A Family of Human MicroRNA Genes from Miniature Inverted-Repeat Transposable Elements

In the paper

“A striking feature of plant MITEs is their apparent preference for insertion in gene regions [49], [50].”

What the sources say

• Supported

  In “Miniature Inverted-repeat Transposable Elements,” 48.3% of rice MITE-containing sequence-tagged connectors matched the rice gene index, versus 11.5% of those lacking MITEs. The paper also describes gene association in maize, while cautioning that the association varies among MITE families. This supports the claim’s qualified wording, “apparent preference.” (LLM, conf=0.90)

  cites [49] L Mao, 2000, Rice transposable elements: a survey of 73,000 sequence-tagged-connectors., Genome Res source
• Supported

  The Discussion (‘A Strong Preference for Genic Targets’) says that insertion into genic regions had been suggested as a feature of MITEs, while noting that earlier database studies could not establish a true preference. The paper reports preferential insertion into genic regions for the Heartbreaker MITE family. The claim’s word ‘apparent’ preserves that distinction; page numbers were not provided in our copy. (LLM, conf=0.91)

  cites [50] Q Zhang, 2000, Recent, extensive, and preferential insertion of members of the miniature inverted-repeat transposable element family Heartbreaker into genic regions of maize., Proc Natl Acad Sci U S A source

In the paper

“Mature miRNAs are processed from longer RNA sequences that form local stem-loop (hairpin) structures [3].”

What the sources say

• Supported

  The supplied passage [3] (labeled Abstract; no page provided) states that miRNAs are processed from transcripts capable of forming local RNA hairpin structures. The biogenesis passage [4] also describes cleavage of a stem-loop precursor to produce the mature miRNA. (LLM, conf=0.95)

  cites [3] DP Bartel, 2004, MicroRNAs: genomics, biogenesis, mechanism, and function., Cell source

In the paper

“There are two models to explain the repressive effects that miRNAs exert on target gene expression: i-translational repression and ii-mRNA degradation [16], [17], [42].”

What the sources say

• ?Not checked — no full text of the sourcecites [16] S Yekta, 2004, MicroRNA-directed cleavage of HOXB8 mRNA., Science source
• Not checked yet

  Checked before — its earlier verdict is held back until a new check runs.

  cites [17] Y Zeng, 2003, MicroRNAs and small interfering RNAs can inhibit mRNA expression by similar mechanisms., Proc Natl Acad Sci U S A source
• Supported

  The Conclusions (page not provided) contrast inhibition of translation without target degradation with a mechanism involving tissue-specific mRNA degradation. The paper favors translational inhibition for most mammalian miRNAs, but recognizes both mechanisms described in the claim. (LLM, conf=0.88)

  cites [42] T Babak, 2004, Probing microRNAs with microarrays: tissue specificity and functional inference., Rna source

In the paper

“The connection between TEs and siRNAs has led to the proposal that origination from TEs distinguishes siRNAs from miRNAs [3].”

What the sources say

• Supported

  In “Mechanism: Distinctions between miRNAs and siRNAs” (page not provided), the paper identifies origin as a distinction: siRNAs often derive from transposons, whereas miRNAs derive from distinct genomic loci. It presents these differences as a basis for distinguishing the two classes; “often” is an important qualification. (LLM, conf=0.88)

  cites [3] DP Bartel, 2004, MicroRNAs: genomics, biogenesis, mechanism, and function., Cell source

In the paper

“This was slightly surprising given that there are 7,850 annotated Made1 sequences in the human genome.”

In the paper

“There are 29 GO biological process categories, encompassing 104 genes, which contain an over-representation of genes from these clusters (Table S3).”

In the paper

“This 754 base pair (bp) EST maps to chromosome chr13 at positions 24,718,360–24,719,104; it includes a nearly full length Made1 element as well as 325 bp of 5′ flanking DNA and 353 bp of sequence 3′ to the element.”

In the paper

“These include genes encoding a cell division cycle protein (ENSG00000004897), a C epsilon type protein kinase (ENSG00000171132) and a centromere/kinetochore protein (ENSG00000086827).”

In the paper

“Visualization of genomic expression data, generated with human genome tilling arrays [30], shows that this particular Made1 is inserted into an intergenic region of the genome that is transcriptionally active (Figure 3).”

In the paper

“the intersection of the target gene sets derived from the miRBase versus Made1 consists of a mere 29 genes, and this figure is only slightly higher than the random expectation of 27 shared targets (P = 0.07 binomial distribution).”

In the paper

“However, as reported here and elsewhere [21], more and more TE-derived miRNAs are being discovered.”

What the sources say

• ?Not checked — no full text of the sourcecites [21] NR Smalheiser, 2005, Mammalian microRNAs derived from genomic repeats., Trends Genet source

In the paper

“TEs, such as Madel, represent a natural source of such lineage-specific miRNAs, which could in turn be responsible for regulatory phenotypes that contribute to evolutionary diversification between species.”

In the paper

“However, a recent report indicated that a number of mammalian miRNAs, including six human miRNAs, are in fact derived from TEs [21].”

What the sources say

• ?Not checked — no full text of the sourcecites [21] NR Smalheiser, 2005, Mammalian microRNAs derived from genomic repeats., Trends Genet source

In the paper

“A number of epigenetic gene silencing mechanisms, such as cytosine methylation [52], genomic imprinting [53] and heterochromatin [54] are thought to have evolved as defense mechanisms against transposition.”

What the sources say

• ?Not checked — no full text of the sourcecites [52] JA Yoder, 1997, Cytosine methylation and the ecology of intragenomic parasites., Trends Genet source
• ?Not checked — no full text of the sourcecites [53] JF McDonald, 2005, Host defenses to transposable elements and the evolution of genomic imprinting., Cytogenet Genome Res source
• ?Not checked — no full text of the sourcecites [54] Z Lippman, 2004, Role of transposable elements in heterochromatin and epigenetic control., Nature source

In the paper

“This would provide ample opportunities for the processing of MITE hairpins by RNA interference enzymatic machinery, which is known to play a particularly important role in plant gene regulation [51].”

What the sources say

• Not checked yet

  Checked before — its earlier verdict is held back until a new check runs.

  cites [51] MA Matzke, 2004, Planting the seeds of a new paradigm., PLoS Biol source

In the paper

“Hsmar1 elements are DNA-type TEs, approximately 1,300 bp in length, which possess a transposase-encoding open reading frame flanked by terminal inverted repeat (TIR) sequences (Figure 2A) [41].”

What the sources say

• ?Not checked — no full text of the sourcecites [41] HM Robertson, 1997, Molecular evolution of an ancient mariner transposon, Hsmar1, in the human genome., Gene source

In the paper

“Muk is an effective silencer of the MuDR DNA-type TE, and the Muk locus consists of an inverted duplication of a partially deleted MuDR element.”

What the sources say

• ?Not checked — no full text of the sourcecites [19] RK Slotkin, 2005, Heritable transposon silencing initiated by a naturally occurring transposon inverted duplication., Nat Genet source

In the paper

“In addition, the dispersed repetitive nature of TE sequences provides for the emergence of multiple novel miRNA genes as well as numerous homologous target sites throughout the genome.”

In the paper

“The evolutionary lineage-specific nature of MITEs could also provide for the generation of novel regulatory phenotypes related to species diversification.”

In the paper

“Therefore, we propose a model whereby Made1 insertions into transcriptionally active genomic regions would yield viable pri-miRNA structures that would be processed into mature miRNA sequences by the RNA interference enzymatic machinery.”

In the paper

“Apparently, Made1 sequences avoid protein coding gene exon regions and thus are poorly represented among potential hsa-mir-548 target sites.”

In the paper

“Consistent with this model, there are a number of cases of siRNAs that originate from TEs in different species [55]–[58].”

What the sources say

• Not checked yet

  Checked before — its earlier verdict is held back until a new check runs.

  cites [55] AA Aravin, 2003, The small RNA profile during Drosophila melanogaster development., Dev Cell source
• Not checked yet

  Checked before — its earlier verdict is held back until a new check runs.

  cites [56] A Hamilton, 2002, Two classes of short interfering RNA in RNA silencing., Embo J source
• Not checked yet

  Checked before — its earlier verdict is held back until a new check runs.

  cites [57] Z Lippman, 2003, Distinct mechanisms determine transposon inheritance and methylation via small interfering RNA and histone modification., PLoS Biol source
• ?Not checked — no full text of the sourcecites [58] D Zilberman, 2003, ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation., Science source

In the paper

“MITEs are widely distributed among eukaryotes [46]”

What the sources say

• ?Not checked — no full text of the sourcecites [46] C Feschotte, 2002, Miniature inverted-repeat transposable elements and their relationship to established DNA transposons. source

In the paper

“When Muk is transcribed, it yields a long (>2 kb) dsRNA hairpin structure that is processed to yield siRNAs.”

What the sources say

• ?Not checked — no full text of the sourcecites [19] RK Slotkin, 2005, Heritable transposon silencing initiated by a naturally occurring transposon inverted duplication., Nat Genet source

In the paper

“For instance, MITEs are particularly prevalent in plants where they were first discovered [47]”

What the sources say

• ?Not checked — no full text of the sourcecites [47] TE Bureau, 1992, Tourist: a large family of small inverted repeat elements frequently associated with maize genes., Plant Cell source

In the paper

“Including these new data, version 8.2 of miRBase, the online microRNA database [11], reports 462 human miRNA genes.”

What the sources say

• Not checked yet

  Checked before — its earlier verdict is held back until a new check runs.

  cites [11] S Griffiths-Jones, 2006, miRBase: microRNA sequences, targets and gene nomenclature., Nucleic Acids Res source

In the paper

“The tight hairpin formed by the element is similar to the structures processed by Drosha and Dicer, and the location of the mature miRNA sequence, in the stem close to the 3′ end of the structure, is consistent with the mode of cleavage thought to be employed by the Dicer (Figure 4B).”

In the paper

“In a similar way, RNA interference by siRNAs is considered to have evolved to silence TEs [18], [20].”

What the sources say

• ?Not checked — no full text of the sourcecites [18] MA Matzke, 2000, Transgene silencing by the host genome defense: implications for the evolution of epigenetic control mechanisms in plants and vertebrates., Plant Mol Biol source
• ?Not checked — no full text of the sourcecites [20] NL Vastenhouw, 2004, RNAi protects the Caenorhabditis elegans germline against transposition., Trends Genet source

In the paper

“the rice genome alone contains ∼90,000 MITEs [48].”

What the sources say

• ?Not checked — no full text of the sourcecites [48] N Jiang, 2004, Using rice to understand the origin and amplification of miniature inverted repeat transposable elements (MITEs)., Curr Opin Plant Biol source

In the paper

“a recent analysis of the human genome detected numerous putative miRNAs that are not evolutionarily conserved [5].”

What the sources say

• ?Not checked — no full text of the sourcecites [5] I Bentwich, 2005, Identification of hundreds of conserved and nonconserved human microRNAs., Nat Genet source

In the paper

“Recently, anti-correlated expression patterns between miRNA sequences and their target mRNAs have provided evidence in favor of the mRNA degradation model [43].”

What the sources say

• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites [43] JC Huang, 2006, Detecting microRNA targets by linking sequence, microRNA and gene expression data.

In the paper

“Such panhandle structures would include long internal loop regions that correspond to the internal open reading frames that are lost when autonomous elements are converted to non-autonomous MITE derivatives.”

In the paper

“Many of the extant miRNA genes characterized today may have evolved beyond recognition to their progenitor TEs, while others may have originated from other genomic re-structuring mechanisms that juxtapose short inverted repeats [59].”

What the sources say

• ?Not checked — no full text of the sourcecites [59] E Allen, 2004, Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana., Nat Genet source

In the paper

“MITEs retain the TIRs, and those same TIRs that were processed from longer RNAs to form siRNA could be similarly processed to form miRNAs.”