RNA in control

 

Blencowe BJ, Khanna M. Molecular biology: RNA in control. Nature. 2007 May 24; 447 (7143): 391-3.

RNA in control

Compartmentalization of the splicing machinery in plant cell nuclei

 

Lorkovi? ZJ, Barta A. Compartmentalization of the splicing machinery in plant cell nuclei. Trends Plant Sci. 2004 Dec; 9 (12): 565-8.

 

The cell nucleus is a membrane-surrounded organelle that contains numerous compartments in addition to chromatin. Compartmentalization of the nucleus is now accepted as an important feature for the organization of nuclear processes and for gene expression. Recent studies on nuclear organization of splicing factors in plant cells provide insights into the compartmentalization of the plant cell nuclei and conservation of nuclear compartments between plants and metazoans.

 Compartmentalization of the splicing machinery in plant cell nuclei

 

Pre-mRNA splicing in higher plants

 

Lorkovi? ZJ, Wieczorek Kirk DA, Lambermon MH, Filipowicz W. Pre-mRNA splicing in higher plants. Trends Plant Sci. 2000 Apr; 5 (4): 160-7.

 

Most plant mRNAs are synthesized as precursors containing one or more intervening sequences (introns) that are removed during the process of splicing. The basic mechanism of spliceosome assembly and intron excision is similar in all eukaryotes. However, the recognition of introns in plants has some unique features, which distinguishes it from the reactions in vertebrates and yeast. Recent progress has occurred in characterizing the splicing signals in plant pre-mRNAs, in identifying the mutants affected in splicing and in discovering new examples of alternatively spliced mRNAs. In combination with information provided by the Arabidopsis genome-sequencing project, these studies are contributing to a better understanding of the splicing process and its role in the regulation of gene expression in plants.

 Pre-mRNA splicing in higher plants

 

Plant serine/arginine-rich proteins and their role in pre-mRAN spicing

 

Reddy AS. Plant serine/arginine-rich proteins and their role in pre-mRNA splicing. Trends Plant Sci. 2004 Nov; 9 (11): 541-7.

 

Pre-messenger RNA (pre-mRNA) splicing, a process by which mature mRNAs are generated by excision of introns and ligation of exons, is an important step in the regulation of gene expression in all eukaryotes. Selection of alternative splice sites in a pre-mRNA generates multiple mRNAs from a single gene that encode structurally and functionally distinct proteins. Alternative splicing of pre-mRNAs contributes greatly to the proteomic complexity of plants and animals and increases the coding potential of a genome. However, the mechanisms that regulate constitutive and alternative splicing of pre-mRNA are not understood in plants. A serine/arginine-rich (SR) family of proteins is implicated in constitutive and alternative splicing of pre-mRNAs. Here I review recent progress in elucidating the roles of serine/arginine-rich proteins in pre-mRNA splicing.

 Plant serine/arginine-rich proteins and their role in pre-mRAN spicing

 

Alternative splicing and proteome diversity in plants: the tip of the iceberg has just emerged

 

Kazan K. Alternative splicing and proteome diversity in plants: the tip of the iceberg has just emerged. Trends Plant Sci. 2003 Oct;8(10):468-71.

 

Alternative splicing has recently emerged as one of the most significant generators of functional complexity in several relatively well-studied animal genomes, but little is known about the extent of this phenomenon in higher plants. However, recent computational and experimental studies discussed here suggest that alternative splicing probably plays a far more significant role in the generation of proteome diversity in plants than was previously thought.

 Alternative splicing and proteome diversity in plants

 

Genome-wide natural antisense transcription: coupling its regulation to its different regulatory mechanisms

 

Lapidot M, Pilpel Y. Genome-wide natural antisense transcription: coupling its regulation to its different regulatory mechanisms. EMBO Rep. 2006 Dec; 7 (12): 1216-22.

 

Many genomic loci contain transcription units on both strands, therefore two oppositely oriented transcripts can overlap. Often, one strand codes for a protein, whereas the transcript from the other strand is non-encoding. Such natural antisense transcripts (NATs) can negatively regulate the conjugated sense transcript. NATs are highly prevalent in a wide range of species--for example, around 15% of human protein-encoding genes have an associated NAT. The regulatory mechanisms by which NATs act are diverse, as are the means to control their expression. Here, we review the current understanding of NAT function and its mechanistic basis, which has been gathered from both individual gene cases and genome-wide studies. In parallel, we survey findings about the regulation of NAT transcription. Finally, we hypothesize that the regulation of antisense transcription might be tailored to its mode of action. According to this model, the observed relationship between the expression patterns of NATs and their targets might indicate the regulatory mechanism that is in action.

 Genome-wide natural antisense transcription-coupling its regulation to its different regulatory mechanisms

 

Plant snoRNAs: functional evolution and new models of gene expression

 

Brown JW, Echeverria M, Qu LH. Plant snoRNAs: functional evolution and new modes of gene expression. Trends Plant Sci. 2003 Jan; 8 (1): 42-9.

 

Small nucleolar RNAs (snoRNAs) are a well-characterized family of non-coding RNAs whose main function is rRNA modification. The diversity and complexity of this gene family continues to expand with the discovery of snoRNAs with non-rRNA or unknown targets. Plants contain more snoRNAs than other eukaryotes and have developed novel expression and processing strategies. The increased number of modifications, which will influence ribosome function, and the novel modes of expression might reflect the environmental conditions to which plants are exposed. Polyploidy and chromosomal rearrangements have generated multiple copies of snoRNA genes, allowing the generation of new snoRNAs for selection. The large snoRNA family in plants is an ideal model for investigation of mechanisms of evolution of gene families in plants.

 

MicroRNAs: Genomics, Biogenesis, Mechanism, and Function

 

David P. Bartel. MicroRNAs: Genomics, Biogenesis, Mechanism, and Function. Cell Volume 116, Issue 2, 23 January 2004, Pages 281-297

 

MicroRNAs (miRNAs) are endogenous 22 nt RNAs that can play important regulatory roles in animals and plants by targeting mRNAs for cleavage or translational repression. Although they escaped notice until relatively recently, miRNAs comprise one of the more abundant classes of gene regulatory molecules in multicellular organisms and likely influence the output of many protein-coding genes.

 

 

Let Me Count the Ways: Mechanisms of Gene Regulation by miRNAs and siRNAs

 

Ligang Wu and Joel G. Belasco Let Me Count the Ways: Mechanisms of Gene Regulation by miRNAs and siRNAs. Molecular Cell. Volume 29, Issue 1, 18 January 2008, Pages 1-7

 

The downregulation of gene expression by miRNAs and siRNAs is a complex process involving both translational repression and accelerated mRNA turnover, each of which appears to occur by multiple mechanisms. Moreover, under certain conditions, miRNAs are also capable of activating translation. A variety of cellular proteins have been implicated in these regulatory mechanisms, yet their exact roles remain largely unresolved.

 

MicroRNAs: Genomics, Biogenesis, Mechanism, and FuLet Me Count the Ways: Mechanisms of Gene Regulati

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