a****o
发帖数: 1786 | 1 Journal Club 1: Paused RNA polymerase and bidirectional transcription
谢绝转载
我来抛砖引玉了，其实不是砖，是坯
In the last issue of 2008, Science published 4 related papers about paused
RNA polymerase and bidirectional transcription. I would like to briefly
summarize the history of these studies and how they would influence our
understanding of transcription.
Paused polymerase
The first well known example of paused (stalling) RNA polymerase was
described about 20 years ago by John Lis and colleagues at Cornell
Uni | m****g
发帖数: 530 | | a***e
发帖数: 1010 | 3 This is a very nice summarization of the recent biggest advancement of the
transcription field.
Although protein coding genes only occupy a small part of the genome, people
have accepted the idea that most of the genome sequences are actually
transcribed. In the last issue of 2008, Science published Lis and colleague
’s work about RNA polymerase II –mediated bi-directional transcription
which excited the people wondering how much we really understand
transcription.
In these papers, researchers | a***e
发帖数: 1010 | 4 http://www.sciencemag.org/content/vol322/issue5909/index.dtl
(1)Nascent RNA Sequencing Reveals Widespread Pausing and Divergent
Initiation at Human Promoters
Leighton J. Core, Joshua J. Waterfall, and John T. Lis
Science 19 December 2008: 1845-1848.
(2)Divergent Transcription from Active Promoters
Amy C. Seila, J. Mauro Calabrese, Stuart S. Levine, Gene W. Yeo, Peter B.
Rahl, Ryan A. Flynn, Richard A. Young, and Phillip A. Sharp
Science 19 December 2008: 1849-1851.
(3) RNA Exosome Depletion Reve | a****o
发帖数: 1786 | 5 果然引来一颗大玉， 待我来琢琢
some of your comments are based on the assupmtion that bidirectional
transcrption happened in the same cell, but I feel it is still a open
question right now. As I pinted out in my last post. If bidirectional
transcription happens in different cell populations, i.e, in some cells,
transcription happen in forward direciton, while in other cells,
transcription happen in reverse direction.The direction of transcription may
be determined stochastically. Sunny Xie group has showed tha
【在 a***e 的大作中提到】
: This is a very nice summarization of the recent biggest advancement of the
: transcription field.
: Although protein coding genes only occupy a small part of the genome, people
: have accepted the idea that most of the genome sequences are actually
: transcribed. In the last issue of 2008, Science published Lis and colleague
: ’s work about RNA polymerase II –mediated bi-directional transcription
: which excited the people wondering how much we really understand
: transcription.
: In these papers, researchers
| a***e
发帖数: 1010 | 6 I agree it is reasonable that the bidirectional transcription can happen in
different cell populations. It is a pity that the authors didn’t compare
whether cell cycle or environmental stimuli can change gene expression
profile of the reverse transcription.
This promoter-proximal bidirectional transcription was also observed in
bacteria. It is speculated the reverse transcription can be quickly
switched to forward transcription (if my memory is right, in a recent N or S
paper).
My biggest int | n********k
发帖数: 2818 | 7 very much interested in the topics but haven't really followed closely and
thought as much as you two since I am not ready to venture into it, it seems
u are about ready to go there:)). I will try to read those papers carefully
and then may comment later...for now, I am just gonna talk some nonsense:)
At the times when the news/papers were out, I was mostly wondering/
interested in how these may have to do with competent transcriptional status
regulation, and the sequential and coupling nature o
【在 a***e 的大作中提到】
: I agree it is reasonable that the bidirectional transcription can happen in
: different cell populations. It is a pity that the authors didn’t compare
: whether cell cycle or environmental stimuli can change gene expression
: profile of the reverse transcription.
: This promoter-proximal bidirectional transcription was also observed in
: bacteria. It is speculated the reverse transcription can be quickly
: switched to forward transcription (if my memory is right, in a recent N or S
: paper).
: My biggest int
| a****o
发帖数: 1786 | 8 In deed, if at any given time, in one cell, there is only one direction of
transcriptioin for a particular gene, this can be a very elegant regulatory
mechanism to either repress the forward transcription, or make the chromatin
structure open and prepare for quick induction when there is inducing
signal.
about the coupling of transcription and splicing, it would be interesting to
test if only forward transcription is capable to recruit splicing machinery
to do the job. since phosphorylation of C
【在 n********k 的大作中提到】
: very much interested in the topics but haven't really followed closely and
: thought as much as you two since I am not ready to venture into it, it seems
: u are about ready to go there:)). I will try to read those papers carefully
: and then may comment later...for now, I am just gonna talk some nonsense:)
: At the times when the news/papers were out, I was mostly wondering/
: interested in how these may have to do with competent transcriptional status
: regulation, and the sequential and coupling nature o
| n********k
发帖数: 2818 | 9
transcription for a particular gene, this can be a very elegant regulatory
mechanism to either repress the forward transcription, or make the
chromatin structure open and prepare for quick induction when there is
inducing signal.
It seems u didn't read the paper as carefully or they didn't discuss this
(??)...the older idea was AS transcription help to keep the forward in check
...however, it doesn't seem it is exactly(or at all) the case with the new
evidence, the second senario is likel
【在 a****o 的大作中提到】
: In deed, if at any given time, in one cell, there is only one direction of
: transcriptioin for a particular gene, this can be a very elegant regulatory
: mechanism to either repress the forward transcription, or make the chromatin
: structure open and prepare for quick induction when there is inducing
: signal.
: about the coupling of transcription and splicing, it would be interesting to
: test if only forward transcription is capable to recruit splicing machinery
: to do the job. since phosphorylation of C
| a****o
发帖数: 1786 | 10 You got me. I read these papers last year and not read them as carefully as
I should.
In my PhD lab, we have jornal club every Friday, everyone (including my boss
) was forced to read at least a paper every week. I miss those good old days.
regulatory
this
check
group.
【在 n********k 的大作中提到】
:
: transcription for a particular gene, this can be a very elegant regulatory
: mechanism to either repress the forward transcription, or make the
: chromatin structure open and prepare for quick induction when there is
: inducing signal.
: It seems u didn't read the paper as carefully or they didn't discuss this
: (??)...the older idea was AS transcription help to keep the forward in check
: ...however, it doesn't seem it is exactly(or at all) the case with the new
: evidence, the second senario is likel
| | | h******u
发帖数: 602 | 11 你们太强了，我最近做transcription elongation相当郁闷，回去好好看看你提的这篇
SCIENCE文章。
【在 a****o 的大作中提到】
: Journal Club 1: Paused RNA polymerase and bidirectional transcription
: 谢绝转载
: 我来抛砖引玉了，其实不是砖，是坯
: In the last issue of 2008, Science published 4 related papers about paused
: RNA polymerase and bidirectional transcription. I would like to briefly
: summarize the history of these studies and how they would influence our
: understanding of transcription.
: Paused polymerase
: The first well known example of paused (stalling) RNA polymerase was
: described about 20 years ago by John Lis and colleagues at Cornell
| D*********t
发帖数: 370 | 12 Interesting...
There's a recent Nature paper by the Grewal lab showing H2A.Z and
heterochromatin is required to suppress antisense transcripts.
http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature08321.html
【在 a****o 的大作中提到】
: Journal Club 1: Paused RNA polymerase and bidirectional transcription
: 谢绝转载
: 我来抛砖引玉了，其实不是砖，是坯
: In the last issue of 2008, Science published 4 related papers about paused
: RNA polymerase and bidirectional transcription. I would like to briefly
: summarize the history of these studies and how they would influence our
: understanding of transcription.
: Paused polymerase
: The first well known example of paused (stalling) RNA polymerase was
: described about 20 years ago by John Lis and colleagues at Cornell
| D*********t
发帖数: 370 | 13 "About RNA polymerase II colliding, according to their data, the reverse
transcription not only happened in the promoter, but also coding region and
3’-UTR. If these bidirectional transcriptions happened in one cell, this
collide is unavoidable, I guess."
Pol II moves only in one direction on one strand. It can transcribe from
different strands – if the sense transcript is produced from the top strand
,
the antisense will be from the bottom strand. So there won't be any
collision.
in
S
question
【在 a***e 的大作中提到】
: I agree it is reasonable that the bidirectional transcription can happen in
: different cell populations. It is a pity that the authors didn’t compare
: whether cell cycle or environmental stimuli can change gene expression
: profile of the reverse transcription.
: This promoter-proximal bidirectional transcription was also observed in
: bacteria. It is speculated the reverse transcription can be quickly
: switched to forward transcription (if my memory is right, in a recent N or S
: paper).
: My biggest int
| a****o
发帖数: 1786 | 14 考古呀
Although RNA polymerase only use one strand as template during transcription
, both strands get into RNA polymerase and separate around Mg ++, so
collision is inevitable for head-to-head transcbing RNA polymerases.It is
not like DNA polymerase, which only take one strand of DNA into its active
center.
and
strand
【在 D*********t 的大作中提到】
: "About RNA polymerase II colliding, according to their data, the reverse
: transcription not only happened in the promoter, but also coding region and
: 3’-UTR. If these bidirectional transcriptions happened in one cell, this
: collide is unavoidable, I guess."
: Pol II moves only in one direction on one strand. It can transcribe from
: different strands – if the sense transcript is produced from the top strand
: ,
: the antisense will be from the bottom strand. So there won't be any
: collision.
:
| D*********t
发帖数: 370 | 15 Good to know. Thx.
transcription
【在 a****o 的大作中提到】
: 考古呀
: Although RNA polymerase only use one strand as template during transcription
: , both strands get into RNA polymerase and separate around Mg ++, so
: collision is inevitable for head-to-head transcbing RNA polymerases.It is
: not like DNA polymerase, which only take one strand of DNA into its active
: center.
:
: and
: strand
| n********k
发帖数: 2818 | 16 u are also in the related field, just print the paper last week, Grewal
continues producing interesting stuff....
【在 D*********t 的大作中提到】
: Interesting...
: There's a recent Nature paper by the Grewal lab showing H2A.Z and
: heterochromatin is required to suppress antisense transcripts.
: http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature08321.html
|
|
