The RNAi Consortium, or TRC, is a public-private partnership whose mission is to create libraries of

small hairpin RNA A short hairpin RNA or small hairpin RNA (shRNA/Hairpin Vector) is an artificial RNA molecule with a tight hairpin turn that can be used to silence target gene expression via RNA interference (RNAi). Expression of shRNA in cells is typically acco ...

s (shRNAs) for 15'000 human and 15'000 mouse

gene In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a ba ...

s. These libraries should help the scientific community to analyse gene function by

RNAi RNA interference (RNAi) is a biological process in which RNA molecules are involved in sequence-specific suppression of gene expression by double-stranded RNA, through translational or transcriptional repression. Historically, RNAi was known by o ...

. The consortium is based at the

Broad Institute The Eli and Edythe L. Broad Institute of MIT and Harvard (IPA: , pronunciation respelling: ), often referred to as the Broad Institute, is a biomedical and genomic research center located in Cambridge, Massachusetts, Cambridge, Massachusetts, U ...

of the

MIT The Massachusetts Institute of Technology (MIT) is a private land-grant research university in Cambridge, Massachusetts. Established in 1861, MIT has played a key role in the development of modern technology and science, and is one of the mo ...

and

Harvard University Harvard University is a private Ivy League research university in Cambridge, Massachusetts. Founded in 1636 as Harvard College and named for its first benefactor, the Puritan clergyman John Harvard, it is the oldest institution of higher le ...

, and includes 6 MIT- and Harvard-associated institutions and 5 international life sciences organizations. Verified RNAi clones and entire libraries are made available both by

Sigma-Aldrich Sigma-Aldrich (formally MilliporeSigma) is an American chemical, life science, and biotechnology company that is owned by the German chemical conglomerate Merck Group. Sigma-Aldrich was created in 1975 by the merger of Sigma Chemical Company a ...

and Open Biosystems.

Hairpin selection

A set of candidate hairpins are selected based on the 1s
Refseq
transcript from each

NCBI The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. The ...

gene. They should be 21mers, be at least 25bp from start of the

coding sequence The coding region of a gene, also known as the coding sequence (CDS), is the portion of a gene's DNA or RNA that codes for protein. Studying the length, composition, regulation, splicing, structures, and functions of coding regions compared to no ...

and no closer than 150bp from its end. Candidates are scored based on various

empirical Empirical evidence for a proposition is evidence, i.e. what supports or counters this proposition, that is constituted by or accessible to sense experience or experimental procedure. Empirical evidence is of central importance to the sciences and ...

rules (see the Broad Institute's web site for a complete lis

and then

BLAST Blast or The Blast may refer to: * Explosion, a rapid increase in volume and release of energy in an extreme manner *Detonation, an exothermic front accelerating through a medium that eventually drives a shock front Film * ''Blast'' (1997 film) ...

ed against 2

transcriptome The transcriptome is the set of all RNA transcripts, including coding and non-coding, in an individual or a population of cells. The term can also sometimes be used to refer to all RNAs, or just mRNA, depending on the particular experiment. The t ...

sets. Hairpins that are unique for a

Unigene UniGene was a NCBI database of the transcriptome and thus, despite the name, not primarily a database for genes. Each entry is a set of transcripts that appear to stem from the same transcription locus (i.e. gene or expressed pseudogene). Informat ...

cluster and a RefSeq NM identifier are preferred. Lastly, the candidates are spaced to have 1 hairpin in the

3' untranslated region In molecular genetics, the three prime untranslated region (3′-UTR) is the section of messenger RNA (mRNA) that immediately follows the translation termination codon. The 3′-UTR often contains regulatory regions that post-transcriptionally ...

and 4 in the coding sequence.

Hairpin vector

Selected hairpins are cloned into the

vector Vector most often refers to: *Euclidean vector, a quantity with a magnitude and a direction *Vector (epidemiology), an agent that carries and transmits an infectious pathogen into another living organism Vector may also refer to: Mathematic ...

pLKO1, which is a multipurpose

plasmid A plasmid is a small, extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently. They are most commonly found as small circular, double-stranded DNA molecules in bacteria; how ...

that can be propagated in

bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among ...

, transfected into

mammal Mammals () are a group of vertebrate animals constituting the class Mammalia (), characterized by the presence of mammary glands which in females produce milk for feeding (nursing) their young, a neocortex (a region of the brain), fur or ...

ian

cell line An immortalised cell line is a population of cells from a multicellular organism which would normally not proliferate indefinitely but, due to mutation, have evaded normal cellular senescence and instead can keep undergoing division. The cell ...

s or used for generation of

lentivirus ''Lentivirus'' is a genus of retroviruses that cause chronic and deadly diseases characterized by long incubation periods, in humans and other mammalian species. The genus includes the human immunodeficiency virus (HIV), which causes AIDS. Lent ...

es. It contains resistance genes against

ampicillin Ampicillin is an antibiotic used to prevent and treat a number of bacterial infections, such as respiratory tract infections, urinary tract infections, meningitis, salmonellosis, and endocarditis. It may also be used to prevent group B strepto ...

and

puromycin Puromycin is an antibiotic protein synthesis inhibitor which causes premature chain termination during translation. Inhibition of translation Puromycin is an aminonucleoside antibiotic, derived from the '' Streptomyces alboniger'' bacterium, ...

Release

Release 1 of the TRC lentiviral shRNA libraries consist of about 35'000 shRNA constructs against 5300 human (25'000 clones) and 2200 mouse genes (10'000 clones). Release 2 of the human shRNA library contained an additional 9'500 clones. Releases occur roughly every quarter. The completing of both mouse and human libraries is envisioned for the end of 2006 or beginning of 2007.

External links

TRC homepage at the Broad Institute

OpenBiosystems TRC intro page
{{DEFAULTSORT:Rnai Consortium Biotechnology companies of the United States Research support companies Harvard University Massachusetts Institute of Technology