2008-Catal Tod-Dehydrogenation of propane on chromiaalumina catalysts promoted by tin

Combinatorial patterns of histone acetylations and methylations in the human genomeZhibin Wang 1,5,Chongzhi Zang 2,5,Jeffrey A Rosenfeld 3–5,Dustin E Schones 1,Artem Barski 1,Suresh Cuddapah 1,Kairong Cui 1,Tae-Young Roh 1,Weiqun Peng 2,Michael Q Zhang 3&Keji Zhao 1Histones are characterized by numerous posttranslational modifications that influence gene transcription 1,2.However,because of the lack of global distribution data in higher eukaryotic systems 3,the extent to which gene-specificcombinatorial patterns of histone modifications exist remains to be determined.Here,we report the patterns derived from the analysis of 39histone modifications in human CD4+T cells.Our data indicate that a large number of patterns are associated with promoters and enhancers.In particular,we identify a common modification module consisting of 17modifications detected at 3,286promoters.These modifications tend to colocalize in the genome and correlate with each other at an individual nucleosome level.Genes associated with this module tend to have higher expression,and addition of more modifications to this module is associated with further increased expression.Our data suggest that these histone modifications may act cooperatively to prepare chromatin for transcriptional activation.Histones are subject to numerous covalent modifications,including methylation and acetylation,that occur mainly at their N-terminal tails and that can affect transcription of genes 1,2,4,5.Extensive studies have established that histone acetylation is primarily associated with gene activation,whereas methylation,depending on its position and state,is associated with either repression or activation 5–10.Various models,including the histone code,the signaling network and the charge neutralization model,have been proposed to account for the function of histone modifications 11–14.The histone code hypothesis suggests that multiple histone modifications act in a combinatorial fashion to specify distinct chromatin states.However,the extent to which combinatorial patterns of histone modifications exist in the genome is unknown.We have now produced genome-wide maps of 18histone acetylations (H2AK5ac,H2AK9ac,H2BK5ac,H2BK12ac,H2BK20ac,H2BK120ac,H3K4ac,H3K9ac,H3K14ac,H3K18ac,H3K23ac,H3K27ac,H3K36ac,H4K5ac,H4K8ac,H4K12ac,H4K16ac and H4K91ac)at an individual nucleosomelevel (see Methods section for data deposition),and analyzed these together with the H2A.Z and 19histone methylation maps we generated previously 15.We first systematically evaluated the specificities of the acetylation antibodies used in this study (Supplementary Methods ,Supplemen-tary Table 1and Supplementary Fig.1online).Competition assays using modified and unmodified peptides indicated that most anti-bodies showed specificity for the desired acetylation (Supplementary Fig.1).The H4K5ac and H3K4ac antibodies demonstrated some crossreactivity toward H4K12ac and H3K9ac,respectively,in a con-dition with excess competitor peptides (Supplementary Fig.1d ,j ),and the H4K91ac antibody did not work in protein blotting.Thus,the results for these modifications should be interpreted with caution.Of note,H2AK9ac has not been reported previously,and H3K4ac has only been identified by mass-spectrometry analysis and has not been previously characterized functionally 16.Protein blotting indicated that these acetylations indeed exist in human CD4+T cells (Supplemen-tary Fig.1j ,o ).We previously analyzed the genome-wide distribution of H2BK5me1(ref.15),and protein blotting data in this study indicated that this methylation exists in human cells and that the H2BK5me1antibody is specific (Supplementary Fig.1p ).Next,we determined the genomic distribution patterns of these histone acetylations using the ChIP-Seq technique 15,which we pre-viously confirmed yields H3K4me3distribution patterns similar to those generated by the ChIP-SAGE (GMAT)strategy 15,17.T o validate the histone acetylation data,we compared the genomic distribution patterns of the K9/K14-diacetylated histone H3from ChIP-SAGE 18with the separately examined patterns of H3K9ac and H3K14ac in this study (Supplementary Fig.2online).We found that the ChIP-Seq acetylation data are reliable and that the previously observed H3K9/K14diacetylation patterns could be primarily attributed to H3K9acetylation.T o examine the distribution of the histone acetylations at different functional regions,we generated composite profiles for the region spanning the transcription start sites (TSSs;Fig.1a –c and Supple-mentary Fig.3online)or the entire gene bodies and extending 5kbReceived 19December 2007;accepted 1April 2008;published online 15June 2008;doi:10.1038/ng.1541Laboratoryof Molecular Immunology,National Heart,Lung,and Blood Institute,US National Institutes of Health,Bethesda,Maryland 20892,USA.2Department ofPhysics,The George Washington University,Washington,D.C.20052,USA.3Cold Spring Harbor Laboratory,Cold Spring Harbor,New York 11724,USA.4Department of Biology,New York University,New York,New York 10003,USA.5These authors contributed equally to this work.Correspondence should be addressed to K.Z.(zhaok@).©2008 N a t u r e P u b l i s h i n g G r o u p h t t p ://w w w .n a t u r e .c o m /n a t u r e g e n e t i c supstream and 5kb downstream for groups of 1,000genes according to their expression (Fig.1d –f and Supplementary Fig.4online).We found that all acetylations positively correlated with gene expression,consistent with their involvement in tran-scriptional activation.However,our dataindicate that different acetylations may targetdifferent regions of genes.For example,H2AK9ac,H2BK5ac,H3K9ac,H3K18ac,H3K27ac,H3K36ac and H4K91ac are mainlylocated in the region surrounding the TSS(Fig.1d and Supplementary Fig.4),whereasH2BK12ac,H2BK20ac,H2BK120ac,H3K4ac,H4K5ac,H4K8ac,H4K12ac and H4K16ac are elevated in the promoter and transcribed regions of active genes (Fig.1f and Supplementary Fig.4).These results are consistent with previous reports that specific*H3K4me3*H3K4me2*H3K4me1*H3K4ac H3K27me3H3K27me2*H3K27me1*H3K27ac H3K9me3H3K9me2*H3K9me1*H3K9ac *H3K79me3*H3K79me2*H3K79me1H3R2me2H3R2me1H3K36me3H3K36me1*H3K36ac H4K20me3H4K20me1H2BK5me1*H2BK5ac *H3K14ac *H3K18ac *H3K23ac*H4K5ac *H4K8ac *H4K12ac *H4K16ac*H4K91ac *H2BK12ac *H2BK20ac *H2BK120ac H2AK5ac H2AK9ac*H2A.Z H4R3me2H3K9acH3K9acN o r m a l i z e d c o u n t sN o r m a l i z e d c o u n t sN o r m a l i z e d c o u n t sPosition relative to TSSPosition relative to TSSN o r m a l i z e d c o u n t sN o r m a l i z e d c o u n t sN o r m a l i z e d c o u n t sH4K12acH4K12acHigh Medium Low SilentHigh Medium Low SilentHigh Medium Low Silentadge1.2E–071E–078E–086E–084E–082E–08–2,000–1,0001,0002,00000cf1.6E–081.4E–081E–081.2E–088E–096E–092E–094E–09–10,000–5,0005,00010,00000Position relative to TSSH3K23acb1.4E–081.2E–088E–091E–086E–092E–094E–09–10,000–5,0005,00010,000H3K23acHigh SilentHigh SilentHigh Silent96Chr20:3461186515543532213125136625616429354155471046478123592224104394525000045300000453500004540000045450000ZMYND85 k b u p 2.5 k b u p t x S t a r t 0.10.20.30.40.500.600.700.800.90t x E n d 2.5 k b d o w n 5 k b d o w n5 k b u p 2.5 k b u p t x S t a r t 0.10.20.30.40.500.600.700.800.90t x E n d 2.5 k b d o w n 5 k b d o w n5 k b u p 2.5 k b u p t x S t a r t 0.10.20.30.40.500.600.700.800.90t x E n d 2.5 k b d o w n 5 k b d o w nFigure 1Three distribution patterns of histone acetylations.(a –c )Normalized tag counts of histone acetylation signalssurrounding the TSS were indicated for highly active,intermediately active (two levels)and silent genes.Each group represents 1,000genes with similar expression,as described in Methods.(d –f )Normalized tag counts of histone acetylation signals of 1,000highly active or silent genes across the gene bodies.The plots extend 5kb 5¢and 3¢of the genic regions (see Methods).txStart,transcription start site;txEnd,transcription end.(g )Chromatin modification patterns at the ZMYND8(PRKCBP1)gene locus.Significant modifications in the –1kb to +1kb region surrounding the TSS (P o 10À7;highlighted in red)are indicated by asterisks on the left.10,00010,0001,0001,000100100908070605040302010101001,00010,0001010010101N u m be r of c o m b i n a t o r i a l p a t t e r n sP e r c e n t a g e o f g e n e s w i t h h i g h e r e x p r e s s i o nF o l d c h a n g e i n e x p r e s s i o n (l o g 2)B,H2AK9ac,H2BK5me1,H3K79me1,me2,me3,H4K12ac,H4K16ac,H4K20me1:62B,H2AK9ac,H2BK5me1,H3K79me1,me2,me3,H4K16ac,H4K20me1:68B,H2BK5me1,H3K79me1,me2,me3,H4K16ac,H4K20me1:74B,H4K16ac:67B:64H3K36me3:135H2AZ,H3K4me1,me2,me3,H3K9me1,H3K27me3:77H2AZ,H3K4me2,me3,H3K9me1,H3K27me3:70H2AZ,H3K4me3,H3K27me3:74H3K4me3,H3K27me3:167H3K4me3:85H3K27me3:630No modification:2007All genes:1254121.510.50–0.5–1–1.5H 2A K 5a c H 2B K 5a c H 2B K 5m e 1H 2B K 12a c H 2B K 20a c H 2B K 120a c H 3K 4a c H 3K 4m e 1H 3K 4m e 2H 3K 4m e 3H 3K 9a c H 3K 9m e 1H 3K 9m e 2H 3K 9m e 3H 3K 14a c H 3K 18a c H 3K 23a c H 3K 27a c H 3K 27m e 1H 3K 27m e 2H 3K 27m e 3H 3K 36a c H 3K 36m e 1H 3K 36m e 3H 3K 79m e 1H 3K 79m e 2H 3K 79m e 3H 3R 2m e 1H 3R 2m e 2H 4K 5a c H 4K 8a c H 4K 12a c H 4K 16a c H 4K 20m e 1H 4K 20m e 3H 4K 91a cH 2A K 9a c H 2A .Z 1Number of genes associatedwith the same patternGene expressiona bcFigure 2Patterns of histone modificationsassociated with promoters.(a )Patterns of histone modifications at promoters.The y axis indicates the number of patterns of 39histonemodifications (see Methods),and the x axis indicates the number of promoters associated with each pattern.(b )Correlation of gene expression with the thirteen most prevalent modification patterns.B,the 17-modification backbone;All,all genes.The number ofpromoters within each pattern is also indicated.The gene expression is determined using DNA microarrays.See Figure 4a for the composition of ‘backbone’.(c )Correlation of each modification with gene expression.The changes in geneexpression (log 2)are calculated by comparing the average expression of the subsets of genes with or without a particular modification.©2008 N a t u r e P u b l i s h i n g G r o u p h t t p ://w w w .n a t u r e .c o m /n a t u r e g e n e t i c shistone acetyl transferases (HATs)can associate with different regions of genes.For example,PCAF associates with the elongation-competent RNA Pol II,whereas p300interacts with the initiation-competent RNA Pol II (ref.19).Additionally,depletion of GCN5or PCAF,but not CBP or p300,affects H4K8ac and H3K14ac 20.The distribution patterns of these histone acetylations and histone methylations are exemplified by the genomic locus for ZMYND8(alsoknown as PRKCBP1),which is expressed in CD4+T cells (Fig.1g ).The promoter region (highlighted in red),which was defined as a 2-kb region surrounding the TSS,is associated with 25modifications (P o 10À7).T o identify the patterns of histone modifications in an unbiased way,we examined each of the 12,541gene promoters for association with each of the 18acetylations,19methylations and H2A.Z.Of the possible patterns,only a small fraction exists at promoters.Of 4,339detected patterns,1,174are associated withmultiple genes and 3,165with only one gene each (Fig.2a ).The 13most prevalent patterns are each associated with more than 62genes.We next examined the expression of genes in these patterns,using the mean expression ofall genes as a reference (Fig.2b ).It seems that we can roughly classify these top patterns into three classes (I,II and III in Fig.2b )accord-ing to expression.Four of six patterns in class I contain H3K27me3and correlate with low expression.These patterns also containH3K4me1/2/3,H3K9me1and H2A.Z butno acetylations.The patterns containing only H3K4me3or no modification also belong to this class.Class II contains H3K36me3or a modification backbone con-sisting of 17modifications (as discussed below),or the backbone plus H4K16ac,which correlates with intermediate gene expression.Class III shows the highest expres-sion,and it includes H2BK5me1,H4K16ac,H4K20me1and H3K79me1/2/3in addition to the modification backbone (Fig.2b ).Our Gene Ontology analysis suggests that genesinvolved in cellular physiology and metabolism are enriched in the active class III patterns,consistent with their house-keeping roles (data not shown).In contrast,many genes involved in development,cell–cell signaling and synaptic transmission are enriched in the inactive class I patterns,consistent with their not being required for mature T-cell function.T o correlate each modification with gene expression,we compared the average gene expression with or without each modification(Fig.2c ).H3K27me3was among a group of repressive marks also including H3K27me2,H3K9me2,H3K9me3and H4K20me3,whereasmost other modifications correlated with activation.Although the modification patterns do not uniquely determine the extent of expression,the H3K79me3and H2BK5ac modifications showed weak correlation with expression within a modification pattern (Supplementary Fig.5online).Chr10:6145000615000061550006160000668100006683000066850000184153984510233151376554783691555178847610612141231632H3K4me3H3K4me2*H3K4me1IL2RACD28RECNS22IFNGH3K27me3H3K27me2*H3K27me1H3K27ac H3K9me3H3K9me2*H3K9me1H3K79me3H3K79me2H3K79me1H3R2me2H3R2me1H3K36me3H3K36me1H4K20me3H4K20me1*H2BK5me1H2BK5ac H4R3me2H3K14ac *H3K18ac *H3K23ac *H4K5ac *H4K8ac H4K12ac H4K16ac *H4K91ac H2BK12ac H2BK20ac *H2BK120ac *H2AK5ac H2AK9ac *H2A.Z H3K36ac H3K9acH3K4acChr12:2511304456175123223511554356379161017464757832345*H3K4me3H3K4me2*H3K4me1H3K27me3H3K27me2*H3K27me1*H3K27ac H3K9me3H3K9me2*H3K9me1H3K79me3H3K79me2H3K79me1H3R2me2H3R2me1H3K36me3H3K36me1H4K20me3H4K20me1H2BK5me1*H2BK5acH4R3me2H3K14ac*H3K18ac*H3K23ac*H4K5ac*H4K8acH4K12ac* H4K16ac * H4K91ac * H2BK12ac * H2BK20ac *H2BK120ac H2AK5acH2AK9ac*H2A.Z*H3K36acH3K9ac *H3K4ac ac d e b0.35F r a c t i o n s o f e n h a n c e r s0.300.250.200.150.100.0510,00010,0001,0001,000Number of enhancers associated with one pattern Enhancers-associated gene expressionP e r c e n t a g e o f e n h a n c e r s w i t h h i g h e r e x p r e s s i o nN u m b e r o f c o m b i n a t o r i a l p a t t e r n s1001001010110H 2A K 5a c H 2A K 9a c H 2B K 5a c H 2B K 5m e 1H 2B K 12a c H 2B K 20a c H 2B K 120a c H 3K 4a c H 3K 4m e 1H 3K 4m e 2H 3K 4m e 3H 3K 9m e 1H 3K 9m e 2H 3K 9m e 3H 3K 14a c H 3K 18a c H 3K 23a c H 3K 27a c H 3K 27m e 1H 3K 27m e 2H 3K 36m e 1H 3K 36m e 3H 3K 79m e 1H 3K 79m e 2H 3K 79m e 3H 3R 2m e 1H 3R 2m e 2H 4K 5a c H 4K 8a c H 4K 12a c H 4K 16a c H 4K 91a cH 4K 20m e 1H 4K 20m e 3H 3K 27m e 3H 3K 36a c H 3K 9a c H 2A .Z 1009080706050403020101101001,00010,000H2AZ, H3K4me1, H3K4me2, H3K4me3, H3K9me1: 21H2AZ, H3K4me2, H3K4me3, H3K9me1: 37H2AZ, H3K4me1: 36 H3K4me1, H4K20me1: 21H3K4me1: 64H3K4me3: 34H3K27me3: 65H3K36me3: 41H4K20me1: 42H2AK5ac: 63No modification: 1,817All enhancers: 4,179H2AZ: 67H2AZ, H3K4me3: 20Figure 3Patterns of histone modifications atenhancers.(a )The histone modification pattern at the CD28RE enhancer (highlighted in red)of the IL2RA gene.Significant modifications are indicated by asterisks on the left.(b )Histone modification patterns at the IFNG gene and its downstream enhancer,CNS22,are shown.Significant modifications at CNS22are indicated by asterisks on the left.(c )The fractions of enhancers associated with each of the 38modifications.(d )Patterns of histonemodifications at 4,179DNase hypersensitivesites.The y axis indicates the number of patterns,and x axis indicates the number of hypersensitive sites associated with each pattern.(e )Correlation analysis of gene expression with the ten largest modification patterns by assigning an enhancer to the TSS of the nearest known gene.All,all DNase I hypersensitive sites.The number of hypersensitive sites associated with each pattern is indicated.©2008 N a t u r e P u b l i s h i n g G r o u p h t t p ://w w w .n a t u r e .c o m /n a t u r e g e n e t i c sEnhancers of transcription have been identified using modification patterns 15,18,21,22.We previously found that all three H3K4methyla-tion states and H2A.Z were detected at enhancers 15.However,others identified enhancers associated with high H3K4me1but very low H3K4me3(refs.21,23).These results suggest that there are distinctive modification patterns at different enhancers.Indeed,the CD28response element (CD28RE)enhancer 24of the IL2RA gene is asso-ciated with 12modifications (P o 10À7),whereas 18modifications are detected at the CNS22enhancer 25of the IFNG gene (Fig.3a ,b ).We next examined histone modification patterns at 4,179intergenic DNase I hypersensitive sites 26,excluding those in promoter regions and miRNA genes,as a set of putative enhancers.As compared to the whole genome,these putative enhancer regions showed an elevated sum of all modifications (Supplementary Fig.6a online).Each of H2A.Z,H3K4me1,H3K4me2,H3K4me3,H3K9me1and H3K18ac associated with more than 20%of enhancers (Fig.3c ).Several modifications were associated with very few enhancers,including both repressive marks (H3K9me2,H3K9me3and H3K27me2)and activating marks (H2AK9ac and H3K14ac)(Fig.3c ).Among the total of 1,389patterns,195are associated with multiple hypersensitive sites and 1,194associated with a distinct hypersensitive site (Fig.3d ).The top 12patterns include those associated with only one modification or combinations of H3K4me1,H3K4me2,H3K4me3,H3K9me1,H3K36me3,H4K20me1and H2A.Z (Fig.3e ).No modifications were detected at 1,817hypersensitive sites,perhaps indicating nucleo-some-free regions or insufficient sequencing.These data suggest that there are multiple patterns associated with enhancers.However,we did not find significant correlations between modification patterns at enhancers and gene expression (Fig.3e and Methods).These results suggest that multiple histone modifications can associate with critical regulatory elements of transcription.T o identify modifications that may function together to modify chromatin,we searched for robust modification features at promoter regions.This analysis revealed a modification ‘backbone’consisting of 17modifica-tions (H2A.Z,H2BK5ac,H2BK12ac,H2BK20ac,H2BK120ac,H3K4ac,H3K4me1,H3K4me2,H3K4me3,H3K9ac,H3K9me1,H3K18ac,H3K27ac,H3K36ac,H4K5ac,H4K8ac and H4K91ac)that were present in 821different patterns and associated with a total of 3,286genes.T o examine whether the modifications in this group tend to coexist,we counted the promoters missing one of these modifica-tions.Notably,only a small number of promoters (0–393)were identified as missing one of these 17modifications,as compared to 3,286promoters that had all 17modifications (Fig.4a ).This back-bone of modifications is robust against perturbations (Supplementary Fig.6b ).Furthermore,none of the promoters possessing the backbone had significant levels of the repressive mark H3K27me3.We verified the existence of the ‘backbone’modification by principal component analysis,which revealed that 16of the 17modifications are highly clustered in the first principal component (Supplementary Fig.7online)and provided further evidence that the modifications in the backbone can be classified in the same group.Genes with this backbone seem to have higher expression than the genes with no modifications (Fig.2b ,class II).The tendency of the 17modifications to coexist suggests that some of these modifications may be present at the same nucleosome.We tested this hypothesis by carrying out a pairwise correlation analysis at a single-nucleosome level of 18histone acetylations,18histone methylations,CTCF,Pol II and H2A.Z using 200-bp windows for the entire genome (see Supplementary Table 2online for the top correlated pairs (r 40.4;P o 0.01)).A heat map based on the mean correlation coefficients indicates that a cluster of strong positively correlated pairs was observed at the lower-right corner (Fig.4b ).All 14modifications within this cluster (r 40.4;P o 0.01)belong to the 17-modification backbone module found at promoters.Another cluster of positively correlated pairs contains modifications enriched in transcribed regions of genes,including H4K20me1,H2BK5me1,H3K9me1,H3K4me1/2and H3K79me1/2/3.Pol II clustered together with these modifications rather than the promoter-centric modifica-tions.Modifications related to gene silencing,including H3K27me2,H3K27me3,H3K9me2and H3K9me3,were clustered together (Fig.4b ).Many correlated pairs,including H3K4me1-H3K9me1(r ¼0.51;P o 0.01),H3K9me1-H3K27me1(r ¼0.31;P o 0.01)PresentAbsentValueH 3K 9m e 2H 3K 9m e 3H 3K 27m e 2H 3K 27m e 3H 3K 14a c H 2A K 9a c H 3K 23a c H 3K 36m e 3H 3K 27m e 1H 3R 2m e 1H 3R 2m e 2H 4R 3m e 2H 4K 20m e 3H 2A K 5a c H 4K 16a c H 4K 12a c C T C F P o l I I H 3K 79m e 1H 3K 79m e 2H 3K 79m e 3H 4K 20m e 1H 2B K 5m e 1H 3K 4m e 1H 3K 4m e 2H 3K 9m e 1H 4K 8a c H 4K 5a c H 2A Z H 3K 4m e 3H 2B K 12a c H 3K 9a c H 3K 18a c H 3K 27a c H 2B K 5a c H 3K 36a c H 3K 4a c H 2B K 20a c H 4K 91a c H 2B K 120a cH2BK120acH4K91ac H2BK20ac H3K4ac H3K36ac H2BK5ac H3K27ac H3K18ac H3K9ac H2BK12ac H3K4me3H2AZ H4K5ac H4K8ac H3K9me1H3K4me2H3K4me1H2BK5me1H4K20me1H3K79me3H3K79me2H3K79me1PolIICTCF H4K12ac H4K16ac H2AK5ac H4K20me3H4R3me2H3R2me2H3R2me1H3K27me1H3K36me3H3K23ac H2AK9ac H3K14ac H3K27me3H3K27me2H3K9me3H3K9me2abFigure 4Correlation of histone modifications in the genome.(a )A group of 17modifications,the ‘backbone’in Figure 2b ,tend to coexist.The numbers of promoters associated with all the 17modifications or missing any one modification (the blue rectangle)are indicated on the right.(b )Tags are binned into nonoverlapping 200-bp bins along the ing the tallies for each bin,we calculated a pairwise Spearman correlation coefficient for each pair of modifications to create a correlation coefficient matrix.A heat map was then generated from this matrix.©2008 N a t u r e P u b l i s h i n g G r o u p h t t p ://w w w .n a t u r e .c o m /n a t u r e g e n e t i c sand H3K9me2-H3K27me2(r ¼0.28;P o 0.01),identified in this study have been detected in one single modified peptide using a mass spectrometry strategy 16.Mutually exclusive acetylation and methylation are detectable at several lysines,including H2BK5,H3K4,H3K9,H3K27and H3K36.However,except for the H3K9acetylation and methylation,little is known about the functional and spatial differences of modification variance at other lysines.Our data indicate that all acetylations of these five lysines areenriched in the promoter regions of active genes (Fig.5),whereas the predominantregion of enrichment for the various methyla-tions depends on the specific lysine.H3K4me1and H3K4me2were elevated in the vicinity of promoters,whereas mono-methylated H2BK5,H3K9and H3K27were elevated throughout the transcribed regions of active genes (Fig.5).Localization in different regions of genes suggests that these modifica-tions have different functions.For example,H3K9ac was elevated in promoter regions,consistent with a role in transcriptional initia-tion 20,whereas H4K12ac was detected at high levels in transcribed regions,suggesting a role in transcriptional elongation 19,27.It has been proposed that histone modifica-tions can cross-talk 28and that multiple mod-ifications with similar functions can reinforce the robustness of a chromatin state 14.In thisreport,we identify a large number of histone modification patterns at promoters and potential enhancers.In particular,we identify a back-bone module consisting of 17modifications that is found at 25%of human promoters.These modifications tend to colocalize at gene promoters,and most of them are correlated with each other at an individual nucleosome level.Although the genes associated with these modifications tend to have higher expression,the histone modificationsChr19:a cegi bdfhj 91964500019650000H2BK5me1H2K36me3H3K36me1H3K4me3H3K4me2H3K4me1H3K27me3H3K27me2H3K27me1H3K9me3H3K9me2H3K9me1H3K9acH3K27ac H3K4acH2BK5acH3K36acZNF101ZNF101SMAPSMAPSMAP 19655000196600001964500019650000196550001966000016716000167165001671700016717500167180001671850016720000167300001674000016715000167200001672500016750000167600001411Chr19:52151143Chr11:911142131321Chr11:516171411Chr11:2211221481 1.6E–07AcMe1Ac Me3Ac Me1Ac Me3Ac Me2Ac Me1Ac Me3Ac Me2Ac Me1Ac Me3AcMe2Ac Me1H 2B K 5 t a g d e n s i t yH 3K 36 t a g d e n s i t yH 3K 4 t a g d e n s i t yH 3K 27 t a g d e n s i t yH 3K 9 t a g d e n s i t y1.4E–071.2E–071E–078E–086E–084E–082E–08–4,000–2,00002,0004,000–4,000–2,00002,0004,000–4,000–2,000–1,000–2,0002,0001,00000–1,000–2,0002,0001,0000–1,000–2,0002,0001,0000–2,000–4,0002,0004,0000–2,000–4,0002,0004,0000–2,000–4,0002,0004,0000–2,000–4,0002,0004,0000–2,000–4,0002,0004,0000–2,000–4,0002,0004,00002,0004,0001.4E–071.2E–071E–078E–086E–084E–082E–081.4E–071.2E–071E–078E–086E–084E–082E–081.4E–071.2E–071E–078E–086E–084E–082E–0801E–088E–096E–094E–092E–0901E–088E–096E–094E–092E–0901.8E–081.6E–081.4E–081.2E–081E–088E–097E–086E–085E–084E–083E–082E–081E–0807E–086E–085E–084E–083E–082E–081E–0807E–088E–086E–085E–084E–083E–082E–081E–087E–088E–086E–085E–084E–083E–082E–081E–082.5E–072E–071.5E–071E–075E–086E–094E–092E–091.2E–081E–088E–096E–094E–092E–0901.2E–081E–088E–096E–094E–092E–0901.2E–081E–088E–096E–094E–092E–0905E–094E–093E–092E–091E–0905E–094E–093E–092.5E–082E–081.5E–081E–085E–0902E–091E–0901.2E–071E–078E–086E–084E–082E–0801.2E–071E–078E–086E–084E–082E–0801.2E–071E–078E–086E–084E–082E–080Figure 5Characteristic spatial distribution of mutually exclusive modifications.(a )Thedistribution of H2BK5me1(upper)and H2BK5ac (lower)surrounding the ZNF101gene.(b )The composite profiles of H2BK5me1(green)and H2BK5ac (red)surround the TSS regions of1,000active genes.(c )The distribution patterns of H3K36me3(upper),H3K36me1(middle)and H3K36ac (lower)surrounding the ZNF101gene.(d )The composite profiles of H3K36ac (red)are compared with the two states of H3K36methylation (H3K36me1and H3K36me3)surrounding the TSS regions of 1,000active genes.(e )The distribution patterns of H3K4ac and the three states of H3K4methylation surrounding the promoter region of the SMAP gene.(f )The composite profiles of H3K4ac (red)are compared with the three states of H3K4methylation (H3K4me1,H3K4me2andH3K4me3)surrounding the TSS regions of 1,000active genes.(g )The distribution patterns of H3K27ac and the three states of H3K27methylation surrounding the SMAP gene.(h )The composite profiles of H3K27ac (red)are compared with the three states of H3K27methylation (H3K27me1,H3K27me2and H3K27me3)surrounding the TSS regions of 1,000active genes.(i )The distribution patterns of H3K9ac and the three states of H3K9methylation surrounding the SMAP gene.(j )The composite files of H3K9ac (red)are compared with the three states of H3K9methylation (H3K9me1,H3K9me2and H3K9me3)surrounding the TSS regions of 1,000active genes.©2008 N a t u r e P u b l i s h i n g G r o u p h t t p ://w w w .n a t u r e .c o m /n a t u r e g e n e t i c s。

Qin HB, Yang ZY, Fan YJ, Zhu Q. Establishment and evaluation of aging models induced by D-galactose in mice.Zhongguo
Zuzhi Gongcheng Yanjiu yu Linchuang Kangfu 2009;13(7): 1275-1278(China)
中国组织工程研究与临床康复 第 13 卷 第 7 期 2009–02–12 出版 Journal of Clinical Rehabilitative Tissue Engineering Research February 12, 2009 Vol.13, No.7
基础医学
D-半乳糖诱导衰老小鼠模型的建立与评价
通讯作者：朱 清，博士，讲师， 南通大学医学院 药理学教研室，江 苏省南通市 226001 zhuqing7883@
中图分类号:R332 文献标识码:B 文章编号:1673-8225 (2009)07-01275-04
收稿日期：2008-09-20 修回日期：2008-12-06 (54200809190025/ W·Z)
ISSN 1673-8225 CN 21-1539/R CODEN: ZLKHAH
1275

秦红兵，等. D-半乳糖诱导衰老小鼠模型的建立与评价
0 引言
D-半乳糖衰老动物模型是由国内学者龚国清等在 1991年根据衰老的代谢紊乱学说而构建的。与其他几种 衰老动物模型如SAMP系小鼠衰老模型、臭氧损伤衰老 模型、去胸腺衰老模型、自然衰老模型等相比，该模型 简便易行，价格低廉，结果稳定，因而广泛应用于药物 抗衰老的研究之中[1-2]。但是D-半乳糖诱导衰老模型在 行为、免疫等方面的衰老研究中的应用，文献相关报道 并不完全一致[3-5]。实验使用D-半乳糖建立亚急性衰老 小ቤተ መጻሕፍቲ ባይዱ模型，并对其进行行为学、生化以及免疫等方面的 评价。

含一个儿茶酚基团ꎬ因此左旋多巴及其衍生物具有一定的抗氧化活性 [７] ꎬ例如ꎬＭａｎｃｈｉｎｅｅｌｌａ 等在实验中
发现ꎬ含多巴环二肽 ｃｙｃｌｏ( ＤＯＰＡ￣ＤＯＰＡ) 与 ｃｙｃｌｏ( ＤＯＰＡ￣Ｐｈｅ) 不仅具有良好的 １ꎬ１ － 二苯基 － ２ － 三硝基
苯肼( ＤＰＰＨ) 自由基清除活性ꎬ而且安全性好ꎬ在实验浓度下对 ＰＣ１２ 细胞没有细胞毒性 [８]
外ꎬ采用 ＤＰＰＨ 自由基清除实验ꎬ以丹参素为对照ꎬ首次研究了这三种环二肽的抗氧化活性
１ 材料与方法
１. １ 实验材料与仪器 Ｆｍｏｃ￣ＤＯＰＡ( Ａｃｅｔｏｎｉｄｅ) ￣ＯＨ 和 Ｈ￣ＤＯＰＡ( Ａｃｅｔｏｎｉｄｅ) ￣ＯＭｅꎬ依据文献报道由实验
室合成 [１５ － １６] ꎻＬ￣脯氨酸甲酯盐酸盐( Ｈ￣Ｐｒｏ￣ＯＭｅＨＣｌ) 、Ｌ￣谷氨酸甲酯盐酸盐( Ｈ￣Ｇｌｕ( ＯｔＢｕ) ￣ＯＭｅＨＣｌ)
及其 ＤＰＰＨ 自由基清除活性测试
张小燕ꎬ任 毅ꎬ何延淼ꎬ胡碧煌ꎬ刘中强
( 热带生物资源教育部重点实验室ꎬ海南大学 生命科学与药学院ꎬ海南 海口 ５７０２２８)
摘 要: 采用缩丙酮保护的左旋多巴( Ｌ￣ＤＯＰＡ) 的儿茶酚基ꎬ在常温下以哌啶催化直链二肽甲酯并使其发生
分子内环化反应ꎬ制备了 Ｌ￣Ｐｒｏ、Ｌ￣Ｇｌｕ 或 Ｄ￣Ｇｌｕ 与 Ｌ￣ＤＯＰＡ 形成的环二肽ꎻ该保护方式成功地规避了微波辐
第 ３８ 第 ２ 期
２０２０ 年 ６ 月
海南大学学报自然科学版
ＮＡＴＵＲＡＬ ＳＣＩＥＮＣＥ ＪＯＵＲＮＡＬ ＯＦ ＨＡＩＮＡＮ ＵＮＩＶＥＲＳＩＴＹ
Ｖｏｌ. ３８ Ｎｏ. ２
Ｊｕｎ ２０２０
文章编号:１００４ － １７２９(２０２０)０２ － ０１２４ － ０８

year 1 (Osuna-Viscarra, 1991; CNA, 2001). Water table drops due to increasing groundwater consumption are a common problem in the aquifers of central and northern Mexico (Brouste et al., 1997; Edmunds et al., 2002; Mahlknecht et al., 2004, 2006a; Esteller and Andreu, 2005; Portugal et al., 2005; Daessle et al., 2006; FloresMarquez et al., 2006; Schoups et al., 2006; Ramos-Leal et al., 2007). Recently, frequent droughts have accelerated this tendency and forced the municipal water and wastewater agency to adopt a water service programme whereby only a portion of the population receives water at any given time. Additionally, extraction of some water wells was halted due to the finding of high arsenic concentrations in the water, which did not comply with the national drinking water standard. As a result, the local population and government have serious concerns about the long-term availability and water quality in this area. In 2002, a ¾140 million USD project to modernize and technically improve the Rio Conchos irrigation districts started with the aim of improving water availability in the Rio Conchos Basin (BECC, 2002). This project would also indirectly benefit Chihuahua City. Nevertheless, the expected benefits of this promising project have yet to reach the region.rgency to