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发表于 2010-5-12 13:12 |只看该作者
回复 20# saturn
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I always miss it as you didn't use reply.) f; Z" r4 T1 a- }: P# `
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For your first answer, why don't you think I have seen such sentence? There is a lot more such sentence than you could imagine. Furthermore, could you exemplify your view with an article or review which clearly claim the miRNA belong to epigenetics, but not merely by post a wiki definition and inference?
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For your second answer, firstly thanks for offering several papers about this theme. I only wonder why you guess I would argue for that funny reason, then answer for it that as if I really don't understand. On the contrary, I have found another article which you didn't mention as  supportive materials. I post the article address instead of PDF because this is from an OA journal:; ?  M9 b8 [; v% r6 z
http://www.biomedcentral.com/1471-2199/10/12
3 ?' _; R7 T" A7 n$ p; vNow the question is to wait for more rigorious corroboration. After all they are published recently.+ B# G/ H; s- b. d

8 z5 L! K* S. O. w4 kp.s.: You "personally think there will be nobody agree with the narrow definition", however how about the author of that review? And, all I know is that at least one expert does not not consider microRNAs an epigenetic mechanism.
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发表于 2010-5-12 18:08 |只看该作者
本帖最后由 saturn 于 2010-5-12 18:12 编辑   k. d# r$ D. g$ O" s. o
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here are several publications elucidate miRNA is an epigenetic regulator
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Review) G1 L( C8 x) V: @) s2 V- f% V& D
Epigenetic mechanisms in glioblastoma multiforme
1 ?, [6 e& _, d% D6 Z: GRaman P. Nagarajana and Joseph F. CostelloCorresponding Author Contact Information, a, E-mail The Corresponding Author. o0 |- K, h1 i& m) G& ^0 D; v& |
aBrain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA
4 |, f# }- Y3 QAvailable online 20 February 2009.( H9 Y  p/ P, V$ j% \3 ~# e: _8 i
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2.7. Aberrant expression of microRNAs in GBM
1 n$ b! N% d" m& YMicroRNAs (miRNAs), non-coding RNAs which are potential epigenetic regulatory effectors, are important in normal mammalian development and dysregulation of their expression has been observed in multiple human cancers. MiRNAs are 19–25 nt in length and are cleaved from 60–110 nt hairpin precursors (pre-miRNAs) derived from larger primary transcripts (pri-miRNAs). MiRNAs can regulate gene expression through interactions with mRNAs in regions of sequence complementary, blocking translation of mRNAs [103].
6 Q9 M+ f1 [4 g. y7 m2 o5 eIn GBM, multiple miRNAs are aberrantly expressed or repressed in both primary tumors and cell lines [104]. Primary GBMs and cell lines overexpress miR-221, whereas a set of brain-enriched miRNAs (miR-128, miR-181a, miR-181b, and miR-181c) shows decreased expression [105]. Reduced miR-128 expression in GBM and consequent reduced cell proliferation in vitro and in xenografts [106] were shown in a separate study. Furthermore, miR-128 regulates the expression of the polycomb complex protein Bmi-1 through binding at the BMI-1 3′-UTR, resulting in decreased Bmi-1 and H3K27me3 levels. In GBM-derived neurosphere cells, miR-128 overexpression blocked stem cell self-renewal, indicating that miR-128 can regulate the stem cell-like capabilities of a subset of GBM cells.
" [/ m7 W, [: D5 |) B2 M4 ?Additional microRNAs are aberrantly expressed in GBM. MiR-124 and miR-137 are underexpressed in primary GBM and anaplastic astrocytoma [107]. MiR-137 expression was increased in GBM cell lines U87 and U251 following treatment with 5-aza-2′-deoxycytidine, suggesting regulation of these microRNAs by DNA methylation. Functionally, miR-124 and miR-137 inhibit proliferation in GBM and can induce differentiation of normal neural and brain tumor stem cells. Additional studies have demonstrated that miR-124 is underexpressed in primary oligodendrogliomas, astroblastomas, and GBM cell lines [108], [109] and [110] indicating a potentially central role for this non-coding RNA in brain tumors. Overall, microRNAs appear to play multiple roles in cancer biology; for example in GBM miR-21 has both anti-apoptotic and pro-invasion functions
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REVIEW
* ]( v+ N% g7 P( i! r6 WThe microRNA network and tumor metastasis3 S/ E( h( q2 w" _: @& g* l7 _
H Zhang, Y Li and M Lai2 L* n3 t3 k) |9 N% s
Department of Pathology, School of Medicine, Zhejiang University, Zhejiang, PR China
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4 U6 N7 t" X5 v. Q' d, QThe reciprocal regulation between miRNA and epigenetic modification in tumor metastasis
4 C: Y+ O! V. |4 w: G( B, g7 w. OEpigenetic modifications include DNA methylation and covalent modification of histones. These alterations are reversible, but very stable, and have a significant impact on the regulation of gene expression, the contribution of which to cancer goes beyond the early stages of tumor transformation to affect metastasis. However, miRNAs have an important role in epigenetic modification, and are also regulated by epigenetic mechanisms in tumor metastasis.
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) l; t+ o* z; u7 zNature Reviews Rheumatology 5, 266-272 (May 2009) | doi:10.1038/nrrheum.2009.55
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Epigenetic control in rheumatoid arthritis synovial fibroblasts' |! h. f$ q; ]- S+ a

2 u; g8 a1 p' }, |+ @7 n0 `3 E  eEmmanuel Karouzakis, Renate E. Gay, Steffen Gay & Michel Neidhart
# B  v/ g9 b9 ^  D8 yAbstract
0 y+ }2 x% Q/ V2 cRheumatoid arthritis synovial fibroblasts (RASFs) are the effector cells of cartilage and bone destruction. These cells show an 'intrinsically' activated and aggressive phenotype that results in the increased production of matrix-degrading enzymes and adhesion molecules, and is conserved over long-term passage in vitro. The three main mechanisms of epigenetic control—DNA methylation, histone modifications and microRNA activity—interact in the development of the RASF phenotype. The extent of global DNA methylation is reduced in synoviocytes in situ and RASFs in vitro. In addition, histone hyperacetylation occurs and specific microRNAs are expressed in RASFs. Normal synovial fibroblasts cultured in a hypomethylating milieu acquire an activated phenotype similar to that of RASFs. These findings suggest that epigenetic control, in particular the control of DNA methylation, is deficient in RASFs. Genome-wide analyses of the epigenome will enable the detection of additional genes involved in the pathogenesis of rheumatoid arthritis, the identification of epigenetic biomarkers, and potentially the development of a therapeutic regimen that targets activated RASFs.
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Leukaemogenesis:more than mutant genes6 s. W' t* v8 |- ?, I0 N
Jianjun Chen*§, Olatoyosi Odenike*§ and Janet D. Rowley*‡% ?( L/ F  K0 I- ]" i
Abstract | Acute leukaemias are characterized by recurring chromosomal aberrations andgene mutations that are crucial to disease pathogenesis. It is now evident that epigenetic modifications, including DNA methylation and histone modifications, substantially contribute to the phenotype of leukaemia cells. An additional layer of epigenetic complexity is the pathogenetic role of microRNAs in leukaemias, and their key role in the transcriptional regulation of tumour suppressor genes and oncogenes. The genetic heterogeneity of acute leukaemias poses therapeutic challenges, but pharmacological agents that target components of the epigenetic machinery are promising as a component of the therapeutic arsenal for this group of diseases.
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$ w; _& l2 Q3 S1 fhope for your comments, by the way could you list some evidences show that miRNA is not an epigenetic effector?(from the expert you mentioned)
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发表于 2010-5-12 18:12 |只看该作者
本帖最后由 saturn 于 2010-5-12 18:21 编辑
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" K7 S9 a9 q' B# A+ W' zto be honest,  i pay less attention to the definition of epigenetic(strict definition), however, personally i think the most important thing in the definition is to  regulate gene expression without changes in DNA sequence, i also think this is accepted by all the researchers in this field. 6 v/ D! O' b: S  J+ d# u! d

" {7 @' P) ~6 N! Hand i also have an another requirement, could you list some exact the same sentence in you last post, such as epigenetic mechanism of DNA methylation or histone modification in the regulation of…… in any papers is OK.
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# p3 W6 S$ |' [! i# Mnothing in the world is absolutely!
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发表于 2010-5-12 19:04 |只看该作者
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here is also another interesting paper related paramutation, also controlled by miRNA" K# h; [/ g$ h
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by the way, if you are really interested, you could search miRNA epigenetic in pubmed, then you could find plenty of papers.
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" [/ Y' h/ p9 {8 H& ~0 Hit is a little funny to discuss this topic with a person who are not in epigenetic field, if you have read some important papers in this field, i suppose you should not ask such a silly question.
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发表于 2010-5-12 21:12 |只看该作者
uh...somebody seemed so irritated about some amateur’s viewpoint...as to call his argument "a silly question", which is still a debate in some expert's mind. But now I can't spare time to defend cauz the this month I'm so buzy. Truely you can see the the sentence you required in many places. I will not show them to you cauz it make no sense to discuss with someone who call other's question a silly one when he could not convince him. Also, you have not convinced many others, although you did not define them as silly......
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发表于 2010-5-12 22:04 |只看该作者
hehe, first i want to say i am not angry with you, i don't know why you said i was irritated,
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5 ?) a2 u* U- _6 m0 U. |second i was wondering why the evidences i showed are not convincing, i think they are all published in good journals, at least better or higher influence than the modern immunology you mentioned before.* k, w% O0 }7 p- s1 g: B( N

' O" @6 o1 T% U( n1 Cthird, don't you think it is a silly question. if you have more knowledge in epigenetic field, you could never ask such a kind of question.
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* G2 l8 S/ @+ z& xfinally, i think i am the first one want to end this discussion with you.4 A9 u% |3 T8 J( D' \
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however, now you could not show any evidence that support your layman's point, you just said i was too busy to discuss with you.
+ _! J# w0 d, T% X6 gok let's stop ! ) S; v4 F+ H9 ?- a4 a. {/ \- z3 Z
everyone is too busy with their experiments, not only you.6 e2 P. D5 A; i" ]
by the way, some time when you have a chance to discuss with the others i think you have to treasure it,  you might learn something from the discussion,
3 I% Y8 Q' L( H/ ^! _  `it is meaningful!
$ a) c& O/ p9 a- a6 y- U8 U% uthat is why so many conferences exist!
4 h0 T5 N7 u. P4 o5 ] i hope next time if you want to discuss something with the others please make sure that you know that field well. and do please not say anything you have no evidence to support your point!
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发表于 2010-5-13 00:24 |只看该作者
哎,除了读写文章,实在不想用鸟语
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8 ~- x& w# k1 A! P) P首先,问题si不silly不是由提出异议者有没有epigenetic背景决定,因为有背景的内行也有不认同此观点的。其次我持m不属于E观点已经贴了一篇NEJM,其没有把m归纳到E中,而只是讲了两者互相影响。持m属于E观点者需要证据充分,而且经的起长久考验;当然你贴了一些paper,我还帮你贴了一篇,但实在太忙没法继续看了,(说自己忙你也有意见啊,况且我也不是忙实验呀,人生不会全都是实验的......), d2 h* t3 h0 g
还有一点被你扯远了:按你的意思,此后发帖者要小心了,没有know that field well者不要乱说,否则要吃亏的......9 r3 P2 F! s: a! \: h6 Q

( ?' `" W4 S1 c- K虽然忙,但是还是抽空google了一下你问我要的句子:% W& E. h# r9 Q2 o* N5 C
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1. The results demonstrate an epigenetic mechanism of DNA methylation in programming of cardiac Prkce gene repression, linking fetal cocaine exposure and pathophysiological consequences in the heart of adult male offspring in a gender-dependent manner.
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  y! f  u; M# E. R) l2. An important aspect of the epigenetic regulation of the PL-I gene is that there are only a few CpGs in the regulatory region and placenta-non-specific transcription factors such as GATA and AP-1 can regulate the placenta-specific genes in combination with the epigenetic mechanism of DNA methylation7 e9 O( O1 \5 _; w: {1 W

. h# ?9 v4 _: i3. Fundamentals of epigenetic gene regulation are reviewed, with an emphasis on the epigenetic mechanism of DNA methylation.' k" v6 X5 x9 f+ M! v2 ]
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4. Therefore, it is possible that Sp1 transactivation and transcriptional repression by MeCP2 are coupled regulatory mechanisms in higher-order eukaryotes and that these two types of regulation also contribute to the epigenetic mechanism of DNA methylation required for proper gene expression. 2 {: b) I9 S- ^; t) Y: f$ p

  F3 @3 u, h: k8 l* k% D# x' V......
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发表于 2010-5-13 07:05 |只看该作者
希望大家平和心态 就事论事 争论可以看到自己的不足 真理是越辨越明。- Z3 |+ D! Z& c" ]4 z4 r  X$ f7 T
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至于其他的事情 不要过分苛求$ u7 ]7 S' r3 [6 j

5 v, B: p: O4 M* i8 k论坛有过一个会员说过一句话,给我印象很深.他说:能在论坛上找到一个人吵架,是很幸福的事情。
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. b& ^. q8 E# M4 R: \. ]6 C# q大家都是好朋友 希望你们在论坛过的开心。

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发表于 2010-5-13 11:48 |只看该作者
友情支持一把土星。
3 ^7 ?% l' J6 v  E! c俺在Epigenetics领域混了有些年头了,俺认为包括miRNA在内的ncRNA是属于表观遗传研究范畴的,俺就懒得引进据点了。NEJM虽说是个很好的杂志,但在基础研究领域发言权还是很弱的。

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发表于 2010-5-13 21:31 |只看该作者
嗯,楼上言是。
' _" ~4 Z/ S5 }- isaturn大哥别在意,其实偶一点也不觉得那个定义多么有理,只是看看有没有办法面对你这个业内人说出个理来,网坛嘛,要是同你在论坛或杂志上pk的话那才叫本事。6 Z) n5 _; G4 k; _
很多周围的人做这方面工作时从来不care miRNA的归属,这也是为什么有些人对此一直持保守意见。4 j6 C- \/ c7 C
海洋版主也真够意思,不仅增加坛了民幸福感,还给偶俩辩论过程加了那么多包包,实在惭愧。以前干细胞研究者到处求助,如今各路好手汇聚此坛,奉献家藏、积淀思想、传秉精神,海洋兄等功不可没
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