RNAs in mammalian cells.

Two RNAs (4.5SH and 4.5SI) with unknown functions share a number of features: short length (about 100 nt), transcription by RNA polymerase III, predominately nuclear localization, the presence in various tissues, and relatively narrow taxonomic distribution (4 and 3 rodent families, respectively).

SNOntology: Myriads of novel snoRNAs or just a mirage?

Background: Small nucleolar RNAs (snoRNAs) are a large group of non-coding RNAs (ncRNAs) that mainly guide 2'-O-methylation (C/D RNAs) and pseudouridylation (H/ACA RNAs) of ribosomal RNAs. The pattern of rRNA modifications and the set of snoRNAs that guide these modifications are conserved in vertebrates. Nearly all snoRNA genes in vertebrates are localized in introns of other genes and are processed from pre-mRNAs.

SINEs.

Short interspersed elements (SINEs) are mobile genetic elements that invade the genomes of many eukaryotes. Since their discovery about 30 years ago, many gaps in our understanding of the biology and function of SINEs have been filled. This review summarizes the past and recent advances in the studies of SINEs.

Additional box B of RNA polymerase III promoter in SINE B1 can be functional.

Many genes of small RNAs and short interspersed elements (SINEs) are transcribed by RNA polymerase III due to an internal promoter that is composed of two boxes (A and B) spaced by 30-45bp. Rodent SINE B1 originated from 7SL RNA, and a 29-bp tandem duplication took place in B1 at an early stage of its evolution. As a result of this duplication, an additional box B (named B') located at a distance of 79-82bp from box A arose in SINE B1.

Nucleotide sequences of B1 SINE and 4.5S(I) RNA support a close relationship of zokors to blind mole rats (Spalacinae) and bamboo rats (Rhizomyinae).

Until recently, zokors (Myospalacinae) were assigned to the Cricetidae family. However, analysis of mitochondrial and nuclear genes suggests a sister relationship between zokors and subterranean rodents of the Spalacidae family, namely blind mole rats (Spalacinae) and bamboo rats (Rhizomyinae). Here, we cloned and sequenced copies of the B1 short interspersed element (SINE) from the genome of zokor Myospalax psilurus.

4.5SI RNA genes and the role of their 5'-flanking sequences in the gene transcription.

4.5S(I) RNA is a small nuclear RNA synthesized by RNA polymerase III and detected in rodents of only four families. Hundreds of copies of this RNA retropseudogenes are interspersed throughout the mouse (Mus musculus) and rat (Rattus norvegicus) genomes.

5'-flanking sequences can dramatically influence 4.5SH RNA gene transcription by RNA-polymerase III.

4.5SH RNA is a 94 nt small nuclear RNA with an unknown function. Hundreds of its genes are present in the genomes of rodents of six families including Muridae.

5S rRNA-derived and tRNA-derived SINEs in fruit bats.

Most short retroposons (SINEs) descend from cellular tRNA of 7SL RNA. Here, four new SINEs were found in megabats (Megachiroptera) but neither in microbats nor in other mammals. Two of them, MEG-RS and MEG-RL, descend from another cellular RNA, 5S rRNA; one (MEG-T2) is a tRNA-derived SINE; and MEG-TR is a hybrid tRNA/5S rRNA SINE.

Analysis of C/D box snoRNA genes in vertebrates: The number of copies decreases in placental mammals.

C/D box small nucleolar RNAs (snoRNAs) guide site-specific 2'-O-methylation of RNAs. Nearly all C/D box snoRNAs with known targets are involved in rRNA modification. In vertebrates, snoRNAs are encoded in introns of various genes and their processing is coupled with splicing of host gene pre-mRNA.

Transcripts synthesized by RNA polymerase III can be polyadenylated in an AAUAAA-dependent manner.

It is well known that nearly all eukaryotic mRNAs contain a 3' poly(A) tail. A polyadenylation signal (AAUAAA) nearby the 3' end of pre-mRNA is required for poly(A) synthesis. The protein complex involved in the pre-mRNA polyadenylation is coupled with RNA polymerase II during the transcription of a gene.

Bov-B-mobilized SINEs in vertebrate genomes.

Two new short retroposon families (SINEs) have been found in the genome of springhare Pedetes capensis (Rodentia). One of them, Ped-1, originated from 5S rRNA, while the other one, Ped-2, originated from tRNA-derived SINE ID. In contrast to most currently active mammalian SINEs mobilized by L1 long retrotransposon (LINE), Ped-1 and Ped-2 are mobilized by Bov-B, a LINE family of the widely distributed RTE clade.

B1 SINEs in different rodent families.

B1 SINEs were studied in 22 families covering all major rodent lineages. The number of B1 copies considerably varies, from 1 x 10(4) in Geomyidae to 1 x 10(6) in Myodonta. B1 sequences can be divided into three main structural variants: B1 with a 20-bp tandem duplication (found in Gliridae, Sciuridae, and Aplodontidae), B1 with a 29-bp duplication (found in other families), and proto-B1 without duplication (pB1).

Molecular evolution of satellite DNA repeats and speciation of lizards of the genus Darevskia (Sauria: Lacertidae).

Satellite DNA repeats were studied in Caucasian populations of 18 rock lizard species of the genus Darevskia. Four subfamilies (Caucasian Lacerta satellites (CLsat)I-IV) were identified, which shared 70%-75% sequence similarity. The distribution of CLsat subfamilies among the species was studied.