- Email: [email protected]
Chromatin goes global
News & Comment
contrast, a different treatment that uncouples the band 3–skeleton interactions, while promoting band 3 aggregation, does induce a lack of stability. For researchers who spend most of their lives dealing with pure lipid bilayers, or single reconstituted proteins, even a ‘simple’ cell such as the erythrocyte appears hopelessly complex. It is somehow comforting that experienced cell scientists
TRENDS in Biochemical Sciences Vol.27 No.1 January 2002
conclude that ‘as simple as the red cell is, it may still require considerable scrutiny before its most fundamental characteristics are fully understood’, and that ‘no single model of membrane stability can explain all of these observations’. In summary, Van Dort et al. should be commended, not just for their exploratory efforts in a largely uncharted territory, but also for reminding us that integral membrane proteins do have a role in
7
stabilizing membrane structure, and that there is such a thing as a membrane skeleton. 1 Van Dort, H.M. et al. (2001) Analysis of integral membrane protein contribution to the deformability and stability of the human erythrocyte membrane. J. Biol. Chem. (epub ahead of print)
Félix M. Goñi [email protected]
Garbage separation in the endoplasmic reticulum How does a cell distinguish between folded and misfolded proteins? Although it might be a while before we can answer this question, we do have a significant understanding about the disposal of misfolded proteins once they have been identified as garbage by the cell. In the secretory pathway, most ‘good’ proteins are sorted from the ‘bad’ at their site of biosynthesis and folding, the endoplasmic reticulum (ER). Conventional wisdom – supported by a plethora of data – has it that properly folded proteins are packaged into ER-to-Golgi transport vesicles, whereas misfolded proteins are retained in the ER and ultimately shunted back to the cytosol where they are degraded by proteasomes. Recent data by Vashist et al. [1] suggest that not all misfolded proteins are created equal. In this paper, the authors demonstrate that two soluble, misfolded substrates require vesicle formation at the ER, and protein retrieval from the Golgi, before degradation. In addition, in a cell-free assay, these substrates were both packaged into vesicles budding from the ER. Vashist et al. describe their identification of a gene, PER17 (for protein processing in the ER), that seems to be responsible specifically for the
packaging of soluble misfolded proteins into ER-to-Golgi transport vesicles. The coat of these vesicles mediates cargo selection, and PER17 was originally identified by genetic interaction with one of the vesicle coat components, SEC13 (hence its alias BST1, bypass of SEC thirteen). Vashist et al. also demonstrate that, in contrast to soluble misfolded proteins, defective transmembrane proteins are disposed of in a conservative fashion: they were retained in the ER and transported back to the cytosol for degradation without a lap through the Golgi. Data from several laboratories suggest that the degradation of soluble and transmembrane proteins also differs in that misfolded soluble proteins require ER lumenal chaperones for export and degradation, whereas transmembrane protein degradation is largely independent of ER chaperones. This might reflect the route of protein entry into the protein translocation channel – for soluble proteins, the protein translocation channel opens from the lumenal side, whereas membrane proteins presumably enter laterally. Therefore, chaperones might be required for targeting to the channel or for opening of the channel from the ER lumen, but not for lateral re-
entry of the transmembrane domain into the channel. Alternatively, misfolded soluble proteins could hitch a ride with the chaperone molecules that escape from the ER and are retrieved from the Golgi complex, in which case, the degradation of soluble proteins should be dependent on a functional retrieval receptor. So what do we make of this? The most satisfactory explanation would be that misfolded proteins are modified in the Golgi and that, upon return of the misfolded protein to the ER, this modification serves as a targeting signal for retrograde transport to the cytosol, analogous to the signal peptide during protein import into the ER. Such retrograde translocation signals have been pursued for a long time. The paper by Vashist et al. widens the scope of this search to include Golgi-specific modifications, and perhaps will bring it to a successful end in the near future.
providing information in a more relevant chromatin context. More recent studies, however, focus on global changes in particular loci, which include many different genes and regulatory regions. The chicken β-globin locus has been particularly useful, not least because an established cell line system exists that represents the various developmental stages of this region. Using the immunoglobulin heavy chain (IgH) locus in the B-cell differentiation
system, Chowdhury and Sen demonstrated the change in patterns of histone acetylation in the 120-kb germline DNA during B-cell maturation [1]. This domain undergoes extensive rearrangements during maturation of the B cell, and these have been suggested to occur in an orderly fashion: D–J recombination is followed by V–DJ recombination, which ultimately produces the mature VDJ configuration. Using pro-B, pre-B and primary B cell lines,
1 Vashist, S. et al. (2001) Distinct retrieval and retention mechanisms are required for the quality control of ER protein folding. J. Cell Biol. 155, 369–380
Karin Römisch [email protected]
Chromatin goes global Transcriptional regulation plays an important role in development. Originally, studies of transcriptional regulation used specific promoter regions, either in the form of naked DNA or in a nucleosome context. In addition, the chromatin immunoprecipitation (ChIP) technique allowed researchers to establish the relationships of certain regulatory proteins, kinases, histone modifications and so on, with given regions of genomic DNA, thereby http://tibs.trends.com
0968-0004/01/$ – see front matter © 2002 Elsevier Science Ltd. All rights reserved.
8
News & Comment
the authors not only explain the mechanism for the order of VDJ rearrangement, but also provide chromatin data for the mechanism of IL-7-mediated V–DJ recombination. Using anti-acetyl-H3 and -H4 antibodies, they show that the V region of the domain is hyperacetylated only in the pre-B cell line undergoing V–DJ recombination, and in primary pro-B cells that have been stimulated with IL-7 to differentiate into pre-B cells. This result is consistent with a previous study in which IL-7Rα-deficient mice exhibit dysregulation of V rearrangement [2]. The authors further show that in pro-B cells undergoing D–J rearrangement, but not in pro-T cells, D and J regions of the domain are hyperacetylated, potentially making that
TRENDS in Biochemical Sciences Vol.27 No.1 January 2002
chromatin region accessible to the recombinase machinery. They also show that the C region, which follows the D and J regions, has little or no acetylation, thus indicating the presence of a potential insulator in the C domain, although no classical insulator elements have been defined as yet.
information about the regulation of differentiation. As acetylation is by no means the only modification, methylation patterns have also been studied for different contexts. The ‘global histone code’ can be predicted to emerge from the combinatorial chromatin modification patterns over large developmentally regulated domains.
… Using the immunoglobulin heavy chain ‘… (IgH) locus … Chowdhury and Sen demonstrated the change in patterns of histone acetylation in … germline DNA during B-cell maturation …’
1 Chowdhury, D. and Sen, R. (2001) Stepwise activation of the immunoglobulin µ heavy chain gene locus. EMBO J. 20, 6394–6403 2 Corcoran, A.E. et al. (1998) Impaired immunoglobulin gene rearrangements in mice lacking the IL-7 receptor. Nature 391, 904–907
The in-depth study of global chromatin modifications no doubt provides useful
Isil Aksan [email protected]
genetic profile that would be consulted before drugs are prescribed.’ However, the clash between pharmacogenomic and economic sense might raise problems. For example, although small racial groups have genetic variants making them vulnerable to some drugs, drug companies might not think it worthwhile to develop alternative drugs for such a small market. Further problems to implementation include inadequate training for clinicians and inadequate funding for genotyping. S de B (http://www.ucsf.edu/pressrel/2001/11/ 111401.html)
The report says that although 32% of assistant professors were women, this fell to 28% for associate professors and 11% for full professors. Every EU member state had a low percentage of women at the senior level of full professor: from 5% in Ireland to 18% in Finland. S de B (http://www.thesis.co.uk/News/story.asp? rank3=1&from=%2Fmain.asp&from_left NavLogin=1&id=8058; http://europa.eu.int/comm/research/growth/ gcc/projects/gender-research.html)
In Brief
A drug just for you Personalization of drug therapies, enabling the prevention of adverse drug reactions (ADRs), could be made possible with pharmacogenomics. A study led by scientists at the University of California (UCSF, San Francisco, CA, USA) is the first systematic assessment of the potential of pharmacogenomics [J. Am. Med. Assoc. (2001) 286, 2270–2279]. To assess the possible contribution of genetic variability to ADRs, the researchers combined a study of variant alleles for drug-metabolizing enzymes, with a study of ADRs. 59% of the drugs cited in the ADR study are metabolized by at least one enzyme that has a naturally occurring variant associated with poor metabolism. However, only 22% of randomly selected drugs sold in the US, and 7% of randomly selected top-selling American drugs, are metabolized by enzymes with this genetic variability. ‘Our study confirms the powerful potential of genetic information to improve drug therapies, but it also emphasizes the importance of considering how genetics will affect both health care practice and the public,’ said Kathryn A. Phillips, lead author on the report and UCSF associate professor of health economics and health services research. ‘In the future,’ the authors conclude, ‘...we may all carry a “gene chip assay report” that contains our unique http://tibs.trends.com
FEU females Females constitute 52% of european union (EU) students. However, they comprise less than one-third of EU researchers, and only one quarter of Europe’s professors. Figures released by Eurostat, the EU’s statistical agency, highlight Germany, Ireland, Belgium and the Netherlands as being poor performers in terms of equal opportunities (9%,12%, 14% and 15%, respectively, of professors from these countries are female). The UK, in which 24% of professors are female, falls just short of the EU average of 26%. However, the UK has more female researchers (36% compared with 28%) than the EU average. Higher scorers for female professors are found in Finland (36%) and Sweden (33%). Eurostat commented, ‘Women are strongly under-represented in higher education teaching … there was a general trend across the EU to have a larger proportion of women at the lowest grade.’
The female craves The effects of drugs, including addiction, appear to impinge more heavily on the brain in the presence of estrogens, according to a study presented at the 2001 meeting of the Society for Neuroscience in San Diego (USA). ‘Years ago, people said that women shouldn’t smoke or drink because we were more likely to become addicted,’ said University of Michigan biopsychologist Jill B. Becker, who conducted the research. Becker continued ‘… when it comes to drug use, women should be extremely cautious, especially younger women who may be experiencing major hormonal swings at just the same time in their lives when many of their peers are first experimenting with nicotine, cocaine and other addictive substances.’ Hormone replacement therapy might also increase a woman’s vulnerability to drug addiction. The underlying mechanism is thought to involve the role of estrogen in boosting female behavior that slows down male rats during sexual activities. A slower
0968-0004/02/$ – see front matter © 2002 Elsevier Science Ltd. All rights reserved.
contrast, a different treatment that uncouples the band 3–skeleton interactions, while promoting band 3 aggregation, does induce a lack of stability. For researchers who spend most of their lives dealing with pure lipid bilayers, or single reconstituted proteins, even a ‘simple’ cell such as the erythrocyte appears hopelessly complex. It is somehow comforting that experienced cell scientists
TRENDS in Biochemical Sciences Vol.27 No.1 January 2002
conclude that ‘as simple as the red cell is, it may still require considerable scrutiny before its most fundamental characteristics are fully understood’, and that ‘no single model of membrane stability can explain all of these observations’. In summary, Van Dort et al. should be commended, not just for their exploratory efforts in a largely uncharted territory, but also for reminding us that integral membrane proteins do have a role in
7
stabilizing membrane structure, and that there is such a thing as a membrane skeleton. 1 Van Dort, H.M. et al. (2001) Analysis of integral membrane protein contribution to the deformability and stability of the human erythrocyte membrane. J. Biol. Chem. (epub ahead of print)
Félix M. Goñi [email protected]
Garbage separation in the endoplasmic reticulum How does a cell distinguish between folded and misfolded proteins? Although it might be a while before we can answer this question, we do have a significant understanding about the disposal of misfolded proteins once they have been identified as garbage by the cell. In the secretory pathway, most ‘good’ proteins are sorted from the ‘bad’ at their site of biosynthesis and folding, the endoplasmic reticulum (ER). Conventional wisdom – supported by a plethora of data – has it that properly folded proteins are packaged into ER-to-Golgi transport vesicles, whereas misfolded proteins are retained in the ER and ultimately shunted back to the cytosol where they are degraded by proteasomes. Recent data by Vashist et al. [1] suggest that not all misfolded proteins are created equal. In this paper, the authors demonstrate that two soluble, misfolded substrates require vesicle formation at the ER, and protein retrieval from the Golgi, before degradation. In addition, in a cell-free assay, these substrates were both packaged into vesicles budding from the ER. Vashist et al. describe their identification of a gene, PER17 (for protein processing in the ER), that seems to be responsible specifically for the
packaging of soluble misfolded proteins into ER-to-Golgi transport vesicles. The coat of these vesicles mediates cargo selection, and PER17 was originally identified by genetic interaction with one of the vesicle coat components, SEC13 (hence its alias BST1, bypass of SEC thirteen). Vashist et al. also demonstrate that, in contrast to soluble misfolded proteins, defective transmembrane proteins are disposed of in a conservative fashion: they were retained in the ER and transported back to the cytosol for degradation without a lap through the Golgi. Data from several laboratories suggest that the degradation of soluble and transmembrane proteins also differs in that misfolded soluble proteins require ER lumenal chaperones for export and degradation, whereas transmembrane protein degradation is largely independent of ER chaperones. This might reflect the route of protein entry into the protein translocation channel – for soluble proteins, the protein translocation channel opens from the lumenal side, whereas membrane proteins presumably enter laterally. Therefore, chaperones might be required for targeting to the channel or for opening of the channel from the ER lumen, but not for lateral re-
entry of the transmembrane domain into the channel. Alternatively, misfolded soluble proteins could hitch a ride with the chaperone molecules that escape from the ER and are retrieved from the Golgi complex, in which case, the degradation of soluble proteins should be dependent on a functional retrieval receptor. So what do we make of this? The most satisfactory explanation would be that misfolded proteins are modified in the Golgi and that, upon return of the misfolded protein to the ER, this modification serves as a targeting signal for retrograde transport to the cytosol, analogous to the signal peptide during protein import into the ER. Such retrograde translocation signals have been pursued for a long time. The paper by Vashist et al. widens the scope of this search to include Golgi-specific modifications, and perhaps will bring it to a successful end in the near future.
providing information in a more relevant chromatin context. More recent studies, however, focus on global changes in particular loci, which include many different genes and regulatory regions. The chicken β-globin locus has been particularly useful, not least because an established cell line system exists that represents the various developmental stages of this region. Using the immunoglobulin heavy chain (IgH) locus in the B-cell differentiation
system, Chowdhury and Sen demonstrated the change in patterns of histone acetylation in the 120-kb germline DNA during B-cell maturation [1]. This domain undergoes extensive rearrangements during maturation of the B cell, and these have been suggested to occur in an orderly fashion: D–J recombination is followed by V–DJ recombination, which ultimately produces the mature VDJ configuration. Using pro-B, pre-B and primary B cell lines,
1 Vashist, S. et al. (2001) Distinct retrieval and retention mechanisms are required for the quality control of ER protein folding. J. Cell Biol. 155, 369–380
Karin Römisch [email protected]
Chromatin goes global Transcriptional regulation plays an important role in development. Originally, studies of transcriptional regulation used specific promoter regions, either in the form of naked DNA or in a nucleosome context. In addition, the chromatin immunoprecipitation (ChIP) technique allowed researchers to establish the relationships of certain regulatory proteins, kinases, histone modifications and so on, with given regions of genomic DNA, thereby http://tibs.trends.com
0968-0004/01/$ – see front matter © 2002 Elsevier Science Ltd. All rights reserved.
8
News & Comment
the authors not only explain the mechanism for the order of VDJ rearrangement, but also provide chromatin data for the mechanism of IL-7-mediated V–DJ recombination. Using anti-acetyl-H3 and -H4 antibodies, they show that the V region of the domain is hyperacetylated only in the pre-B cell line undergoing V–DJ recombination, and in primary pro-B cells that have been stimulated with IL-7 to differentiate into pre-B cells. This result is consistent with a previous study in which IL-7Rα-deficient mice exhibit dysregulation of V rearrangement [2]. The authors further show that in pro-B cells undergoing D–J rearrangement, but not in pro-T cells, D and J regions of the domain are hyperacetylated, potentially making that
TRENDS in Biochemical Sciences Vol.27 No.1 January 2002
chromatin region accessible to the recombinase machinery. They also show that the C region, which follows the D and J regions, has little or no acetylation, thus indicating the presence of a potential insulator in the C domain, although no classical insulator elements have been defined as yet.
information about the regulation of differentiation. As acetylation is by no means the only modification, methylation patterns have also been studied for different contexts. The ‘global histone code’ can be predicted to emerge from the combinatorial chromatin modification patterns over large developmentally regulated domains.
… Using the immunoglobulin heavy chain ‘… (IgH) locus … Chowdhury and Sen demonstrated the change in patterns of histone acetylation in … germline DNA during B-cell maturation …’
1 Chowdhury, D. and Sen, R. (2001) Stepwise activation of the immunoglobulin µ heavy chain gene locus. EMBO J. 20, 6394–6403 2 Corcoran, A.E. et al. (1998) Impaired immunoglobulin gene rearrangements in mice lacking the IL-7 receptor. Nature 391, 904–907
The in-depth study of global chromatin modifications no doubt provides useful
Isil Aksan [email protected]
genetic profile that would be consulted before drugs are prescribed.’ However, the clash between pharmacogenomic and economic sense might raise problems. For example, although small racial groups have genetic variants making them vulnerable to some drugs, drug companies might not think it worthwhile to develop alternative drugs for such a small market. Further problems to implementation include inadequate training for clinicians and inadequate funding for genotyping. S de B (http://www.ucsf.edu/pressrel/2001/11/ 111401.html)
The report says that although 32% of assistant professors were women, this fell to 28% for associate professors and 11% for full professors. Every EU member state had a low percentage of women at the senior level of full professor: from 5% in Ireland to 18% in Finland. S de B (http://www.thesis.co.uk/News/story.asp? rank3=1&from=%2Fmain.asp&from_left NavLogin=1&id=8058; http://europa.eu.int/comm/research/growth/ gcc/projects/gender-research.html)
In Brief
A drug just for you Personalization of drug therapies, enabling the prevention of adverse drug reactions (ADRs), could be made possible with pharmacogenomics. A study led by scientists at the University of California (UCSF, San Francisco, CA, USA) is the first systematic assessment of the potential of pharmacogenomics [J. Am. Med. Assoc. (2001) 286, 2270–2279]. To assess the possible contribution of genetic variability to ADRs, the researchers combined a study of variant alleles for drug-metabolizing enzymes, with a study of ADRs. 59% of the drugs cited in the ADR study are metabolized by at least one enzyme that has a naturally occurring variant associated with poor metabolism. However, only 22% of randomly selected drugs sold in the US, and 7% of randomly selected top-selling American drugs, are metabolized by enzymes with this genetic variability. ‘Our study confirms the powerful potential of genetic information to improve drug therapies, but it also emphasizes the importance of considering how genetics will affect both health care practice and the public,’ said Kathryn A. Phillips, lead author on the report and UCSF associate professor of health economics and health services research. ‘In the future,’ the authors conclude, ‘...we may all carry a “gene chip assay report” that contains our unique http://tibs.trends.com
FEU females Females constitute 52% of european union (EU) students. However, they comprise less than one-third of EU researchers, and only one quarter of Europe’s professors. Figures released by Eurostat, the EU’s statistical agency, highlight Germany, Ireland, Belgium and the Netherlands as being poor performers in terms of equal opportunities (9%,12%, 14% and 15%, respectively, of professors from these countries are female). The UK, in which 24% of professors are female, falls just short of the EU average of 26%. However, the UK has more female researchers (36% compared with 28%) than the EU average. Higher scorers for female professors are found in Finland (36%) and Sweden (33%). Eurostat commented, ‘Women are strongly under-represented in higher education teaching … there was a general trend across the EU to have a larger proportion of women at the lowest grade.’
The female craves The effects of drugs, including addiction, appear to impinge more heavily on the brain in the presence of estrogens, according to a study presented at the 2001 meeting of the Society for Neuroscience in San Diego (USA). ‘Years ago, people said that women shouldn’t smoke or drink because we were more likely to become addicted,’ said University of Michigan biopsychologist Jill B. Becker, who conducted the research. Becker continued ‘… when it comes to drug use, women should be extremely cautious, especially younger women who may be experiencing major hormonal swings at just the same time in their lives when many of their peers are first experimenting with nicotine, cocaine and other addictive substances.’ Hormone replacement therapy might also increase a woman’s vulnerability to drug addiction. The underlying mechanism is thought to involve the role of estrogen in boosting female behavior that slows down male rats during sexual activities. A slower
0968-0004/02/$ – see front matter © 2002 Elsevier Science Ltd. All rights reserved.