Nascent rna transcription rna small nuclear. Medical search. Frequent questions

In molecular biology, small nucleolar RNAs (snoRNAs) are a class of small RNA molecules that primarily guide chemical modifications of other RNAs, mainly ribosomal RNAs, transfer RNAs and small nuclear RNAs. (wikipedia.org)
More than 80% of RNA in most cells consists of rRNA rRNAs and dozens of ribosomal proteins form ribosomes. (freezingblue.com)
They do so by catalyzing site-specific pseudouridylation of ribosomal and spliceosomal small nuclear RNAs, by processing ribosomal RNAs, and by stabilizing telomerase RNA. (silverchair.com)
RNA polymerase produces all types of RNA, including messenger RNA (mRNA), transfer RNA (tRNA), ribosomal RNA (rRNA), microRNA (miRNA), and even non-coding RNAs and ribozymes. (sciencefacts.net)
This mitochondrial RNA colocalizes with components of the cytoplasmic machinery that makes and imports nuclear-encoded proteins - that is, a ribosomal protein (S6), a nascent peptide associated protein (NAC), and the translocase in the outer membrane (Tom22). (biomedcentral.com)
In most human cells, mitochondria contain 10 3 -10 4 copies of a circular genome of 16,569 base-pairs that encodes two ribosomal RNAs, 22 tRNAs, and 13 polypeptides that form parts of the respiratory-chain located in the inner mitochondrial membrane [ 9 , 10 ]. (biomedcentral.com)
Small nucleolar RNAs (snoRNA) are commonly known to be involved in the processing of precursor ribosomal RNA (pre-rRNA) and small nuclear RNAs (snRNAs). (hindawi.com)
Specific tertiary structure types are observed for transfer RNA (tRNA), ribosomal RNA (rRNA), small nuclear RNA (snRNA), certain introns, and ribozymes. (biosyn.com)
RNP-based processive anti-termination underlies the switching from immediate-early to delayed-early gene expression in other lambdoid phages as well as ribosomal RNA synthesis in Escherichia coli . (fu-berlin.de)
Huang YH, Said N, Loll B, Wahl MC (2019) Structural basis for the function of SuhB as a transcription factor in ribosomal RNA synthesis. (fu-berlin.de)

piRNA-guided slicing of transposon transcripts enforces their transcriptional silencing via specifying the nuclear piRNA repertoire. (oeaw.ac.at)
Set1 binds nascent transcripts through its dRRM. (prinsesmaximacentrum.nl)
In addition, we uncovered that Set1 binds to different classes of RNAs to levels that largely exceed the levels of binding to the general population of transcripts, suggesting the Set1 persists on these RNAs after transcription. (prinsesmaximacentrum.nl)
Sequential assembly of the human spliceosome on RNA transcripts regulates splicing across the human transcriptome. (biomedcentral.com)
Interestingly, cells without intact IGCs continue to synthesize nascent transcripts. (rupress.org)
Mitochondrial DNA (mtDNA) genes are long known to be co-transcribed in polycistrones, yet it remains impossible to study nascent mtDNA transcripts quantitatively in vivo using existing tools. (biorxiv.org)
To this end we used deep sequencing (GRO-seq and PRO-seq) and analyzed nascent mtDNA-encoded RNA transcripts in diverse human cell lines and metazoan organisms. (biorxiv.org)
These obstacles interfered with comparative in-vivo investigation of mtDNA transcription in diverse conditions, and hampered expanding the study of mtDNA nascent transcripts to organisms lacking an mtDNA reference sequence. (biorxiv.org)
For this step to be efficiently executed, the viral Trans-Activator of Transcription, Tat, acts as a master regulator of transcription elongation by tethering SEC to the HIV trans-activator response (TAR) stem-loop RNA on the viral short transcripts, and synergistically enhancing RNAPII pause-release and elongation. (biomedcentral.com)
The nascent transcripts from HIV-1 Longer Terminal Do it again (LTR) include a exclusive structured RNA domains inside the 5′-nontranslated area referred to as the transactivation response (TAR) component which is crucial for effective transcription of viral promoter in response to Tat [3,4]. (thetechnoant.info)
TFs are enriched in RNA polymerase II complexes that produce nascent RNA transcripts, using co-transcribed genes from chromatin loops as their templates. (mechanobio.info)
MicroRNAs (miRNAs) are small regulatory non-coding RNAs, resulting from the cleavage of long primary transcripts (pri-miRNAs) in the nucleus by the Microprocessor complex generating precursors (pre-miRNAs) that are then exported to the cytoplasm and processed into mature miRNAs. (mdpi.com)
To explore how repeated drug exposure alters gene regulatory networks in the brain, we combined capped small (cs)RNA-seq, which accurately captures nascent-like initiating transcripts from total RNA, with Hi-C and single nuclei (sn)ATAC-seq. (figshare.com)

In order to carry out modification, each snoRNA associates with at least four core proteins in an RNA/protein complex referred to as a small nucleolar ribonucleoprotein particle (snoRNP). (wikipedia.org)
The proteins associated with each RNA depend on the type of snoRNA molecule (see snoRNA guide families below). (wikipedia.org)
This process is carried out by the human spliceosome machinery, in which over 300 proteins sequentially assemble with uridine-rich small nuclear RNA molecules (U snRNAs) to form distinct small nuclear ribonucleoprotein complexes (snRNPs). (biomedcentral.com)
Conversely, overexpression of a catalytically inactive mutant, Clk/STY(K190R), causes retention of hypophosphorylated SR proteins in nuclear speckles. (rupress.org)
In eukaryotes, DNA is packed inside the cell nucleus in the form of chromatin, which consists of DNA, proteins such as histones, and RNA. (nature.com)
We propose that the accumulating RNA recruits RNA-binding proteins that together tend to separate from transcriptionally inactive euchromatin. (nature.com)
It has been suggested, for example, that nuclear bodies, including those formed from RNA and RNA-binding proteins (RBPs), can displace transcriptionally inactive chromatin 18 . (nature.com)
As the active nuclear compartment contains high levels of RNA and RNA-binding proteins 1 , 5 , this provides a potential mechanism for the selective exclusion of inactive chromatin from the active compartment. (nature.com)
These RNPs consist of four core proteins and one RNA, but it is not known how they assemble. (silverchair.com)
NAF1 and all of the core proteins except GAR1 are recruited to the site of transcription. (silverchair.com)
Both proteins are essential for stable H/ACA RNA accumulation. (silverchair.com)
Serine and arginine-rich (SR) proteins are RNA-binding proteins (RBPs) known as constitutive and alternative splicing regulators. (molcells.org)
Diverse SR proteins play partially overlapping but distinct roles in transcription-coupled splicing and mRNA processing in the nucleus. (molcells.org)
This mini-review will summarize the roles of SR proteins as RNA binders, regulators, and connectors from transcription in the nucleus to translation in the cytoplasm. (molcells.org)
In this mini-review, the essential functions of SR proteins in splicing regulation, with a focus on their roles as RNA binders in the ribonucleoprotein complex (RNP) will be summarized. (molcells.org)
The messenger RNAs (mRNAs) produced from transcription are further used to encode functional proteins or make non-coding RNAs, such as tRNA, rRNA, and miRNA. (sciencefacts.net)
Then, proteins encoded by the nuclear genome and destined for the mitochondria will be made close to mitochondrial-encoded proteins so that they can be assembled efficiently into mitochondrial complexes. (biomedcentral.com)
Box C/D RNAs are associated with four snoRNP core proteins: NOP56, NOP58, fibrillarin, and 15.5 kDa [ 5 - 7 ]. (hindawi.com)
Box C/D RNAs contain the following functional elements: boxes C and D, which are essential for snoRNA interaction with specific proteins, and a guide sequence that determines the nucleotide to be modified (Figure 1(a) ). (hindawi.com)
Bioinformatic algorithms allowing predicting of biomolecular folding for proteins, peptides, and RNAs, even though sometimes successful, have all their limitations. (biosyn.com)
RNA molecules in solution may adopt secondary structures that are only partially determined by thermodynamics since RNA molecules can undergo conformational changes during interaction with other RNAs, RNA binding proteins or RNA binding peptides. (biosyn.com)
Since RNA-binding proteins (RBPs) are key players in the post-transcriptional regulation of gene expression precise knowledge of their binding sites is critical for determining their molecular function and for understanding their roles in cell development and disease. (biosyn.com)
Numerous fundamental cellular processes, including virtually every aspect of gene expression and regulation, depend on the cooperation of RNAs and proteins. (fu-berlin.de)
Specific RNAs and proteins associate to build up some of the most complex macromolecular machineries of living cells, such as ribosomes and spliceosomes, which mediate particular steps of gene expression. (fu-berlin.de)
RNAs and proteins can also engage in more transient interactions, for example during co-transcriptional regulation of RNA polymerases or during post-transcriptional regulation of (pre-)mRNA life cycles. (fu-berlin.de)
We investigate the molecular mechanisms, by which RNAs and proteins cooperate to bring about the biological functions of selected RNPs involved in transcription and pre-mRNA splicing. (fu-berlin.de)
NF90ctelevision can be a C-terminal variant [30] from the NF90 double-stranded RNA (dsRNA)-binding proteins that was originally reported like a putative transcription element knowing the antigen receptor response component (ARE) in the IL-2 gene regulatory area [31]. (thetechnoant.info)
Nab3 and Nrd1 are yeast heterogeneous nuclear ribonucleoprotein (hnRNP)-like proteins that heterodimerize and bind RNA. (chksignal.com)
The self-association property of Nab3 adds to the previously documented interactions between these hnRNP-like proteins, RNA polymerase II, and the nascent transcript, Selleck Entinostat leading to a network of nucleoprotein interactions that define a higher order Nrd1-Nab3 complex. (chksignal.com)
His fields of research comprise RNA-mediated gene silencing processes with a focus on epigenetic phenomena, including studies on RNA-directed DNA methylation, the characterization of virus silencing suppressor proteins, the development of plant bioreactor platforms and viroid research. (degruyter.com)
Viroids are non-encapsidated, single-stranded (ss), 250-400 nucleotide (nt)-long circular RNA molecules that do not encode proteins (1, 2). (degruyter.com)
That is, guide RNAs-rather than proteins-serve as the catalysts in RNA editing. (openstax.org)
Although speculative, the process of RNA editing may be a holdover from a primordial time when RNA molecules, instead of proteins, were responsible for catalyzing reactions. (openstax.org)

RNA polymerase II (RNAP II) produces precursors of mRNAs and most snRNA and microRNAs. (sciencefacts.net)
The artificial box C/D RNA directed to the branch point adenosine of the second intron, as well as the analogue directed to the last nucleotide of the second exon of the HSPA8 pre-mRNA caused the most prominent influence on the level of HSPA8 mRNAs. (hindawi.com)
Bioinformatics analysis revealed that some of these orphan RNAs were complementary to pre-mRNAs or mature mRNAs [ 10 ]. (hindawi.com)
The MZT marks the transfer of control of development from the mother to the zygote as maternal mRNAs are degraded, transcription from the zygotic genome begins, and embryonic development becomes dependent on zygotic gene products ( Tadros and Lipshitz, 2009 ). (elifesciences.org)
The RNA recognition motif protein CP33A is a global ligand of chloroplast mRNAs and is essential for plastid biogenesis and plant development. (uni-halle.de)
Many eukaryotic precursor messenger RNAs (pre-mRNAs) bear coding regions (exons) interspersed with non-coding intervening sequences (introns). (fu-berlin.de)
After transcription, eukaryotic pre-mRNAs must undergo several processing steps before they can be translated. (openstax.org)

This class includes RNAs derived from SET1, Ty1 retrotransposons, specific transcription factors genes and snRNAs (small nuclear RNAs). (prinsesmaximacentrum.nl)
In the vast majority of eukaryotes, OXPHOS is operated by genes encoded by two genomes - most in the nuclear genome (nDNA) and 37 in the short circular mitochondrial genome (mtDNA). (biorxiv.org)
This bi-genomic division is accompanied by profoundly different transcription regulatory system: whereas nDNA-encoded genes are transcribed individually by RNA polymerase 2 and the general nuclear transcription machinery, mtDNA transcription is long known to be regulated mainly by a dedicated RNA polymerase (POLRMT) and mtDNA-specific transcription factors (TFAM and TFB2) ( Shutt and Shadel 2010 ). (biorxiv.org)
However, as mtDNA transcription was mostly studied in vitro, little remains known about the mode and tempo of in vivo OXPHOS genes' transcription residing on the mtDNA. (biorxiv.org)
The sigma (σ) factor of the RNA polymerase is encoded by nuclear genes. (sciencefacts.net)
Finally, effects of FUS on HIV gene transcription are also exhibited genome wide, where FUS mainly occupies gene promoters at transcription starting sites, while its knockdown leads to an increase in AFF4 and Cdk9 occupancy on gene promoters of FUS affected genes. (biomedcentral.com)
The sex-biased lincRNA genes are enriched for nearby and correspondingly sex-biased accessible chromatin regions, as well as sex-biased binding sites for growth hormone-regulated transcriptional activators (STAT5, hepatocyte nuclear factor 6 [HNF6], FOXA1, and FOXA2) and transcriptional repressors (CUX2 and BCL6). (omicsdi.org)
Genes in active, inactive, and poised chromatin states exhibited differential responsiveness to ligand-activated nuclear receptors and distinct enrichments for functional gene categories. (omicsdi.org)
Although more highly transcribed genes acquire methylation earlier, the major transitions in the oocyte transcriptome occur well before the de novo methylation phase, indicating that transcription is generally not rate limiting in conferring permissiveness to DNA methylation. (biomedcentral.com)
These findings suggest a scenario where collisions between DNA replication and transcription are frequent, leading to increased genetic variability, as seen by the increase SNP levels at chromosome subtelomeres and in DGF-1 genes containing putative origins. (biomedcentral.com)
Despite 20,000 genes being present in each haploid nucleus, the number of transcription foci is limited to around 2000. (mechanobio.info)
The limitation in the ratio of transcriptional foci per genes to be transcribed is overcome by a phenomenon where groups of genes share the same transcription machinery. (mechanobio.info)
In order for these distant genes to be transcribed by the same transcription factory, they must first co-localize with this machinery. (mechanobio.info)
Some miRNAs are hosted in pri-miRNAs annotated as long non-coding RNAs (lncRNAs) and defined as MIRHGs (for miRNA Host Genes). (mdpi.com)
Recent studies revealed classes of recurrent DNA double-strand breaks (DSBs) in neural stem/progenitor cells, including transcription-associated, promoter-proximal breaks and recurrent DSB clusters in late-replicating, long neural genes that may give rise to somatic brain mosaicism. (stanford.edu)
In participating UK research institutions, investigators can publish open access in Genome Research, Genes & Development, RNA, and Learning & Memory without article publication charges and all staff can read the entire renowned Cold Spring Harbor journal collection. (cshlpress.com)
Other genes in the mitochondrial genome encode 40- to 80-nucleotide guide RNAs. (openstax.org)

After transcription, nascent rRNA molecules (termed pre-rRNA) undergo a series of processing steps to generate the mature rRNA molecule. (wikipedia.org)
Over the last decades, a variety of RNA methods have been developed for the study of RNA-DNA, RNA-RNA, and RNA-protein interactions including RNA complexes with ligand molecules. (biosyn.com)
RNA molecules are functionally diverse and involved in many cellular processes such as catalysis, ligand binding, and protein recognition. (biosyn.com)
RNA molecules are structural flexible and can adopt different structures. (biosyn.com)
RNAs are single-stranded molecules and the unlinked monomer building blocks are known as nucleotides. (biosyn.com)
RNA molecules are generally folded into compact and defined tertiary structures. (biosyn.com)
The aptamer is a kind of short DNA or RNA sequence that can specifically bind to target molecules, and could be widely used as the active targeting agents of nanoplatforms to achieve active-targeted therapy of tumors. (bvsalud.org)
Therefore, the overall goal of our work is to discover how DNA replication is regulated both in the large chromosomes of cells and in the "mini-chromosomes" of viruses and small extrachromosomal DNA molecules. (nih.gov)
At least in plants, DNA regions that become de novo methylated can be defined by homologous RNA molecules in a process termed RNA-directed DNA methylation (RdDM). (degruyter.com)
Viroids are pathogenic circular, non-coding, single-stranded RNA molecules. (degruyter.com)
Upon inoculation, mature Pospiviroidae RNA molecules enter the plant cell nucleus. (degruyter.com)
This process is entirely mediated by RNA molecules. (openstax.org)

Full phase separation is prevented because RNA remains tethered to transcribed euchromatin through RNA polymerases. (nature.com)
Bacteria transcribe their genomes with the help of multi-subunit RNA polymerases (RNAPs), which comprise two large β and β' subunits that form the active site, two regulatory α subunits and an ω subunit that supports RNAP assembly. (fu-berlin.de)

RNA polymerase I (RNAP I) synthesizes pre-rRNA 45S, which matures into the ribosome 's 28S, 18S, and 5.8S subunits. (sciencefacts.net)

The snoRNA molecule contains an antisense element (a stretch of 10-20 nucleotides), which are base complementary to the sequence surrounding the base (nucleotide) targeted for modification in the pre-RNA molecule. (wikipedia.org)
A conserved region of 10-21 nucleotides upstream of the D box is complementary to the methylation site of the target RNA and enables the snoRNA to form an RNA duplex with the RNA. (wikipedia.org)
Once RNA polymerase attaches to the promoter (where RNA polymerase begins transcribing a gene), it moves along the DNA template in the 5 to 3' direction, adding nucleotides to the growing RNA chain. (sciencefacts.net)
The INCB39110 TAR RNA component stretches between nucleotides +1 and +59 and forms a well balanced RNA stem-loop framework [5,6]. (thetechnoant.info)
We demonstrated that DNA synthesis occurs discontinuously only on one arm of replication forks (the arm where the direction of synthesis is opposite to the direction of fork movement) through the repeated initiation, synthesis and joining of Okazaki fragments (transient nascent DNA chains of 40 to 300 nucleotides). (nih.gov)
However, the guide RNA has more A nucleotides than the pre-mRNA has U nucleotides with which to bind. (openstax.org)

rRNAs and snRNAs are the main natural targets of 2′-O-methylation that is mediated by box C/D RNAs. (hindawi.com)
In the female germline, DNA methylation is acquired late in oogenesis from an essentially unmethylated baseline and is established largely as a consequence of transcription events. (biomedcentral.com)
however, little is known about the kinetics of methylation gain genome wide and the reasons for asynchrony in methylation at imprinted loci. (biomedcentral.com)
Given the predominant role of transcription, we sought to investigate whether transcription timing is rate limiting for de novo methylation and determines the asynchrony of methylation events. (biomedcentral.com)
We also identified differential enrichment of transcription factor binding motifs in CGIs acquiring methylation early or late in oocyte growth. (biomedcentral.com)
As a result, there is highly programmed methylation of a defined set of ~2000 CGIs in oocytes, mostly on account of their location within active transcription units. (biomedcentral.com)
Since then, he has been working as a postodoc in Dr. Wassenegger's lab (RLP AgroScience GmbH, AlPlanta) and his main field of interest is RNA-interference (RNAi) and RNA-directed DNA methylation (RdDM) in plants. (degruyter.com)
The recruitment of this machinery results in the production of viroid-derived small RNAs (vd-sRNAs) that mediate RNA degradation and DNA methylation of cognate sequences. (degruyter.com)

We show that accumulation of RNA induces formation of transcription pockets which displace transcriptionally inactive chromatin. (nature.com)
Long intergenic noncoding RNAs (lincRNAs) are increasingly recognized as key chromatin regulators, yet few studies have characterized lincRNAs in a single tissue under diverse conditions. (omicsdi.org)
Here, we analyzed 45 mouse liver RNA sequencing (RNA-Seq) data sets collected under diverse conditions to systematically characterize 4,961 liver lincRNAs, 59% of them novel, with regard to gene structures, species conservation, chromatin accessibility, transcription factor binding, and epigenetic states. (omicsdi.org)
This integrative analysis of liver lincRNA chromatin states, transcription factor occupancy, and growth hormone regulation provides novel insights into the expression of sex-specific lincRNAs and their potential for regulation of sex differences in liver physiology and disease. (omicsdi.org)
Chances are consequently, that Tat facilitates chromatin adjustments, thereby advertising initiation and transcription elongation in some sequential, coordinated occasions that result in high degrees of HIV transcription [11]. (thetechnoant.info)
In keeping with this look at, we mentioned that Tat/TAR-specified CDK9 (P-TEFb) kinase activity is crucial for the phosphorylation of RNAP II, transcription elongation elements SPT5 and Tat-SF1 as well as the induction histone H3 lysine 4 and lysine 36 methylations during transcriptional activation of integrated HIV-1 chromatin [12]. (thetechnoant.info)
Chromatin loops from the same or from different chromosome territories often share transcription factories (TFs). (mechanobio.info)

To investigate the functional relevance of RNA binding, we performed UV RNA crosslinking (CRAC) for Set1 and RNA polymerase II in parallel with ChIP-seq experiments. (prinsesmaximacentrum.nl)
Recombinant HIPKs and DYRK1A are auto-activated and phosphorylate the negative elongation factor SPT5, the transcription factor c-Myc, and the C-terminal domain of RNA polymerase II, suggesting a direct function in transcriptional regulation. (nature.com)
Within SEC two elongation factors, positive transcription elongation factor b (P-TEFb) and elongation factor for RNA polymerase II 2 (ELL2) are key components. (biomedcentral.com)
Genetic and biochemical evidence reveals that they are integral to the termination of transcription of short non-coding RNAs by RNA polymerase II. (chksignal.com)
The mutations included a Nab3 self-association defect, a Nab3-Nrd1 heterodimerization defect, a Nrd1-polymerase II binding defect, and an Nab3-RNA recognition motif mutation. (chksignal.com)

Structure of the human core transcription-export complex reveals a hub for multivalent interactions. (oeaw.ac.at)
In general, RRM domains recognize RNA, whereas RS domains participate in diverse protein-protein and protein-RNA interactions. (molcells.org)
Also, it contains some elements for non-sequence-specific interactions with DNA and nascent RNA. (sciencefacts.net)
It contains the other part of the active center responsible for RNA synthesis and the rest of the elements for non-sequence-specific interactions with DNA and nascent RNA. (sciencefacts.net)
b) Base-pairing interactions between an artificial box C/D RNA and target RNAs. (hindawi.com)
The characterization of RNA and RNA interactions is closely related to transcription, for example, gene expression levels are investigated within a biological context. (biosyn.com)
The mapping of RNA-protein or RNA-RNA interactions by protein pull-down or affinity pull-down methods allow studying RNA structures, as well as RNA-protein, and RNA-RNA interactions. (biosyn.com)
These data strengthen the idea that a multiplicity of interactions is needed to assemble a higher order Nrd1-Nab3 complex that coats specific nascent RNAs in preparation for termination. (chksignal.com)

The nucleotide to be modified in the target RNA is usually located at the 5th position upstream from the D box (or D' box). (wikipedia.org)
The growing RNA chain is extended one nucleotide at a time in the 5'→3' direction using nucleoside triphosphates ( ATP , CTP, UTP, and GTP). (sciencefacts.net)
We identify their source as a subset of stable, overlapping nuclear hybrids with a specific nucleotide signature. (stanford.edu)

However, both the accumulation of splicing factors at sites of pre-mRNA synthesis as well as pre-mRNA splicing are dramatically reduced, demonstrating that IGC disassembly perturbs coordination between transcription and pre-mRNA splicing in mammalian cell nuclei. (rupress.org)
IGCs are composed of particles measuring 20-25 nm in diameter, and they contain numerous factors that are involved in RNA synthesis and processing. (rupress.org)
It is part of the active center responsible for RNA synthesis. (sciencefacts.net)
RNA synthesis is terminated intrinsically, when the elongation complex transcribes a stable RNA hairpin followed by a uridine-rich stretch, or with the aid of transcription termination factor ρ. (fu-berlin.de)

Each snoRNA molecule acts as a guide for only one (or two) individual modifications in a target RNA. (wikipedia.org)
The snoRNA-dependent modifications are catalyzed by small nucleolar ribonucleoprotein particles (snoRNPs). (hindawi.com)
a) Schematics of a guide box C/D snoRNA structure and the interaction between a snoRNA and target RNAs. (hindawi.com)

To examine the involvement of interchromatin granule clusters (IGCs) in transcription and pre-mRNA splicing in mammalian cell nuclei, the serine-arginine (SR) protein kinase cdc2-like kinase (Clk)/STY was used as a tool to manipulate IGC integrity in vivo. (rupress.org)
By interrogating the site of H/ACA RNA transcription, we dissected their biogenesis in single cells and delineated the role of the non-core protein NAF1 in the process. (silverchair.com)
Protein-coding regions of the resulting RNAs are translated by ribosomes within the mitochondrion. (biomedcentral.com)
Strikingly, we found that liver-specific lincRNA gene promoters are more highly species conserved and have a significantly higher frequency of proximal binding by liver transcription factors than liver-specific protein-coding gene promoters. (omicsdi.org)
Moreover, RNA-protein complexes (RNPs) provide glimpses at the molecular ancestry of modern cells, which most likely evolved from an RNA-dominated world. (fu-berlin.de)
In these processes, transcript-borne regulatory RNAs alone or in conjunction with protein factors assemble on the surface of RNAP and accompany the enzyme during further transcription by an RNA looping mechanism, rendering the elongation complex resistant to pause and/or termination signals downstream of the original modification site. (fu-berlin.de)
Presumably, this process involves the interaction between the host's bromodomain-containing viroid RNA-binding protein 1 (VIRP1) and the viroid's TR domain (6). (degruyter.com)
A beta-hairpin comprising the nuclear localization sequence sustains the self-associated states of nucleosome assembly protein 1. (colorado.edu)

A universal method for the rapid isolation of all known classes of functional silencing small RNAs. (oeaw.ac.at)
We study the functional interplay of pausing, termination and continued transcription, which constitutes a pervasive gene regulatory principle in bacteria. (fu-berlin.de)
If smORFs present within lncRNAs can encode functional small peptides, they can also constitute cis -regulatory elements involved in lncRNA decay. (mdpi.com)

Euchromatin, which is permissive for transcription, is spatially organized into transcriptionally inactive domains interspersed with pockets of transcriptional activity. (nature.com)
Hepatic Long Intergenic Noncoding RNAs: High Promoter Conservation and Dynamic, Sex-Dependent Transcriptional Regulation by Growth Hormone. (omicsdi.org)

Inasmuch as artificial box C/D RNAs decreased viability of transfected human cells, we propose that natural snoRNAs as well as their artificial analogues can influence the maturation of complementary pre-mRNA and can be effective regulators of vital cellular processes. (hindawi.com)
Using such an approach, it was shown that introducing sequences complementary to a selected pre-mRNA into box C/D RNA structures allowed knockdown of the target mRNA [ 13 ]. (hindawi.com)

This enables the snoRNP to recognise and bind to the target RNA. (wikipedia.org)

Here we show that the Set1 complex (Set1C) directly binds RNA in vitro through the regions that comprise the double RNA recognition motifs (dRRM) and N-SET domain within Set1 and its subunit Spp1. (prinsesmaximacentrum.nl)
RNAPs not only transcribe DNA but are also responsible for proofreading the newly synthesized RNA strand and taking part in the recognition of the transcription start and termination sites. (sciencefacts.net)
terminus but nevertheless can rescue, in trans, the phenotype resulting from a mutation in the RNA recognition motif of Nab3. (chksignal.com)

We also closely collaborate with the Joint Research Group MX of Helmholtz-Zentrum Berlin and Freie Universität at the local BESSY II storage ring, where we aim at exploiting MX-based fragment screening to develop small molecule probes and modulators of RNP function. (fu-berlin.de)
The inhibitors of Tat/TAR axis consist of TAR RNA decoys [15,16], little molecule inhibitors and ribozyme [17-24]. (thetechnoant.info)
These data support a model in which multiple Nrd1-Nab3 heterodimers polymerize onto substrate RNA to effect termination, allowing complementation of one mutant Nab3 molecule by another lacking a different function. (chksignal.com)

Telomerase works the RNA -domain to dependent association of epidermal core lipids to the 3' G-rich heterotrimeric acid membrane. (erik-mill.de)

Postel Z, Poux C, Gallina S, Varre JS, Gode C, Schmitt E, Meyer E, Van Rossum F, Touzet P (2022) Reproductive isolation among lineages of Silene nutans (Caryophyllaceae): A potential involvement of plastid-nuclear incompatibilities. (uni-halle.de)
Saleh O, Dwiani S, Rott J, K hn K (2022) Nascent Transcript Sequencing for the Mapping of Promoters in Arabidopsis thaliana Mitochondria. (uni-halle.de)

Our observations show that FUS regulates both HIV and global gene transcription and modulates viral latency, thus can potentially serve as a target for future therapy that sets to reactivate HIV from its latent state. (biomedcentral.com)

For the class II DYRK ortholog from D. melanogaster it was demonstrated that the critical tyrosine is cis -auto-phosphorylated by the nascent kinase in a transitory intermediate state during maturation at the ribosome 3 . (nature.com)
To expand understanding of the role of snoRNAs in control of gene expression, in this study we tested the ability of artificial box C/D RNAs to affect the maturation of target pre-mRNA. (hindawi.com)
A Member of the Arabidopsis Mitochondrial Transcription Termination Factor Family Is Required for Maturation of Chloroplast Transfer RNAIle(GAU). (uni-halle.de)
Determining mitochondrial transcript termini for the study of transcription start sites and transcript 5′ end maturation. (uni-halle.de)
Comet assays on nascent DNA revealed a marked delay in nascent DNA maturation in multiple conditions previously linked to R-loop accumulation. (stanford.edu)

Combining EM and immuno-labeling on locus-specific head-on TRCs in bacteria, we observed the frequent accumulation of DNA:RNA hybrids behind replication forks. (stanford.edu)
These findings establish RNA-DNA hybrids as immunogenic species that aberrantly accumulate in the cytoplasm after R-loop processing, linking R-loop accumulation to cell death through the innate immune response. (stanford.edu)

Surprisingly, accurate detection of human mtDNA transcription initiation sites (TIS) in the heavy and light strands revealed a novel conserved transcription pausing site near the light strand TIS, upstream to the transcription-replication transition region. (biorxiv.org)
The kinetics of replication and transcription (monitored by immunolabelling after incorporating bromodeoxyuridine or bromouridine) reveal that each genome replicates independently of others in a focus, and that newly-made RNA remains in a focus (residence half-time ~43 min) long after it has been made. (biomedcentral.com)
Collision between replication and transcription is considered especially problematic, as each are catalyzed by large multiprotein machines, and can occur co-directionally, when the replication fork and transcription machinery are moving in the same direction, or on the leading strand and is head-on, when the fork and transcription are moving towards each other. (biomedcentral.com)
Background Examination of sponsor cell-based inhibitors of HIV-1 transcription could be very important to attenuating viral replication. (thetechnoant.info)
We analyzed the TAR RNA binding properties of NF90ctelevision and show it attenuates HIV-1 replication partly by inhibition of Tat-mediated transactivation of HIV-1 MYL2 LTR. (thetechnoant.info)
2) What are the requirements for DNA replication and transcription at the beginning of mammalian development? (nih.gov)
Direct visualization of transcription-replication conflicts reveals post-replicative DNA:RNA hybrids. (stanford.edu)
Transcription-replication collisions (TRCs) are crucial determinants of genome instability. (stanford.edu)

The C-terminal part of NF90 includes an arginine, glycine-rich (RGG) domains, like the motifs which mediate RNA binding by hnRNP-U and nucleolin [34]. (thetechnoant.info)

Competition for PRPF8 availability alters the transcription-coupled splicing of RNAs in which weak 5′ splice sites predominate, enabling diversification of human gene expression during biological processes like mitosis. (biomedcentral.com)
Recent global analyses of SR-RNA interaction maps have advanced our understanding of SR-regulated gene expression. (molcells.org)
Results were integrated with genome-wide binding data for five transcription factors implicated in growth hormone-regulated, sex-biased liver gene expression, leading to the following findings. (omicsdi.org)
Therapeutic tiny or short modified antisense oligonucleotides (Tiny ASOs) can block gene expression or modulate splice-switching! (biosyn.com)
Genome regulation encompasses all facets of gene expression, from the biochemical modifications of DNA, to the physical arrangement of chromosomes and the activity of the transcription machinery. (mechanobio.info)
One possibility is that the mitochondria, being remnants of ancient prokaryotes, have an equally ancient RNA-based method for regulating gene expression. (openstax.org)

The nascent RNA binding complex SFiNX licenses piRNA-guided heterochromatin formation. (oeaw.ac.at)
RNA polymerase V (RNAP V) has RNAs involved in siRNA-directed heterochromatin formation in plants. (sciencefacts.net)

Our approach paves the path towards in vivo, quantitative, reference sequence-free analysis of mtDNA transcription in all eukaryotes. (biorxiv.org)
Eukaryotes have many different nuclear RNAPs, and each recognizes a different promoter sequence, synthesizing some form of the RNA or the other. (sciencefacts.net)

Our analyses indicate that NAF1 binds NAP57 and escorts it to the nascent H/ACA RNA and that GAR1 then replaces NAF1 to yield mature H/ACA RNPs in Cajal bodies and nucleoli. (silverchair.com)

Because maturing oocytes and early embryos lack appreciable transcription, posttranscriptional regulatory processes control their development. (elifesciences.org)
Pausing and termination can be further modulated by elongation factors, such as N-utilization substances A and G. Some regulatory factors or RNAs can stably insulate RNAP from the destabilizing effects of terminators over long distances (processive anti-termination). (fu-berlin.de)
Interrogating over 100,000 active transcription start regions (TSRs) revealed that most TSRs had hallmarks of bonafide enhancers and highlighted the KLF/SP1, RFX, and AP1 transcription factors families as central to establishing brain-specific gene regulatory programs. (figshare.com)
Analysis of rats with addiction-like behaviors versus controls identified addiction-associated repression of transcription at regulatory enhancers recognized by nuclear receptor subfamily 3 group C (NR3C) factors, including glucocorticoid receptors. (figshare.com)

Here, we show that alterations in RNA splicing patterns across the human transcriptome that occur in conditions of restricted cellular PRPF8 abundance are defined by the altered splicing of introns with weak 5′ splice sites. (biomedcentral.com)

These post-replicative structures are linked to fork slowing and reversal across conflict regions and are distinct from physiological DNA:RNA hybrids at Okazaki fragments. (stanford.edu)

Within the tightly packed nuclear interior, which lacks defining membranes, various structurally distinct compartments and nuclear bodies (NBs) exist. (rupress.org)

RNA polymerase IV (RNAP IV) produces siRNA in plants. (sciencefacts.net)
We developed a generic automated eukaryotic short interfering RNA (siRNA) analysis tool, called RAPID. (uni-frankfurt.de)
Our tool captures diverse siRNA characteristics from small RNA sequencing data and provides easily navigable visualisations. (uni-frankfurt.de)

A heterochromatin-dependent transcription machinery drives piRNA expression. (oeaw.ac.at)
As transcription silencing is key for establishing the HIV reservoir, significant efforts have been made to understand the mechanism that regulate HIV gene transcription, and the role of the elongation machinery in promoting this step. (biomedcentral.com)
Members of the Pospiviroidae family replicate in the nucleus through double-stranded RNA intermediates, attracting the host RNA silencing machinery. (degruyter.com)

However, while the role of the super elongation complex (SEC) in enhancing transcription activation of HIV is well established, the function of SEC in modulating viral latency is less defined and its cell partners are yet to be identified. (biomedcentral.com)
Early studies on the regulation of gene transcription of the proviral human immunodeficiency virus (HIV) have laid the foundations to our current understanding of how metazoan transcription elongation is regulated [ 1 ]. (biomedcentral.com)
Cdk9 also phosphorylates the serine 2 of the heptapeptide repeats (YSPTSPS) of the C-terminal domain (CTD) of RNAPII to enhance elongation of transcription. (biomedcentral.com)
The principal part of Tat may actually be to market set up of pre-initiation complicated, thereby advertising both transcription initiation and elongation of HIV-1 promoter [4]. (thetechnoant.info)

Concordantly, depletion of FUS elevates the occupancy of AFF4 and Cdk9 on the viral promoter and activates HIV gene transcription. (biomedcentral.com)

The core enzyme (ββ′α 2 ω) consists of five subunits: two alpha (α) subunits of 36 kDa, a beta (β) subunit of 150 kDa, a beta prime subunit (β′) of 155 kDa, and a small omega (ω) subunit. (sciencefacts.net)

The combination of different biochemical methods with computational modelling allows scientists to gain insight into molecular processes in which RNA is involved. (biosyn.com)
RNA is a long, polymer of ribonucleoside monophosphate molecular units or building blocks joined together by phosphodiester linkages. (biosyn.com)

Both immunofluorescence and transmission electron microscopy analyses of cells overexpressing Clk/STY indicate that IGC components are completely redistributed to a diffuse nuclear localization, leaving no residual structure. (rupress.org)
NF90 offers two dsRNA binding motifs, a putative nuclear localization sign (NLS), and a leucine-rich nuclear export sign (NES). (thetechnoant.info)
Pol β is the smallest polymerase in family X. Other members of the family have a nuclear localization signal (NLS), a BRCA1 C-terminal (BRCT) domain, and a proline rich region. (biomedcentral.com)

Krupp F, Said N, Huang YH, Loll B, Bürger J, Mielke T, Spahn CMT, Wahl MC (2019) Structural basis for the action of an all-purpose transcription anti-termination factor. (fu-berlin.de)

This pausing site correlated with the presence of a bacterial pausing sequence motif, yet the transcription pausing index varied quantitatively among the cell lines. (biorxiv.org)
Analysis of non-human organisms enabled de novo mtDNA sequence assembly, as well as detection of previously unknown mtDNA TIS, pausing, and transcription termination sites with unprecedented accuracy. (biorxiv.org)

Finally, mtDNA transcription termination sites have been either mapped in-vitro, or were associated with MTERF binding sites ( Christianson and Clayton 1986 ), thus, again, limiting the capability to in-vivo map transcription terminations sites in diverse organisms. (biorxiv.org)
RNA-based processive anti-termination is exemplified by the polymerase utilization ( put ) signal of phage HK022. (fu-berlin.de)

RNA-sequencing analysis further reveals that stripe and interstripe iridophores have different transcriptomic states, while cryogenic-scanning-electron-microscopy and micro-X-ray diffraction identify different crystal-arrays architectures, indicating that stripe and interstripe iridophores are different cell types. (janelia.org)

The 3' ends of guide RNAs have a long poly-U tail, and these U bases are inserted in regions of the pre-mRNA transcript at which the guide RNAs are looped. (openstax.org)

SnoRNAs are commonly referred to as guide RNAs but should not be confused with the guide RNAs that direct RNA editing in trypanosomes or the guide RNAs (gRNAs) used by Cas9 for CRISPR gene editing. (wikipedia.org)
RNA editing is not just a phenomenon of trypanosomes. (openstax.org)

R-loops are RNA-DNA-hybrid-containing nucleic acids with important cellular roles. (stanford.edu)

Uppercase letters in the target pre-mRNA sequences correspond to exons, and small letters indicate the intron sequences. (hindawi.com)

Some causative mutations arise in the nuclear genome (for example, in NDUFS4 , 7 , and 8 in Leigh and Leigh-like syndromes), others in the mitochondrial one. (biomedcentral.com)
Mitochondrial run-on transcription assay using biotin labeling. (uni-halle.de)

Here we identify a new population of RNA-DNA hybrids in the cytoplasm that are R-loop-processing products. (stanford.edu)

Anatomy13

Organisms18

Chemicals and Drugs129

Analytical, Diagnostic and Therapeutic Techniques and Equipment21

Phenomena and Processes76

Information Science3

Ribosomal10

Transcripts13

Proteins33

MRNAs7

Genes17

Molecules12

Polymerases2

RRNA1

Nucleotides6

Methylation8

Chromatin7

Polymerase II5

Interactions8

Nucleotide3

Synthesis4

SnoRNA3

Protein8

Functional3

Transcriptional2

Complementary2

Bind1

Recognition3

Molecule3

Telomerase1

20222

Regulates1

Maturation5

Accumulation2

Replication8

Mediate1

Gene expression6

Heterochromatin formation2

Eukaryotes2

Binds1

Regulatory4

Introns1

Okazaki1

Distinct1

SiRNA3

Machinery3

Elongation4

Promoter1

Subunit1

Molecular2

Localization3

20191

Sequence2

Termination2

Reveals1

Transcript1

Trypanosomes2

Cellular1

Exons1

Mitochondrial2

Cytoplasm1