A new paradigm for developmental biology

Mattick, John S.

doi:10.1242/jeb.005017

Cited by 213 publications

(187 citation statements)

References 358 publications

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“…This model is also consistent with the hypothesis advanced by Mattick and associates that most important genetic regulatory action in higher cells does not necessarily occur by specific interactions by proteins with DNA or RNA, or DNA molecules interacting with DNA, but at the level of long and short RNA regulatory molecules communicating with other RNA molecules as well as with other DNA and protein assemblies [38,39,50].…”

Section: Rt-mediated Long Dna Conversion Transcription Factories Andsupporting

confidence: 91%

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Genesis of ancestral haplotypes: RNA modifications and reverse transcription–mediated polymorphisms

et al. 2011

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how mutations in newly synthesized RNA might be copied back to DNA thus accounting for some of the genome-wide strand biases (e.g. the A-to-G vs T-to-C component of the strand biased spectrum). We hypothesize that the genesis of PFBs and extended AHs occurs during mutagenic episodes in evolution (e.g. retroviral infections) and that many of the critical DNA sequence diversifying events occur first at the RNA level e.g. recombination between RNA strings resulting in tandem and dispersed RNA duplications (retroduplications), RNA mutations via adenosine-to-inosine pre-mRNA editing events as well as error prone RNA synthesis. These are then copied back into DNA by a cellular reverse transcription (RT) process (also likely to be error-prone) we have called "RTmediated long DNA conversion" (RT-LDC). Finally we suggest that all these activities and others can be envisaged as being brought physically under the umbrella of special sites in the nucleus involved in transcription known as "Transcription Factories" (TF).

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Section: Rt-mediated Long Dna Conversion Transcription Factories Andsupporting

confidence: 91%

“…Before we proceed to a more formal analysis relating somatic gene diversification processes focused on rearranged Ig genes (1-2 Kb scale) to the Mb scale of the genome, it is important to discuss the work of Mattick and associates [38,39]. They established two important facts about the higher mammalian genome:…”

Section: Polak and Arndt Genome-wide Snp Analysesmentioning

confidence: 99%

Genesis of ancestral haplotypes: RNA modifications and reverse transcription–mediated polymorphisms

et al. 2011

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“…35 In addition, RNA has also been implicated as an epigenetic factor whereby processes including chromatin remodeling, transcription factor binding, and transcription are affected by RNA signaling (reviewed by Mattick). 36 Further studies of donor cells epigenetic contributions would benefit from the inclusion of histone modification and regulatory RNA-related effects on developmental competence.…”

Section: Discussionmentioning

confidence: 99%

Correlation of Developmental Differences of Nuclear Transfer Embryos Cells to the Methylation Profiles of Nuclear Transfer Donor Cells in Swine

Bonk¹,

Cheong²,

Li³

et al. 2007

Epigenetics

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Methylation of DNA is the most commonly studied epigenetic mechanism of developmental competence and somatic cell nuclear transfer (SCNT). Previous studies of epigenetics and the SCNT procedures have examined the effects of different culture media on donor cells and reconstructed embryos, and the methylation status of specific genes in the fetus or live offspring. Here we used a microarray based approach to identify the methylation profiles of SCNT donor cells including three clonal porcine fetal fibroblast-like cell sublines and adult somatic cells selected from kidney and mammary tissues. The methylation profiles of the donor cells were then analyzed with respect to their ability to direct development to the blastocyst stage after nuclear transfer. Clonal cell lines A2, A7 and A8 had blastocyst rates of 11.7% a , 16.7% ab and 20.0% b , respectively ( ab p < 0.05). Adult somatic cells included kidney, mammary (large), and mammary (small) also had different blastocyst rates ( ab p < 0.05) of 4.2% a , 10.7% ab and 18.3% b , respectively. For clonal donor cells and for adult somatic cell groups the donor cells with the highest blastocyst rates also had methylation profiles with the lowest similarity to the methylation profiles of the in vivo-produced blastocysts. Conversely, the donor cells with the lowest blastocyst rates had methylation profiles with the highest similarity to the methylation profiles of the in vivo-produced blastocysts. Our findings show there is an inverse correlation to the similarity of the methylation profiles of the donor cells and the in vivo-produced embryos, and to the blastocyst rates following SCNT. ABBREVIATIoNSA2, A7, A8, designation for three different donor cell populations; ANOVA, analysis of variance; BSA, bovine serum albumin;

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“…56 The observation and characterization of these small RNA species has significantly changed the perception of how gene expression is controlled. 57 It has also become apparent that many non-coding RNAs (ncRNA) [58][59][60] are present within the cell and that the majority of the entire human genome appears to be transcribed. 61,62 It is also very intriguing that ncRNA expression profiles do not appear to be conserved between various organisms, 63 suggesting a role for ncRNAs in the differential aspects of various species.…”

Section: Non Coding Rnasmentioning

confidence: 99%