Abstract
Eukaryotic histone deacetylation, critical for maintaining nucleosome structure and regulating gene expression, is mediated by histone deacetylases (HDACs).
Analysis：
主语：Eucharyotic histone deacetylation
谓语：is mediated by
表语：histone deacetylase （HDACs）
句子critical for maintaining nucleosome structure and regulating gene expression 前面有先行词histone deacetylation 因此是定语从句省略了which is
完整句子应该是：
Eukaryotic histone deacetylation which is critical for maintaining nucleosome structure and regulating gene expression, ......
这里的用法是：定语从句省略主格关系代词的用法
即主格关系代词+be+分词省略主格关系代词+be，但是这里好像后面是critical for 其实这个是副词修饰maintaing
所以我们可以去除ciritical for 在看这个句子：就是主格关系代词which + be 动词is的结构所以可以省略
Eukaryotic histone deacetylation which is maintaining nucleosome structure and regulating gene expression, ......
Although nucleosomes have been reported to regulate mRNA polyadenylation in humans, the role of HDACs in regulating polyadenylation has not been uncovered.
Although引导的让步状语从句，Although nucleosomes（主语） have been reported to （谓语） regulate mRNA polyadenylation（宾语） in humans （地点状语）。
the role of HDACs（主语）（which was省略） in regulating polyadenylation has not been（谓语） uncovered（表语）
Taking （现在分词作状语）advantage of phenotypic studies on Arabidopsis, HDA6 (one of HDACs) was found to be a critical part of many biological processes.
知识点：伴随状语
由于从句和主句主语一致，为了避免重复，状语从句主语省略，同时动词变成动名词。
Because I felt tired， I went to bed ealier.
Feeling tired, I went to bed ealier
When she saw the dog，she ran off
Seeing the dog，she ran off
这里乍看前后主语不一致后面好似HDA6，前面从句好像是we， 仔细观察我们发现，HDA6 是was found （by us省略），所以主语还是we ，前后一致，只是科学描述为了避免主观性，把主动变被动了。
Here, we report that HDA6 affects mRNA polyadenylation in Arabidopsis. Poly(A) sites of up-regulated transcripts are closer to the histone acetylation peaks in hda6 compared to the wild-type Col-0.
Here，地点状语
we （主语）report（谓语） that （宾语从句） “HDA6 （主语）affects （谓语） mRNA polyadenylation （宾语）in Arabidopsis （地点状语）.”
HDA6 is required for the deacetylation of histones around DNA on nucleosomes, which solely coincides with up-regulated or uniquely presented poly(A) sites in hda6.
主语: HDA6
谓语：is required for
宾语： the deacetylation of histones around DNA on nucleosomes（状语）
which solely coincides with up-regulated or uniquely presented poly(A) sites in hda6. 非限制定语从句其中which为主语 solely状语
coincide with 谓语
or 链接两个同位语宾语
in hda6 状语
Furthermore, defective HDA6 results in an overrepresentation of the canonical poly(A) signal (AAUAAA) usage.
Furthermore：状语
主语：defective（定语） HDA6
位语：results in
宾语：an overrepresentation of the canonical poly(A) signal (AAUAAA) usage.
Chromatin loci for generating AAUAAA-type transcripts have a comparatively low H3K9K14ac around poly(A) sites when compared to other noncanonical poly(A) signal–containing transcripts.
主语：Chromatin loci
位语： have
宾语： a comparatively low H3K9K14ac around poly(A) sites
状语：when compared to other noncanonical poly(A) signal–containing transcripts
其中 for generating AAUAAA-type transcripts=which is for generating AAUAAA-type transcripts
These results indicate that HDA6 regulates polyadenylation in a histone deacetylation–dependent manner in Arabidopsis.
主语：These results
位语：indicate
宾语：HDA6 （主语） regulates（谓语） polyadenylation （宾语） in a histone deacetylation–dependent manner in Arabidopsis （复合状语）
Introduction
As one of the post-transcriptional modifications of mRNA, the polyadenylation process can critically regulate the gene expression in eukaryotes (Tian and Manley 2017).
主语： the polyadenylation process
谓语：regulate
宾语：the gene expression
状语或宾补：in eukaryotes
知识点：宾补
所谓“补”就是补充说明，宾补呢，就是对宾语的补充。英语中，做宾补的部分一把是名词、形容词、介词短语和非谓语动词。所谓的非谓语动词，就是分词和不定式，分词又包括过去分词和现在分词。
1. 名词做宾补：
We call her Goldilocks.
2. 形容词的宾补：
My work keeps me busy.
3. 介词短语的宾语补语：
I left a case on the train.
4. 动名词短语的宾语补语：
Don't keep me waiting too long.
5. 不定式作宾补：
I asked him to help me.
6. 过去分词作宾补：
Could you make yourself understood?
7. 除了以上情况，有些副词也可以做宾补：
Let me in.
Don't let your parents down.
Don't let the dog out.
Put your shoes away.
方式状语：As one of the post-transcriptional modifications of mRNA,
知识点：
as 用作介词，当它后面接名词时，既可以表示“时间”，也可以“身份”。表示“时间”就是时间状语，表示“身份”则是方式状语，意为“以......身份（做某事）”。
例如：
1. 表示时间：
As a small boy, he was rather naughty.
She loved singing as a child and started vocal training at 12.
2. 表示身份：
As a teacher, you should be strict with your students.
He's not in the first grade as a musician.
as到底是表示“时间”还是“身份”，可以从后面接的名词和语境上判断出来。
As a student, you should study hard. 在这个句子中，as表示“身份”，意为“作为”。“作为一名学生，你应该努力学习。”
This universally required 3′ end processing for RNA polymerase II (Pol II)-dependent transcripts is mainly mediated by a protein complex which recognizes a poly(A) signal, cleavages the pre-mRNA, and synthesizes the poly(A) tail (Clerici et al. 2018).
主语：This 相当于it
谓语：required
宾语：3′ end processing
for RNA polymerase II (Pol II)-dependent transcripts is mainly mediated by a protein complex
for 引导的原因状语从句，
知识点：
because 表示原因,回答why 的问句
比如： why are you absent?
Because i am ill.
for 一般不表示原因，表理由，一般不放句首
比较这两个句子：
The day breaks, for the birds are singing.
The day breaks because the sun is rising.
鸟叫不是天亮的直接原因，只是因为鸟叫，而推断天亮了．
而太阳出来了是直接原因，因为太阳出来了，所以天亮了
which recognizes a poly(A) signal, cleavages the pre-mRNA, and synthesizes the poly(A) tail (Clerici et al. 2018).
which引导的限制性定语从句
主语：which
谓语：and 连接的复合谓语：recognizes，cleavages ，synthesizes
宾语：三个动词后面的词
Recent studies revealed that alternative polyadenylation (APA) sites can be positioned at either the 3′ untranslated region (UTR) or outside of the 3′ UTR (Deng and Cao 2017; Tian and Manley 2017).
主语：studies
谓语：revealed
宾语：that that alternative polyadenylation (APA) sites can be positioned at either the 3′ untranslated region (UTR) or outside of the 3′ UTR
APA results in increased diversity of transcripts and may affect mRNA stability, localization, and exportation.
主语：APA
谓语： results in ， may affect
宾语： increased diversity of transcripts ，mRNA stability, localization, and exportation.
Consequently, the expression of these genes may be regulated by APA.
主语： the expression of these genes
谓语：may be regulated
宾语：by APA.
状语：Consequently
By using high throughput sequencing approaches, it was found that over 50% of genes contain more than two poly(A) sites in eukaryotes (Xing and Li 2011; Tian and Manley 2017).
By using high throughput sequencing approaches
by+doing是“介词by动名词”，在句子中作状语，可在在句尾，句首。如果在句中，前后都要用逗号隔开。举例说明:
He studied English by teaching himself when he was young.
By teaching himself he studied English when he was young.
He, by teaching himself, studied English when he was young.
主语：it（形式主语），真正主语是that引导的名词性从句（over 50% of genes（主语） contain （谓语）more than two poly(A) sites （宾语） in eukaryotes（状语））
谓语：was
Poly(A) signal is mainly recognized by cleavage and polyadenylation specificity factors (CPSFs) (Clerici et al. 2018).
主语：Poly(A) signal
谓语：is mainly recognized by
宾语：cleavage and polyadenylation specificity factors (CPSFs)
Although CPSFs are highly conserved between mammals and plants (Zhang et al. 2008a; Hunt et al. 2012), the poly(A) signal
compositions are quite different.
主语：the poly(A) signal compositions
谓语：are
表语： quite （状语） different.
让步状语从句：Although CPSFs are highly conserved between mammals and plants
More than 50% of transcripts from mammals use the canonical poly(A) signal AAUAAA for polyadenylation (Tian and Manley 2017), whereas the transcripts using AAUAAA only account for about 10% of plant transcripts (Wu et al. 2011b; Xing and Li 2011).
主语： 50% of transcripts from mammals （地点状语）
谓语：use
宾语：the canonical poly(A) signal AAUAAA
宾补：for polyadenylation
The other 40% and 50% of plant transcripts contain 1-nt variations of AAUAAA and other poly(A) signals (Loke et al. 2005), respectively.
主语：The other 40% and 50% of plant transcripts
谓语：contain
宾语：1-nt variations of AAUAAA and other poly(A) signals
This distinguished characteristic of poly(A) signal reflects a more complex polyadenylation mechanism in plants that is not yet understood.
主语： characteristic of poly(A) signal
谓语：reflects
宾语： a more complex polyadenylation mechanism （in plants）
先行词为mechanism的宾语从句： that is not yet understood.（主系表结构）
Nucleosomes are formed when histone proteins are wrapped with DNA.
主语：*Nucleosomes
谓语：are
表语：formed
状语从句：when histone proteins are wrapped with DNA
These nucleosomes are then packed into highly condensed chromatins in the eukaryotic nucleus.
主语：These nucleosomes
谓语：are packed into
宾语：highly condensed chromatins
状语：in the eukaryotic nucleus
It was reported that the nucleosome position affects the usage of proximal or distal poly(A) sites, suggesting the regulatory role of chromatin status in orchestrating mRNA polyadenylation (Huang et al. 2013; Lee and Chen 2013).
主语：形式主语it，真正主语是that引导的主语从句
谓语：was reported
suggestting （that）引导的结果状语从句，解释结果：suggesting the regulatory role of chromatin status in orchestrating mRNA polyadenylation
Overall, the compactness of chromatin is determined by histone modifications such as methylation and acetylation.
主语：the compactness of chromatin
谓语： is determined by
宾语：histone modifications
定语：such as methylation and acetylation解释前面histone modification，定语前置后置的原则就是长的后面，短的前面，当时被动的后面，比如a cake eaten by her
Within these modifications, histone acetylation is known to be associated with the accessibility of chromatin and the recruitment of DNA-binding proteins to activate gene expression.
主语： histone acetylation
谓语：is known to
宾语：be associated with the accessibility of chromatin and the recruitment of DNA-binding proteins
状语：to activate gene expression 不定时作目的状语
状语：介词短语作状语，修饰整个句子Within these modifications
However, acetylation of the histones can be erased by histone deacetylases (HDACs), resulting in structural changes to the chromatin. Thus, the dynamic acetylation of a histone is an epigenetic hallmark to gate transcription activation.
主语：acetylation of the histones
谓语： can be erased by
宾语：histone deacetylases (HDACs)
状语1：resulting in structural changes to the chromatin （动名词词组作结果状语）
插入语：however，
插入语：一般被逗号，破折号，句子的其他成分隔开
类似的：
Frankly，he is a good guy，obviously，
HDA6 (encoded byAT5G63110), one of the HDACs, is associated with heterochromatin formation and gene repression (Tan et al. 2018).
主语： HDA6
谓语：is associated with
宾语：heterochromatin formation and gene repression
同位语：one of the HDACs
同样还有：English，a world wide language，is playing a key role in our school
In addition, HDA6 is also involved in other biological processes, such as stress tolerance, flowering time, and circadian rhythm in Arabidopsis (Yuet al. 2011; Kim et al. 2017; Wang et al. 2017; Hung et al. 2018).
主语： HDA6
谓语： is also involved in
宾语：other biological processes
非限制性定语：such as stress tolerance, flowering time, and circadian rhythm
状语：In addition，相当于additionally
例如 Your bonus this year is a one-week vacation in Hawaii. Additionally/In addition, you'll receive $3,000 in cash.
A recent study has revealed that nuclear retention of HDA6 results in gene silencing (Zhu et al. 2019).
主语：A recent study
谓语：has revealed
宾语：that nuclear retention of HDA6 results in gene silencing
Essentially, HDA6 deficiency could also result in a significant increase of histone H3K9ac, H3K14ac, (To et al. 2011), and gene activation (Earley et al. 2006; Tanaka et al. 2008; Yu et al. 2017).
主语：HDA6 deficiency
谓语：could also result in
宾语：a significant increase of histone H3K9ac, H3K14ac, (To et al. 2011), and gene activation（and 介导的多宾语）
状语：Essentially，副词作状语，修饰真个句子
It was reported that H3K9ac is required for the maximal Pol II pausing release to initiate and elongate transcription (Gates et al.
2017).
主语：it（形式主语）
谓语：reported
真在主语：that H3K9ac is required for the maximal Pol II pausing release to initiate and elongate transcription（目的状语）
The hyperacetylation of H3K9ac in coding and intergenic regions is correlated with transcription, reflecting the global regulatory role of histone acetylation on gene expression (Kurdistani et al. 2004).
主语：The hyperacetylation of H3K9ac in coding and intergenic regions
谓语：is correlated with
宾语：transcription,
状语： reflecting the global regulatory role of histone acetylation on gene expression（动名词词组作结果状语）
By facing the challenge of environmental stress, H3K9ac is associated with the expression of induced stress response genes (Kim et al. 2008; Chinnusamy and Zhu 2009).
主语：H3K9ac
谓语： is associated with
宾语： the expression of induced stress response genes
状语：By facing the challenge of environmental stress, by引导的方式状语
The other type of histone acetylation, H3K14ac, co-occurs with H3K9ac at gene regulatory elements, suggesting their coordinated regulatory role in gene expression (Karmodiya et al. 2012).
主语：The other type of histone acetylation
同位语：H3K14ac
谓语： co-occurs with
宾语：H3K9ac
宾补： at gene regulatory elements
状语：suggesting their coordinated regulatory role in gene expression（动名词词组作结果状语）
Moreover, H3K14ac can crosstalk with H3K4 dimethylation during stress responses in soybeans (Wu et al. 2011a).
主语：H3K14ac
谓语： can crosstalk with
宾语：H3K4 dimethylation
状语：during stress responses in soybeans
状语2：Moreover
Together, these results indicate that H3K9ac and H3K14ac are important histone epigenetic hallmarks for regulating gene
expression.
主语：these results
谓语：indicate
宾语：that H3K9ac and H3K14ac are important histone epigenetic hallmarks for regulating gene
expression（由于前面主系表全有这里for是介词短语做状语）
状语：Together，修饰整个句子
However, their roles in essential RNA maturation processes, polyadenylation, and APA are unknown.
主语：and 连接的多个主语their roles in essential RNA maturation processes, polyadenylation, and APA
谓语：are unknown
插入语：However，一般被逗号，破折号，句子的其他成分隔开
Thus, we carried out poly(A) tag sequencing (PAT-seq) and ChIP-seq of histone acetylation on wild type and HDA6 mutants
of Arabidopsis to uncover the crosstalk between histone deacetylation and mRNA 3′ end processing.
主语：we
谓语： carried out
宾语：poly(A) tag sequencing (PAT-seq) and ChIP-seq of histone acetylation
目的状语： to uncover the crosstalk between histone deacetylation and mRNA 3′ end processing.
插入语或状语：Thus
Results
PAT-seq, which uniquely sequences the 3′ end of mRNA, was applied for Col-0 and HDA6 mutants to uncover the effect of HDA6 on polyadenylation of Arabidopsis.
主语：PAT-seq
谓语：was applied for
宾语：Col-0 and HDA6 mutants
目的状语：to uncover the effect of HDA6 on polyadenylation of Arabidopsis
非限制性定语从句：which uniquely sequences the 3′ end of mRNA
An overview of the experimental and computational analysis scheme is summarized in Supplemental Figure S1.
主语：overview
谓语： is summarized in
宾语：Supplemental Figure S1
It has been shown that mRNA polyadenylation sites are not exclusively positioned in the 3′ UTR (Wu et al.2011b).
主语：it（形式）
谓语：has been shown
主语从句：mRNA polyadenylation sites are not exclusively positioned in the 3′ UTR (Wu et al.2011b).
例子：Further, [状语] it [形式主语] has recently been shown [谓语] something. [主语]
They can be located anywhere with a suitable poly(A) signal, resulting in truncated or prolonged mRNA isoforms (Supplemental Fig. S2A).
主语：They
谓语：can be
状语：anywhere
伴随状语2：with a suitable poly(A) signal
resulting in truncated or prolonged mRNA isoforms （动名词词组作结果状语）
About 50% of genes and intergenic loci were identified with more than two poly(A) sites (Fig. 1A).
主语：About 50% of genes and intergenic loci
谓语：were identified with
宾语：more than two poly(A) sites
Principle component analysis of PAT-seq data shows a good repeatability of this PAT-seq experiment (Supplemental Fig. S2B).
主语：Principle component analysis of PAT-seq data
谓语：shows
宾语：a good repeatability of this PAT-seq experiment
Furthermore, the percentage of reads clustered into each poly(A) site in a gene is calculated to represent the poly(A) site usage (PSU).
主语：the percentage of reads clustered into each poly(A) site in a gene（定语后置）
谓语： is calculated to
宾语：represent the poly(A) site usage (PSU)
By excluding intergenic poly(A) sites, we identified 10,681 genes with ≥2 poly(A) sites.
主语：we
谓语：identified
宾语：10,681 genes
方式状语：By excluding intergenic poly(A) sites
定语：with ≥2 poly(A) sites
DESeq2 was used to calculate the p and adjusted P value (padj) of each poly(A) site.
主语：DESeq2
谓语：was used to
宾语（宾补）：calculate the p and adjusted P value (padj) of each poly(A) site.
To explore the effect of HDA6 on APA, different thresholds were used.
主语：different thresholds
谓语：were
表语：used
目的状语： To explore the effect of HDA6 on APA
According to the published threshold of absolute value of PSU changes (|△PSU|≥0.05, P < 0.05) (Zheng et al. 2018), 1310 (978 + 279 + 53) genes were identified with significant APA events (Fig. 1B, red circle).
主语：1310 (978 + 279 + 53) genes
谓语：were identified with
宾语：significant APA events
状语：条件状语According to the published threshold of absolute value of PSU changes
Within these, about 25.34% (279 + 53) of genes have a larger (|△PSU|≥0.2) shift of poly(A) site usage (Fig. 1B, blue circle).
主语：25.34% (279 + 53) of genes
谓语：have
宾语： larger (|△PSU|≥0.2) shift of poly(A) site usage
条件状语：Within these
However, if the threshold was set to |△PSU|≥0.2 and padj < 0.05, only 53 genes were identified with significant APA events (Fig. 1B, green circle; Supplemental Table S1).
插入语：However
主语：only 53 genes
谓语：were identified with
宾语：significant APA events
条件状语从句： if the threshold was set to |△PSU|≥0.2 and padj < 0.05
These results indicate that HDA6 affects mRNA polyadenylation and APA of genes by different measures.
主语：These results
谓语：indicate
宾语：that HDA6 affects mRNA polyadenylation and APA of genes by different measures（方式状语）.
The cumulative distribution curves present genome-wide polyadenylation profiles of hda6 and Col-0 and are folded at 50% cumulative frequency to show the median PSU (Supplemental Fig.S2C).
主语：The cumulative distribution curves
谓语：present ；are folded at
宾语：genome-wide polyadenylation profiles of hda6 and Col-0； 50% cumulative frequency
Although there is no large difference between the cumulative distribution curves of hda6 and Col-0, a Kolmogorov–Smirnov test (K-S test) shows a significant difference in the PSU profiles of hda6 and Col-0, reflecting that HDA6 has an impact on polyadenylation in Arabidopsis.
主语：a Kolmogorov–Smirnov test
谓语：shows
宾语：a significant difference in the PSU profiles of hda6 and Col-0
让步状语从句：Although there is no large difference between the cumulative distribution curves of hda6 and Col-0,
动名词引导结果状语从句：reflecting that HDA6 has an impact on polyadenylation in Arabidopsis
These results were further confirmed by the PAT-seq of another HDA6 mutant allele, sil1 (Liu et al. 2012) with a K-S test P value < 2.2 × 10−16 (Supplemental Fig. S2D).
主语：These results
谓语： were further confirmed by
宾语：the PAT-seq of another HDA6 mutant allele
Furthermore, by CDF plot again, we found that the PSU profile of DE poly(A) sites (n = 1387; threshold: padj < 0.05)
has a significant difference between hda6 and Col-0 (Fig. 1C).
主语：we
谓语：found
宾语：that the PSU profile of DE poly(A) sites (n = 1387; threshold: padj < 0.05) has a significant difference between hda6 and Col-0 (Fig. 1C)
状语：Furthermore
状语：by CDF plot again
**A heat map of these PSU profiles also illustrates that the PSUs of most DE poly(A) sites were varied between hda6 and Col-0, and this was consistent among replicates (Fig. 1D). **
主语：A heat map of these PSU profiles
谓语：illustrates
宾语：the PSUs of most DE poly(A) sites were varied between hda6 and Col-0
并列句：and this was consistent among replicates
To evaluate the potential that DE poly(A) sites resulted from the total gene expression variation, RT-qPCR was carried out
with a pair of primers which quantified the DE poly(A) sites and a pair of primers located on the 5′ end of genes which quantified
the total gene expression levels (Supplemental Fig. S3; Supplemental Table S2).
主语： RT-qPCR
谓语：was carried out with
宾语： a pair of primers which quantified the DE poly(A) sites（定语从句）
a pair of primers located on the 5′ end of genes（定语后置） which quantified the total gene expression levels （定语从句）
目的状语从句： To evaluate the potential that DE poly(A) sites resulted from the total gene expression variation
Results showed that DE poly(A) sites identified by DESeq2 were validated by RT-qPCR, and variation of their corresponding total gene expression levels was neither significant (Supplemental Fig. S3A–D) nor in an opposite direction (Supplemental Fig. S3E–H).
主语：Results
谓语：showed
宾语：and 介导的双宾语从句： DE poly(A) sites identified by DESeq2 were validated by RT-qPCR, and variation of their corresponding total gene expression levels was neither significant (Supplemental Fig. S3A–D) nor in an opposite direction
As a control, we selected AT1G35680 and AT2G38310 genes with non-DE poly(A) sites in the PAT-seq experiment.
As a control：as 用作介词，当它后面接名词时，既可以表示“时间”，也可以“身份”。表示“时间”就是时间状语，表示“身份”则是方式状语，意为“以......身份（做某事）”。
主语：we
谓语：selected
宾语： AT1G35680 and AT2G38310 genes
宾补： with non-DE poly(A) sites
定语：in the PAT-seq experiment
As shown in Supplemental Figure S3I, RT-qPCR confirmed that AT1G35680 was indeed not a DE poly(A) site gene.
方式状语：As shown in Supplemental Figure S3I,
As shown=As it is shown or As is shown
- Enter the word as it is shown in the box below. 输入下面显示验证字母。（方式状语。as 从句不缺成分，主句是行为动词enter）
可以省略为：Enter the word as shown in the box below.
- As is shown above, the laser beam is much more powerful.（比较状语。as 充当从句主语，传统语法叫“定语从句”。）
如上所显示，激光束比其他光束要强烈得多。
可以省略为：As shown above, the laser beam is much more powerful.
主语：RT-qPCR
谓语：confirmed
宾语：that AT1G35680 was indeed not a DE poly(A) site gene
For the second control gene AT2G38310, while its 3′ UTR was significantly down-regulated in hda6 by the RT-qPCR experiment, the total gene expression level also had the same trend (Supplemental Fig. S3J).
主语：the total gene expression level
谓语： had
宾语： the same trend
状语：For the second control gene AT2G38310,
while引导的让步状语从句： while（=although） its 3′ UTR was significantly down-regulated in hda6 by the RT-qPCR experiment
It indicates that the variation of the 3′ UTR of AT2G38310 may be induced by the repression of gene expression in hda6, and it was not identified as a DE poly(A) site in the PAT-seq analysis.
主语：it
谓语：indicates
宾语： the variation of the 3′ UTR of AT2G38310 may be induced by the repression of gene expression in hda6, and it was not identified as a DE poly(A) site in the PAT-seq analysis
Taken together, DE poly(A) sites identified by PAT-seq were mainly contributed by the change in polyadenylation activity in
hda6, and these results suggest that HDA6 affects mRNA polyadenylation
主语：DE poly(A) sites identified by PAT-seq
谓语：were mainly contributed by
宾语：the change in polyadenylation activity in hda6
and 连接并列句：, （由于和前面不是并列关系，所以这个and前面加，如果不加，就是and连接的两个并列宾语从句）and these results suggest that HDA6 affects mRNA polyadenylation
Histone acetyltransferase inhibitor minimizes the molecular effect of HDA6 mutation
主语：Histone acetyltransferase inhibitor
谓语：minimizes
宾语： the molecular effect of HDA6 mutation
It was demonstrated that defective HDA6 results in an increased gene expression (Earley et al. 2006; Tanaka et al. 2008; Yu et al.2017).
主语：it
谓语：was demonstrated
真正主语： that defective HDA6 results in an increased gene expression
Thus, we asked whether defective HDA6 causes differential expression of transcript isoforms.
主语：we
谓语：asked
宾语从句：whether defective HDA6 causes differential expression of transcript isoforms
状语：Thus
We found that more differentially expressed transcripts are up-regulated in hda6 (Fig. 2A).
主语：We
谓语：found
宾语： that more differentially expressed transcripts are up-regulated in hda6
Within the 1387 transcripts with DE poly(A) sites, 882 are up-regulated and 505 are down-regulated.
主语：882 ；505
谓语：are ；are
宾语：up-regulated；down-regulated.
状语：Within the 1387 transcripts with DE poly(A) sites
Since HDA6 functions in deacetylation of chromatins, we asked whether the effects of HDA6 on polyadenylation can be minimized under a low histone acetylation level.
主语：we
谓语：asked
宾语： whether the effects of HDA6 on polyadenylation can be minimized under a low histone acetylation level （whether作引导词不能省略，含义(是否)，有实际含义。）
原因状语从句：Since HDA6 functions in deacetylation of chromatins,
原因状语从句引导词：beacuse，for，as ，since
A histone acetyltransferase inhibitor, MB-3, was used to reduce the histone acetylation levels of hda6, sil1, and Col-0.
主语：A histone acetyltransferase inhibitor,
同位语：MB-3
谓语：was used to
宾语： reduce the histone acetylation levels of hda6, sil1, and Col-0
PAT-seq of MB-3-treated seedlings shows that the variances of those 1387 HDA6-dependent poly(A) sites are minimized (Fig.2B)
主语：PAT-seq of MB-3-treated seedlings
谓语：shows
宾语：that the variances of those 1387 HDA6-dependent poly(A) sites are minimized
Within those 1387 poly(A) sites, 929 show no significant difference after MB-3 treatment.
主语： 929
谓语：show
宾语：no significant difference
状语1：Within those 1387 poly(A) sites
状语2：after MB-3 treatment
The numbers of both up- and downregulated poly(A) sites are reduced a lot.
主语：The numbers of both up- and downregulated poly(A) sites
谓语：are reduced
状语：a lot
Under normal conditions, the majority of DE poly(A) sites resided in protein coding genes (Fig. 2C, red boxes) and are mainly located in the 3′ UTR (Fig. 2D, red boxes).
主语：the majority of DE poly(A) sites；
谓语：resided in；are mainly located in
宾语： protein coding genes；3′ UTR
状语：Under normal conditions
The interquartile ranges of boxplots and median values are minimized under MB-3 treatment, indicating that MB-3 treatment significantly reduces the variance of transcription expression levels among these three different gene types (Fig. 2C).
主语：The interquartile ranges of boxplots and median values
谓语： are minimized
状语1：under MB-3 treatment
状语2： indicating that MB-3 treatment significantly reduces the variance of transcription expression levels among these three different gene types （动名词词组引导结果状语从句）
The median expression level (dashed lines in red boxes) of DE poly(A) sites is slightly down in the
3′ UTR (canonical poly(A) site), whereas it is up-regulated in most other noncanonical poly(A) sites, such as the intergenic regions and introns (Fig. 2D, red boxes).
主语：The median expression level (dashed lines in red boxes) of DE poly(A) sites
谓语： is
表语：down
状语：in the 3′ UTR (canonical poly(A) site),
状语从句： whereas it is up-regulated in most other noncanonical poly(A) site
whereas 为从属连词，表示对比意义。从句位于主句之后时，分析为对比状语从句（=while on the contrary)
非限制性定语：such as stress tolerance, flowering time, and circadian rhythm
The up-regulating pattern is also observed in sil1, although the expression pattern of CDS poly(A) transcripts is different from hda6 (Supplemental Fig. S2G).
主语：The up-regulating pattern
谓语： is also observed in
宾语：sil1
让步状语从句：although the expression pattern of CDS poly(A) transcripts is different from hda6 (Supplemental Fig. S2G).
MB-3 treatment also reduces the ΔPSU values of 1387 DE poly(A) sites (Fig. 2E), which reflects the assertion
that MB-3 partially patches the effect of mutated HDA6.
主语：*MB-3 treatment
谓语：reduces
宾语：ΔPSU values of 1387 DE poly(A) sites
非限制性定语从句：which reflects the assertion that MB-3 partially patches the effect of mutated HDA6（that引导的同位语从句）
This trend was also found in MB-3 treatment on sil1 (Supplemental Fig. S2H).
主语：This trend
谓语：as also found in
宾语：MB-3 treatment
Gene Ontology enrichment analyses show that genes with significant upand down- regulated poly(A) sites are
both enriched in terms related to stress response (Supplemental Fig. S4A,B, green dashed box).
主语：Gene Ontology enrichment analyses
谓语： show
宾语：that genes with significant upand down- regulated poly(A) sites are
both enriched in terms related to stress response
Genes with up-regulated poly(A) sites are also significantly enriched in translation-associated terms
(Supplemental Fig. S4A, red dashed box), whereas genes with down-regulated poly(A) sites are also enriched in light response-associated terms (Supplemental Fig. S4B, orange dashed box).
主语：Genes with up-regulated poly(A) sites
谓语：are also significantly enriched in
宾语： translation-associated terms
比较状语从句：whereas genes with down-regulated poly(A) sites are also enriched in light response-associated terms
By checking the PAT-seq profiles, we found distinct APA on AT2G29500 encoding a HSP20-like protein, AT5G67300 encoding MYB DOMAIN PROTEIN 44 (MYB44), AT5G52882 encoding a Ploop protein in the nucleoside triphosphate hydrolases superfamily, and AT4G26090 encoding a leucine-rich repeat protein RPS2 (Supplemental Fig. S4C).
主语：we
谓语：found
宾语：and 引导的多个宾语
方式状语从句：By checking the PAT-seq profiles
Under MB-3 treatment, poly(A) sites of these genes in hda6 and sil1 are similar to Col-0 but rather different in the nontreated samples, reflecting that the mutation effect of HDA6 is abolished under low chromatin acetylation level
主语：poly(A) sites of these genes in hda6 and sil1
谓语：are similar to
宾语： Col-0
状语1：Under MB-3 treatment
but并列连词，连接两个句子，由于前面和后面句子主语谓语一致，为了避免重复，后面句子主语+谓语省略
伴随状语从句表示结果：reflecting that the mutation effect of HDA6 is abolished under low chromatin acetylation level
状语从句变成伴随状语从句顺序：1.去掉连词，2.去掉主语，3.动词变形
例如：Though he is young，he is very cute
Being young，he is very cute
After he finished his work，he went shopping
Finishing his work，he went shopping
These distinct APA genes between hda6 and Col-0 may contribute to the phenotypic outcomes of hda6, such as affecting abiotic stress tolerance by AT5G52882 and MYB44 (Ali et al. 2013; Kim et al. 2017), altering heat shock tolerance by HSP20-like gene (Popova et al. 2013), and changing sensitivity to pathogen infection by RPS2 (Bhandari et al. 2019).
主语：These distinct APA genes between hda6 and Col-0
谓语：contribute to
宾语：the phenotypic outcomes of hda6
非限制性定语：such as affecting abiotic stress tolerance by AT5G52882 and MYB44 (Ali et al. 2013; Kim et al. 2017)， altering heat shock tolerance by HSP20-like gene (Popova et al. 2013), and changing sensitivity to pathogen infection by RPS2
One of the important effects of APA is changing the tandem 3′-UTR length of mRNA (Tian and Manley 2017; Chen et al. 2018;Srivastava et al. 2018).
主语：One of the important effects of APA
谓语：is changing
宾语：the tandem 3′-UTR length of mRNA
This molecular effect connects to various post-transcriptional regulations, including alteration of mRNA
stability, the gain or loss of miRNA, and/or RNA-binding protein targets (Mayr 2017).
主语：This molecular effect
谓语：connects to
宾语：various post-transcriptional regulations
状语：including alteration of mRNA stability, the gain or loss of miRNA, and/or RNA-binding protein targets
By genome-wide calculation of the weighted 3′-UTR length of genes, we found that 3′ UTR lengthening events
(1157) are more abundant than 3′ UTR shortening events (373) in hda6 compared to Col-0 (Fig. 3A).
主语：we
谓语：found
宾语：that 3′ UTR lengthening events (1157) are more abundant than 3′ UTR shortening events (373) in hda6 compared to Col-0
These results suggest that HDA6 may play a role in ensuring proper 3′-UTR length for gene expression, indicating a connection between histone acetylation and 3′-UTR length control.
主语：These results
谓语：suggest
宾语：that HDA6 may play a role in ensuring proper 3′-UTR length for gene expression
动名词引导结果状语：indicating a connection between histone acetylation and 3′-UTR length control.
The length of the 3′ UTR was reported to be correlated with total gene expression (not at the individual transcript level) under certain conditions or in specific tissues (Zheng et al. 2018; Fu et al. 2019).
主语：The length of the 3′ UTR
谓语：was reported to
宾语：be correlated with total gene expression
状语：under certain conditions or in specific tissues
RNA-seq data of the seedlings of hda6 and Col-0 from the NCBI Sequence Read Archive (SRA; https://www.ncbi.nlm.nih.gov/sra) database were downloaded to obtain complete gene expression profiles.
主语：RNA-seq data of the seedlings of hda6 and Col-0 from the NCBI Sequence Read Archive database
谓语：were downloaded to
宾语：obtain complete gene expression profiles
We did not observe a clear relationship between 3′-UTR length and gene expression.
主语：We
谓语：did not observe
宾语：a clear relationship between 3′-UTR length and gene expression
However, 3′ UTR lengthening and shortening events coincide with those of stable genes that are not significantly affected by the mutation of HDA6 (Fig. 3B).
主语：3′ UTR lengthening and shortening events
谓语： coincide with
宾语：those of stable genes
定语从句： that are not significantly affected by the mutation of HDA6
状语：However
Figure 3C shows that decreased poly(A) site usage is coupled with an increase of another poly(A) site usage on the 3′ UTR of AT2G30720 and AT3G15518, which may explain the minor variance in total gene expression.
主语：Figure 3C
谓语：shows
宾语：that decreased poly(A) site usage is coupled with an increase of another poly(A) site usage on the 3′ UTR of AT2G30720 and AT3G15518
非限制性定语从句：which may explain the minor variance in total gene expression
Again, MB-3 treatment abolished the difference of poly(A) profile alteration of AT2G30720 and AT3G15518 between mutants and Col-0, reflecting that the 3′ UTR APA may depend on deacetylation by HDA6.
主语：MB-3 treatment
谓语：abolished
宾语：the difference of poly(A) profile alteration of AT2G30720 and AT3G15518 between mutants and Col-0
伴随状语：reflecting that the 3′ UTR APA may depend on deacetylation by HDA6.
状语：Again
In general, these evidences indicate that defective HDA6 results in both gene expression activation and 3′-UTR length variance.
主语：these evidences
谓语：indicate
宾语：that defective HDA6 results in both gene expression activation and 3′-UTR length variance
状语：In general,
However, 3′ UTR APA in hda6 is independent of the transcription activity but associated with histone acetylation status.
主语：3′ UTR APA in hda6
谓语：is independent of ；associated with
宾语： the transcription activity ； histone acetylation
状语：However
Furthermore, tandem 3′ UTR sequences of genes with a switching of 3′-UTR length were submitted to the psRNATarget webserver (Dai et al. 2018) for identifying potential small RNA targets.
主语： tandem 3′ UTR sequences of genes with a switching of 3′-UTR length
谓语： were submitted to
宾语：the psRNATarget webserver (Dai et al. 2018)
状语： for identifying potential small RNA targets
For lengthening events, psRNATarget reported 832 pairs of small RNAs interacting with said 3′ UTRs that may support cleavage inhibition, and 203 pairs of interactions that may be subject to translation inhibition (Supplemental Table S3).
主语：psRNATarget
谓语：reported
宾语：832 pairs of small RNAs (which were) interacting with 3′ UTRs
定语从句省略：主格关系代词+be+分词可以省略主格关系代词+be
例如: The boy who is standing by the dor is my brother
The boy standing by the door is my brother
I received a letter which was written in English
I received a letter written in English
与此相同的还有伴随状语从句省略：
主句和从句主语相同时候可以省略连接词和主语，同时谓语变成分词形式
例如： Because I feel tired， I went to sleep
Feeling tired, I went to sleep
对于832 pairs of small RNAs (which were) interacting with 3′ UTRs 省略引导词做主语，因此是定语从句，状语从句引导词是连接副词一般不做成分。
定语从句：that may support cleavage inhibition
状语：For lengthening events
For shortening events, psRNATarget predicted 233 cleavage inhibition and 43 translation inhibition pairs (Supplemental Table S4).
主语：psRNATarget
谓语：predicted
宾语：233 cleavage inhibition and 43 translation inhibition pairs
目的状语：For shortening events
These data suggest that the lengthening of the 3′ UTR in hda6 may increase possibilities of small RNA targeting for cleavage or translation inhibition, whereas the shortening of the 3′ UTR in hda6 may result in transcripts escaping from small RNA targeting.
主语：These data
谓语：suggest
宾语： that the lengthening of the 3′ UTR in hda6 may increase possibilities of small RNA targeting for cleavage or translation inhibition
非限制性定语从句:whereas the shortening of the 3′ UTR in hda6 may result in transcripts escaping from small RNA targeting
Thus, mRNA stability may be affected by the switch of 3′-UTR length.
主语：mRNA stability
谓语：may be affected by
宾语：the switch of 3′-UTR length
选自：http://www.genome.org/cgi/doi/10.1101/gr.255232.119.