Uncommon Descent Serving The Intelligent Design Community

RNA measurements may yield less insight than assumed

Share
Facebook
Twitter
LinkedIn
Flipboard
Print
Email

From Phys.org:

The majority of RNA expression differences between individuals have no connection to the abundance of a corresponding protein, report scientists from the University of Chicago and Stanford University in Science on Dec. 18. The findings point to a yet-unidentified cellular mechanism that regulates gene expression and suggest studies that rely only on RNA measurements to characterize gene function require further analysis.

“The chief assumption for studies of RNA differences is that they ultimately reflect differences in an end product, which is protein,” said senior study author Yoav Gilad, PhD, professor of human genetics at the University of Chicago. “But it turns out in most cases this may not be true.”

Interesting, when we consider the high hopes placed in RNA world.

See also: Welcome to “RNA world,” the five-star hotel of origin-of-life theories

Follow UD News at Twitter!

Comments
High-throughput characterization of protein–RNA interactions doi: 10.1093/bfgp/elu047 RNA-binding proteins (RBPs) are important regulators of eukaryotic gene expression. Genomes typically encode dozens to hundreds of proteins containing RNA-binding domains, which collectively recognize diverse RNA sequences and structures. Recent advances in high-throughput methods for assaying the targets of RBPs in vitro and in vivo allow large-scale derivation of RNA-binding motifs as well as determination of RNA–protein interactions in living cells. In parallel, many computational methods have been developed to analyze and interpret these data. The interplay between RNA secondary structure and RBP binding has also been a growing theme. Integrating RNA–protein interaction data with observations of post-transcriptional regulation will enhance our understanding of the roles of these important proteins. http://bfg.oxfordjournals.org/content/early/2014/12/13/bfgp.elu047.short?rss=1
Dionisio
December 25, 2014
December
12
Dec
25
25
2014
10:33 PM
10
10
33
PM
PDT
gpuccio Merry Christmas! Thank you for the encouraging words. I appreciate them very much, specially coming from you, who could teach a few things to many of us here! :)Dionisio
December 24, 2014
December
12
Dec
24
24
2014
02:46 PM
2
02
46
PM
PDT
Connecting the Cytoskeleton to the Endoplasmic Reticulum and Golgi DOI: http://dx.doi.org/10.1016/j.cub.2014.05.033 A tendency in cell biology is to divide and conquer. For example, decades of painstaking work have led to an understanding of endoplasmic reticulum (ER) and Golgi structure, dynamics, and transport. In parallel, cytoskeletal researchers have revealed a fantastic diversity of structure and cellular function in both actin and microtubules. Increasingly, these areas overlap, necessitating an understanding of both organelle and cytoskeletal biology. This review addresses connections between the actin/microtubule cytoskeletons and organelles in animal cells, focusing on three key areas: ER structure and function; ER-to-Golgi transport; and Golgi structure and function. Making these connections has been challenging for several reasons: the small sizes and dynamic characteristics of some components; the fact that organelle-specific cytoskeletal elements can easily be obscured by more abundant cytoskeletal structures; and the difficulties in imaging membranes and cytoskeleton simultaneously, especially at the ultrastructural level. One major concept is that the cytoskeleton is frequently used to generate force for membrane movement, with two potential consequences: translocation of the organelle, or deformation of the organelle membrane. While initially discussing issues common to metazoan cells in general, we subsequently highlight specific features of neurons, since these highly polarized cells present unique challenges for organellar distribution and dynamics. http://www.cell.com/current-biology/abstract/S0960-9822(14)00598-3Dionisio
December 24, 2014
December
12
Dec
24
24
2014
01:55 PM
1
01
55
PM
PDT
Dionisio: Merry Christmas to you! :) (And please, go on with your very good work).gpuccio
December 24, 2014
December
12
Dec
24
24
2014
10:31 AM
10
10
31
AM
PDT
Axonal Transport: Cargo-Specific Mechanisms of Motility and Regulation DOI: http://dx.doi.org/10.1016/j.neuron.2014.10.019 Axonal transport is essential for neuronal function, and many neurodevelopmental and neurodegenerative diseases result from mutations in the axonal transport machinery. Anterograde transport supplies distal axons with newly synthesized proteins and lipids, including synaptic components required to maintain presynaptic activity. Retrograde transport is required to maintain homeostasis by removing aging proteins and organelles from the distal axon for degradation and recycling of components. Retrograde axonal transport also plays a major role in neurotrophic and injury response signaling. http://www.cell.com/neuron/abstract/S0896-6273(14)00917-9Dionisio
December 24, 2014
December
12
Dec
24
24
2014
09:45 AM
9
09
45
AM
PDT
AVS Thank you for your nice comments. :) Merry Christmas!Dionisio
December 24, 2014
December
12
Dec
24
24
2014
09:14 AM
9
09
14
AM
PDT
hrun0815 Thank you for your nice comments. :) Merry Christmas!Dionisio
December 24, 2014
December
12
Dec
24
24
2014
09:12 AM
9
09
12
AM
PDT
wd400 Thank you for your nice comments. :) Merry Christmas!Dionisio
December 24, 2014
December
12
Dec
24
24
2014
09:10 AM
9
09
10
AM
PDT
I don't think anyone was the least bit upset but the contents of your posts Dionisio. The sheer volume of them is kind of annoyingly spammy. And when you combine all the links with your refusal to discuss any topic in any detail you end up looking a bit a squid -- retreating rapidly while sending forth a (l)ink cloud to try cover your lack of any argument. So, no "discomfort", just mild;y amused bewilderment about what you think you are achieving.wd400
December 24, 2014
December
12
Dec
24
24
2014
08:54 AM
8
08
54
AM
PDT
AVS:
So Joe, I take it you are unable to find a scientific source that only claims ATP synthase evolved and does not provide evidence for this claim?
That isn't my claim. Obviously you have other issues.
Also, it’s not that evolution can’t be modeled, the problem is it is too complex a process for us to successfully model right now.
Again your equivocation is duly noted. Evolution can be modeled. Unguided evolution producing something of note cannot be. As I said you think your ignorance means something but it doesn't.Joe
December 24, 2014
December
12
Dec
24
24
2014
08:38 AM
8
08
38
AM
PDT
Wow, Dionisio. That's some mighty delusion. Can you point to any place where the content of your C/P jobs was actually discussed? That's like claiming that BA77's posts stimulate discussion.hrun0815
December 24, 2014
December
12
Dec
24
24
2014
08:34 AM
8
08
34
AM
PDT
News, As you can see, this thread got reactivated after I posted a few related references to recent research reports, which apparently caused some itching and discomfort to some commenters here. :) Let's ignore the whiners, specially when they're barking up the wrong trees. Let's keep moving on. :) Marry Christmas!Dionisio
December 24, 2014
December
12
Dec
24
24
2014
07:01 AM
7
07
01
AM
PDT
Endosomal transport of septin mRNA and protein indicates local translation on endosomes and is required for correct septin filamentation DOI 10.1002/embr.201338037 Endosomes transport lipids and proteins over long distances by shuttling along microtubules. They also carry mRNAs on their surface, but the precise molecular function of this trafficking process is unknown. http://embor.embopress.org/content/15/1/94
the precise molecular function of this trafficking process is unknown What else is new? Many things are still unknown. Which means that more research is required. More resources have to be invested in that research. As new discoveries are made, more light is shed on the biological big picture, unveiling elaborate cellular and molecular processes, amazingly orchestrated choreographies, that demand further explanation. This is simply fascinating. That's why we look forward, with much anticipation, to reading newer reports coming out of research labs. Rejoice! :)Dionisio
December 24, 2014
December
12
Dec
24
24
2014
04:55 AM
4
04
55
AM
PDT
#163 addendum
DOI: 10.1126/science.1256898 The eukaryotic cell contains membrane-bound organelles with distinct functionality and composition. Preservation of organelle identity depends on the highly selective transfer of proteins and lipids between compartments. Central to this are transport carriers called vesicles. Mechanisms are required not only for the selective incorporation of specific cargos into vesicles as they bud off a donor organelle, but also for the correct delivery to an acceptor organelle. SNARE proteins on the vesicle and destination organelle drive membrane fusion after arrival and have been implicated in contributing to specificity in choice of organelle. However, upstream of the fusion step, a process called tethering is thought to initially attach the vesicle to the destination organelle and then bring it close to allow the SNARE proteins on opposite membranes to interact. The importance of tethering in conferring specificity to membrane traffic is currently unclear. http://www.sciencemag.org/content/346/6209/1256898.abstract
Dionisio
December 24, 2014
December
12
Dec
24
24
2014
04:27 AM
4
04
27
AM
PDT
All you need to know is described in sufficient details at the very beginning. Just look carefully, so you can see it. If you miss it, then it’ll be described again, even more clear, at the very end. But don’t wait till then. Try to get it now. :)
Ah, yes, Dionisio. You are just a student who just posts interesting material for others. But you refuse to tell anybody what specifically is interesting. Or my assessment of you is actually accurate: you 'literature bluff' yourself through these threads and scared witless of being nailed down on any specific statement lest you be wrong and your ignorance is exposed.hrun0815
December 24, 2014
December
12
Dec
24
24
2014
12:00 AM
12
12
00
AM
PDT
‘How do molecules in the cell find their proper destinations’, is a profound question in my book.
I think many biologists agree with you. A countless amount of work has been done on that specific question for a long time. So much so that Günter Blobel was awarded the Nobel prize "for the discovery that proteins have intrinsic signals that govern their transport and localization in the cell" 15 years ago. (Cue two standard ID retorts: 1) you didn't provide enough details! 2) How did it get there in the first place?)hrun0815
December 23, 2014
December
12
Dec
23
23
2014
11:54 PM
11
11
54
PM
PDT
Well I at least thought you’d take a guess Dio, but I guess not. Those proteins are coat proteins and it’s interesting that you couldn’t name them because 4 posts after linking that video, you linked us to another site that defined those same coat proteins and put a virtually identical picture right at the top of the page. So the question is, do you actually read the stuff you post? Sorry Dio, you failed your first exam. “That's why we look forward, with much anticipation, to reading the next reports coming out of research labs.” Maybe you really do read them, but does Dio actually learn anything from them? Certainly doesn’t seem like it. The autodidactic school system seems to be failing you Dio, you must have a bad teacher.AVS
December 23, 2014
December
12
Dec
23
23
2014
10:28 PM
10
10
28
PM
PDT
The specificity of vesicle traffic to the Golgi is encoded in the golgin coiled-coil proteins DOI: 10.1126/science.1256898 http://www.sciencemag.org/content/346/6209/1256898.abstractDionisio
December 23, 2014
December
12
Dec
23
23
2014
10:12 PM
10
10
12
PM
PDT
Intracellular express -- why transport protein molecules have brakes Check out all these videos: http://article.wn.com/view/2010/05/21/Intracellular_express_why_transport_protein_molecules_have_b/Dionisio
December 23, 2014
December
12
Dec
23
23
2014
10:07 PM
10
10
07
PM
PDT
A Day in the Life of a Motor Protein https://www.youtube.com/embed/tMKlPDBRJ1EDionisio
December 23, 2014
December
12
Dec
23
23
2014
09:57 PM
9
09
57
PM
PDT
I take it you don't know what those proteins are Dio?AVS
December 23, 2014
December
12
Dec
23
23
2014
09:44 PM
9
09
44
PM
PDT
Cellular Uptake Mechanisms and Endosomal Trafficking of Supercharged Proteins DOI: http://dx.doi.org/10.1016/j.chembiol.2012.06.014 Supercharged proteins (SCPs) can deliver functional macromolecules into the cytoplasm of mammalian cells more potently than unstructured cationic peptides. Thus far, neither the structural features of SCPs that determine their delivery effectiveness nor their intracellular fate postendocytosis, has been studied. http://www.cell.com/chemistry-biology/abstract/S1074-5521(12)00222-0Dionisio
December 23, 2014
December
12
Dec
23
23
2014
09:43 PM
9
09
43
PM
PDT
BmCREC Is an Endoplasmic Reticulum (ER) Resident Protein and Required for ER/Golgi Morphology http://www.jbc.org/content/288/37/26649.abstractDionisio
December 23, 2014
December
12
Dec
23
23
2014
09:31 PM
9
09
31
PM
PDT
Apoptosis-linked Gene-2 (ALG-2)/Sec31 Interactions Regulate Endoplasmic Reticulum (ER)-to-Golgi Transport A POTENTIAL EFFECTOR PATHWAY FOR LUMINAL CALCIUM* doi: 10.1074/jbc.M114.561829 Luminal calcium released from secretory organelles has been suggested to play a regulatory role in vesicle transport at several steps in the secretory pathway; however, its functional roles and effector pathways have not been elucidated. http://www.jbc.org/content/289/34/23609.abstractDionisio
December 23, 2014
December
12
Dec
23
23
2014
09:18 PM
9
09
18
PM
PDT
I will believe you Dio, don't worry. So what is it?AVS
December 23, 2014
December
12
Dec
23
23
2014
09:17 PM
9
09
17
PM
PDT
At the very beginning and end of what? I take it you don’t know what they are?
Can't tell you what it is, you won't believe me. You gotta find it yourself. Look carefully, you'll see it. It's amazing. Can't miss it. :)Dionisio
December 23, 2014
December
12
Dec
23
23
2014
09:15 PM
9
09
15
PM
PDT
Cofilin recruits F-actin to SPCA1 and promotes Ca2+-mediated secretory cargo sorting doi: 10.1083/jcb.201311052 http://jcb.rupress.org/content/206/5/635.abstractDionisio
December 23, 2014
December
12
Dec
23
23
2014
09:10 PM
9
09
10
PM
PDT
Cab45 is required for Ca2+-dependent secretory cargo sorting at the trans-Golgi network doi: 10.1083/jcb.201207180 http://jcb.rupress.org/content/199/7/1057.abstractDionisio
December 23, 2014
December
12
Dec
23
23
2014
09:00 PM
9
09
00
PM
PDT
At the very beginning and end of what? I take it you don't know what they are?AVS
December 23, 2014
December
12
Dec
23
23
2014
08:59 PM
8
08
59
PM
PDT
Hey Dio, at about the 1:45 mark of that new protein packing video I can’t tell what those greenish things are, did you come across it by any chance?
All you need to know is described in sufficient details at the very beginning. Just look carefully, so you can see it. If you miss it, then it'll be described again, even more clear, at the very end. But don't wait till then. Try to get it now. :)Dionisio
December 23, 2014
December
12
Dec
23
23
2014
08:56 PM
8
08
56
PM
PDT
1 2 3 6

Leave a Reply