MicroRNAs: Genomics, Biogenesis, Mechanism, and Function

Two different methods of presenting quantitative gene expression exist: absolute and relative quantification. Absolute quantification calculates the copy number of the gene usually by relating the PCR signal to a standard curve. Relative gene expression presents the data of the gene of interest relative to some calibrator or internal control gene. A widely used method to present relative gene expression is the comparative C(T) method also referred to as the 2 (-DeltaDeltaC(T)) method. This protocol provides an overview of the comparative C(T) method for quantitative gene expression studies. Also presented here are various examples to present quantitative gene expression data using this method.

/pdf/analyzing-real-time-pcr-data-by-the-comparative-c-t-method-tnacbujy1o.pdf

Analyzing real-time PCR data by the comparative C(T) method.

http://bartellab.wi.mit.edu/publication_reprints/Bartel_Cell09.pdf

MicroRNAs: Target Recognition and Regulatory Functions

Motivation: Biological sequence data is accumulating rapidly, motivating the development of improved high-throughput methods for sequence classification.

Results: UBLAST and USEARCH are new algorithms enabling sensitive local and global search of large sequence databases at exceptionally high speeds. They are often orders of magnitude faster than BLAST in practical applications, though sensitivity to distant protein relationships is lower. UCLUST is a new clustering method that exploits USEARCH to assign sequences to clusters. UCLUST offers several advantages over the widely used program CD-HIT, including higher speed, lower memory use, improved sensitivity, clustering at lower identities and classification of much larger datasets.

Availability: Binaries are available at no charge for non-commercial use at http://www.drive5.com/usearch

Contact: [email protected]

Supplementary information:Supplementary data are available at Bioinformatics online.

/pdf/search-and-clustering-orders-of-magnitude-faster-than-blast-1c8ksdt7ke.pdf

Search and clustering orders of magnitude faster than BLAST

Pfam is a widely used database of protein families and domains. This article describes a set of major updates that we have implemented in the latest release (version 24.0). The most important change is that we now use HMMER3, the latest version of the popular profile hidden Markov model package. This software is approximately 100 times faster than HMMER2 and is more sensitive due to the routine use of the forward algorithm. The move to HMMER3 has necessitated numerous changes to Pfam that are described in detail. Pfam release 24.0 contains 11,912 families, of which a large number have been significantly updated during the past two years. Pfam is available via servers in the UK (http://pfam.sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/).

/pdf/the-pfam-protein-families-database-3t3lguk949.pdf

The Pfam protein families database

/pdf/enhanced-genome-assembly-and-a-new-official-gene-set-for-2xjev7zm11.pdf

Enhanced genome assembly and a new official gene set for Tribolium castaneum - from a draft to a reference genome

Background The dynamics of gene expression is implicated in an increasing number of fundamental biological processes, including cell fate decisions, inflammation and stem cell heterogeneity. However, the prevalence of the underlying network structures which drive dynamical behaviour, such as bistability, robusteness and noise reduction, remain mostly unexplored. Results We integrate transcription factor binding-site (TFBS) and microRNA target data to generate a gene interaction networks across 28 human tissues. These networks were interrogated to identify network structures previously identified to drive dynamical gene expression, including oscillations. Auto-regulatory motifs were identified in 56% of Transcription Factors (TFs) investigated while 49% of autoregulators were found to regulate and be regulated by a microRNA, forming dual feedback motifs. Both the autoregulatory motif and the microRNA dual feedback motif were found more often than expected by chance within the network (p Conclusion Autoregulation is prevalent amongst human TFs. TFs which autoregulate have more interactions with microRNAs than non-autoregulatory genes. The enrichment of oscillatory type motifs within the human transcriptional network indicates that more genes may be dynamically expressed in this way than previously thought. These data provide a resource for the identification of TFs which regulate the dynamical properties of human gene expression.

/pdf/feedback-motifs-tuned-by-micrornas-in-human-transcriptional-4ez0o3pr1e.pdf

Feedback motifs tuned by microRNAs in human transcriptional networks

The Structural and Biological Relationships of Cereal Proteins involved in Type I Allergy

Aims To identify differential expression of shorter non-coding RNA (ncRNA) genes associated with autism spectrum disorders (ASD). Background ncRNA are functional molecules that derive from non-translated DNA sequence. The HUGO Gene Nomenclature Committee (HGNC) have approved ncRNA gene classes with alignment to the reference human genome. One subset is microRNA (miRNA), which are highly conserved, short RNA molecules that regulate gene expression by direct post-transcriptional repression of messenger RNA. Several miRNA genes are implicated in the development and regulation of the nervous system. Expression of miRNA genes in ASD cohorts have been examined by multiple research groups. Other shorter classes of ncRNA have been examined less. A comprehensive systematic review examining expression of shorter ncRNA gene classes in ASD is timely to inform the direction of research. Methods We extracted data from studies examining ncRNA gene expression in ASD compared with non-ASD controls. We included studies on miRNA, piwi-interacting RNA (piRNA), small NF90 (ILF3) associated RNA (snaR), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), transfer RNA (tRNA), vault RNA (vtRNA) and Y RNA. The following electronic databases were searched: Cochrane Library, EMBASE, PubMed, Web of Science, PsycINFO, ERIC, AMED and CINAHL for papers published from January 2000 to May 2022. Studies were screened by two independent investigators with a third resolving discrepancies. Data was extracted from eligible papers. Results Forty-eight eligible studies were included in our systematic review with the majority examining miRNA gene expression alone. Sixty-four miRNA genes had differential expression in ASD compared to controls as reported in two or more studies, but often in opposing directions. Four miRNA genes had differential expression in the same direction in the same tissue type in at least 3 separate studies. Increased expression was reported in miR-106b-5p, miR-155-5p and miR-146a-5p in blood, post-mortem brain, and across several tissue types, respectively. Decreased expression was reported in miR-328-3p in bloods samples. Seven studies examined differential expression from other classes of ncRNA, including piRNA, snRNA, snoRNA and Y RNA. No individual ncRNA genes were reported in more than one study. Six studies reported differentially expressed snoRNA genes in ASD. A meta-analysis was not possible because of inconsistent methodologies, disparate tissue types examined, and varying forms of data presented. Conclusion There is limited but promising evidence associating the expression of certain miRNA genes and ASD, although the studies are of variable methodological quality and the results are largely inconsistent. There is emerging evidence associating differential expression of snoRNA genes in ASD. It is not currently possible to say whether the reports of differential expression in ncRNA may relate to ASD aetiology, a response to shared environmental factors linked to ASD such as sleep and nutrition, other molecular functions, human diversity, or chance findings. To improve our understanding of any potential association, we recommend improved and standardised methodologies and reporting of raw data. Further high-quality research is required to shine a light on possible associations, which may yet yield important information.

/pdf/a-systematic-review-of-non-coding-rna-genes-with-kafw8zfz.pdf

Sam Griffiths-Jones

Papers

Enhanced genome assembly and a new official gene set for Tribolium castaneum - from a draft to a reference genome

Feedback motifs tuned by microRNAs in human transcriptional networks

The Structural and Biological Relationships of Cereal Proteins involved in Type I Allergy

A systematic review of non-coding RNA genes with differential expression profiles associated with autism spectrum disorders

Plant protein families